Day 1 - Wednesday, 17th May Day 2 - Thursday, 18th May Day 3 - Friday, 19th May
11:00 - 11:30 BST 12:00 - 12:30 CEST 06:00 - 06:30 EDT 03:00 - 03:30 PDT 20:00 - 20:30 AEST
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HOW TO GET STARTED WITH NANOPORE SEQUENCING AND PLAN YOUR EXPERIMENT

online
Akelia Wauchope-Odumbo, Technical Services Manager – Americas
Akelia Wauchope-Odumbo

Title

How to get started with nanopore sequencing and plan your experiment

 

Summary

Learn everything you need to know to get started with nanopore sequencing. This masterclass provides an overview of the nanopore workflow, from extraction and library preparation through to analysis, with guidance on how to design your experiment.

 

Learning Objectives

This masterclass provides an introduction to nanopore sequencing and an overview of what you need to know to perform your first experiment with Oxford Nanopore technology.

In this session, you will learn:

  • How nanopore sequencing technology works

  • The key benefits of nanopore sequencing

  • What to consider when planning and performing your first nanopore sequencing experiment

  • Where to find online learning resources that will support you through the process

 

Biography

Akelia received her PhD from the University of Maryland Baltimore County, USA, where she worked on the multicellular green algae, Volvox carteri, developing molecular tools and gene knockdown systems.

Her postdoctoral work at Synaptic Research involved the optimization of algae and bacterial protein expression for therapeutic nanobodies. As a GENEWIZ project manager, she facilitated various client projects. In 2016, she accepted a role within the Technical Services team at Oxford Nanopore and is now a Technical Services Manager for the Americas region.

 

Keywords

Bioinformatics, Clinical research, Data analysis tool, Human genomics

 

Products

Adaptive sampling, Direct RNA, EPI2ME, Flongle, GridION, MinION Mk1B, PromethION P2/P2 Solo

11:35 - 12:25 BST 12:35 - 13:25 CEST 06:35 - 07:25 EDT 03:35 - 04:25 PDT 20:35 - 21:25 AEST
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HOW TO EXTRACT HIGH-QUALITY DNA AND RNA

online
Vânia Costa, Field Applications Scientist
Vânia Costa

Title

How to extract high-quality DNA and RNA

 

Summary

Find out how to get the best from your samples, with our masterclass detailing how to extract and store the highest quality DNA and RNA to achieve optimal sequencing performance in your experiment.

 

Learning Objectives

This masterclass will teach you how to determine the best extraction method for your sample type and experimental goals, and the steps involved in ensuring a high-quality DNA or RNA extraction. In this session, you will learn:

  • How to determine the right extraction method for your workflow

  • The steps involved in extraction of high-quality DNA and RNA

  • How to optimise extraction for your sample type and perform quality checks

  • Best practices for handling and preserving nucleic acids

 

Biography

Vânia Costa is a Technical Applications Scientist at Oxford Nanopore Technologies. Prior to joining the Technical Services team, her role within the Applications team was to test and optimize RNA and DNA extraction methods for a variety of sample types for downstream analysis with nanopore devices.

 

Keywords

Clinical research, Gene expression, Human genomics

 

Products

Automation, Direct RNA, Short fragment mode

12:55 - 13:25 BST 13:55 - 14:25 CEST 07:55 - 08:25 EDT 04:55 - 05:25 PDT 21:55 - 22:25 AEST
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HOW TO SELECT THE RIGHT LIBRARY PREP WORKFLOW FOR YOUR EXPERIMENT

online
Nikita Fiji, Senior Field Application Scientist
Nikita Fiji

Title

How to select the right library prep workflow for your experiment

 

Summary

Learn about the benefits of different nanopore sequencing techniques — including whole-genome and targeted approaches, PCR and PCR-free options, and multiplexed sequencing — and how to choose the right library prep workflow for your experimental needs.

 

Learning Objectives

This masterclass will introduce what you need to know to choose the right library preparation workflow for your experiment.

In this session, you will learn:

  • What to consider before you begin preparing your samples

  • The variety of library preparation options available for sequencing RNA, DNA, and cDNA

  • The applications and benefits of the different nanopore sequencing techniques, including PCR-free and targeted approaches

  • How to select the right sequencing kit for your application and experimental goals

 

Biography

Nikita Fiji graduated from St. Xavier’s College, India, with a BS degree in Life Sciences, majoring in Biochemistry. She received her Master’s degree in Biotechnology from VIT University, India. Nikita has worked in the field of next-generation sequencing (NGS) for over seven years. She has been at Oxford Nanopore for two years and has extensive experience supporting custom NGS projects. Prior to joining Oxford Nanopore, she was an FAS for Illumina platforms and a Product Specialist for a core NGS facility in Dubai.

 

Keywords

Epigenetics, Human genomics, Clinical research

 

Products

VolTRAX, Automation, Q20+, Adaptive sampling, Cas9 targeted sequencing, Direct RNA, Duplex reads

13:30 - 14:20 BST 14:30 - 15:20 CEST 08:30 - 09:20 EDT 05:30 - 06:20 PDT 22:30 - 23:20 AEST
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HOW TO LOAD A PROMETHION FLOW CELL

online
Thomas Collette, Tech Transfer Sequencing & Validation Scientist
Thomas Collette

Title

How to load a PromethION Flow Cell

 

Summary

Learn how to load a PromethION Flow Cell in this interactive, hands-on demo, which includes additional information on loading Flongle and MinION Flow Cells.

 

Learning Objectives

In this practical demonstration masterclass, you will learn:

  • How to prepare a PromethION Flow Cell prior to sample loading

  • How to load a sequencing library onto a PromethION Flow Cell

  • The basics of loading Flongle and MinION Flow Cells

 

Biography

Thomas grew up in Oxford and did his undergraduate degree in biochemistry at the University of Warwick, UK. During this time, he learnt about nanopore sequencing and was immediately hooked. Soon after finishing his degree, Thomas applied for a job within the Tech Transfer team. He has spent the last two and a half years with this team and enjoys working within this growing company.

 

Products

PromethION P2/P2 Solo, PromethION P24/P48, Flongle, R10 Flow Cells, MinION Mk1B, MinION Mk1C

 

14:40 - 15:30 BST 15:40 - 16:30 CEST 09:40 - 10:30 EDT 06:40 - 07:30 PDT 23:40 - 00:30 AEST
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HOW TO GET STARTED WITH DATA ANALYSIS

online
Bryant Catano, Product Support Scientist
Bryant Catano

Title

How to get started with data analysis

 

Summary

Learn the principles of how to analyse nanopore sequencing data, including the file types involved, the platforms available for analysing your data, and how to basecall your data and detect methylation — no previous data analysis experience necessary.

 

Learning Objectives

This masterclass will introduce the principles of analysing nanopore sequencing data.

In this session, you will learn:

  • How real-time nanopore sequencing data is converted into basecalls, and how to basecall your data and directly detect methylation

  • The options available for nanopore data analysis, for every level of experience, and how to select the right method for your experiment

  • The different file formats involved in nanopore sequencing data analysis

  • How to use adaptive sampling for real-time targeted methylation analysis via reduced-representation methylation sequencing (RRMS)

 

Biography

Bryant Catano is a Product Support Scientist at Oxford Nanopore Technologies. In his role he helps manage the global support strategy for hardware and software issues. His graduate work at William Paterson University, USA, investigated the bacterial communities associating with various strains of Karenia brevis, a marine dinoflagellate responsible for toxic algal blooms along the Gulf of Mexico. Prior to switching fields to molecular biology, he worked as an organic chemist specializing in transition-metal-catalyzed reaction methodology.

 

Keywords

Bioinformatics, Clinical research, Data analysis tool, Epigenetics, Human genomics

 

Products

EPI2ME, EPI2ME Labs, Adaptive sampling, Duplex reads, Q20+

15:35 - 16:25 BST 16:35 - 17:25 CEST 10:35 - 11:25 EDT 07:35 - 08:25 PDT 00:35 - 01:25 AEST
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HOW TO TAKE YOUR DATA ANALYSIS FURTHER

online
Dilrini De Silva, Field Applications Scientist (Bioinformatics) - EMEAI Region
Dilrini De Silva

Title

How to take your data analysis further

 

Summary

Discover the approaches available for comprehensive analysis of your nanopore sequencing data, from generating assemblies, to calling variants — including single nucleotide variants and structural variants — and analysing single-cell transcriptomes. 

 

Learning Objectives

Take your data analysis skills to the next level with this masterclass, where you will learn:

  • How to generate high-quality assemblies with nanopore sequencing data, including small and large genome assembly and metagenomic assembly approaches

  • All about analysis workflows for calling variants — including structural variants (SVs) and single nucleotide variants (SNVs)

  • How to perform transcriptomic analysis, including at the single-cell level

 

Biography

Dilrini has a background in bioinformatics with several years of postdoctoral expertise in genomic and clinical research at the John Radcliffe Hospital, University of Oxford and at Cancer Research UK, Cambridge Institute, University of Cambridge.

 

Keywords

Assembly, Bioinformatics, Chromatin conformation, Clinical research, Data analysis tool, Epigenetics, Gene expression, Human genomics, Infectious disease, Metagenomics, Microbiology, Microbiome, Phasing, Single cell and spatial

 

Products

EPI2ME, EPI2ME Labs, Adaptive sampling

16:40 - 17:30 BST 17:40 - 18:30 CEST 11:40 - 12:30 EDT 08:40 - 09:30 PDT 01:40 - 02:30 AEST
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HOW TO PERFORM TUMOUR-NORMAL NANOPORE SEQUENCING

online
Philipp Rescheneder, Director, Genomic Applications Bioinformatics
Philipp Rescheneder

Title

How to perform tumour-normal nanopore sequencing

 

Summary

Find out how nanopore sequencing enables comprehensive analysis of cancer genomes in this end-to-end masterclass introducing how to perform tumour-normal sequencing.

 

Learning Objectives

In this cancer research-focused masterclass, you will learn:

  • The benefits of nanopore sequencing for comprehensive characterisation of cancer genomes

  • How to perform paired tumour-normal nanopore sequencing of clinical research samples, with best practice guidance through each step

  • How nanopore sequencing enabled haplotype-resolved analysis of variants of interest in a worked example of matched tumour-normal sequencing of clinical research samples

 

Biography

Philipp Rescheneder works as a bioinformatician in the Applications team at Oxford Nanopore. He and his teams identify, benchmark, and adapt the most appropriate tools and workflows for analysing Oxford Nanopore data in the context of a wide range of applications, including variant calling, assembly, and modification calling. Furthermore, he is responsible for transferring this knowledge to enable pilot and proof-of-concept experiments showing the applicability of nanopore sequencing to existing and novel use cases.

 

Keywords

Assembly, Bioinformatics, Cancer research, Data analysis tool, Epigenetics, Human genomics, Phasing

 

Products

PromethION P2/P2 Solo, PromethION P24/P48

10:00 - 10:20 BST 11:00 - 11:20 CEST 05:00 - 05:20 EDT 02:00 - 02:20 PDT 19:00 - 19:20 AEST
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WELCOME TO LONDON CALLING 2023

online onsite
Gordon Sanghera, CEO, Oxford Nanopore Technologies
Gordon Sanghera

Talk Title 

Welcome to London Calling 2023

 

Biography

Gordon Sanghera is co-founder of Oxford Nanopore with Spike Willcocks and Hagan Bayley. He was appointed CEO in May 2005 and has led the company through multiple finance rounds, and in 2021, a listing on the London Stock Exchange. The company has developed a new generation of nanopore-based sensing technology. The first products enable the real-time, high-performance, accessible, and scalable analysis of DNA and RNA, and this new class of sensing has the potential to expand into proteomics and metabolomics.

Fully bespoke manufacturing capability has been built from the ground up, integrating state-of-the-art electronics with silicon fab technology, combining the chemistry and biology. The company has been commercially distributing sequencing platforms since 2015, including the handheld and portable MinION and Flongle, and the high-throughput benchtop devices, GridION and PromethION. These platforms are used in more than 100 countries to understand the biology of humans and diseases such as cancer, plants, animals, bacteria, viruses, and whole environments.

Dr. Sanghera’s PhD in bioelectronic technology was followed by a career at MediSense — an Oxford spin-out that delivered a new generation glucose technology to the market — where he held positions including VP World Wide Marketing, Research Director, and Manufacturing Process Development Director. During this time, he was instrumental in the launch of several generations of blood glucose bio-electronic systems for the consumer and hospital medical markets.

Emma White, Senior Director, Marketing Operations, Oxford Nanopore Technologies
Emma White

Title 

Welcome to London Calling 2023 

 

Biography 

Emma White is Senior Director of Marketing Operations responsible for developing and communicating the vision and brand, and leading global marketing operations at Oxford Nanopore. Emma is an experienced marketer; having held various marketing roles in multi-national life science companies. At Oxford Nanopore she leads a multi-disciplinary and cross-functional team that shares information and customer stories both inside and outside of the Nanopore Community. Emma and her team are also responsible for the organisation of events such as the Nanopore Community Meeting and London Calling. 

Auditorium
10:20 - 10:45 BST 11:20 - 11:45 CEST 05:20 - 05:45 EDT 02:20 - 02:45 PDT 19:20 - 19:45 AEST
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PLENARY 1

online onsite
Genomics England long-read cancer whole-genome sequencing pilot
Helen Webb, Genomics England, UK
Helen Webb

Talk title

Genomics England long-read cancer whole-genome sequencing pilot

 

Abstract

Genomics England are currently running a pilot study to investigate the use of Oxford Nanopore sequencing in large-scale, clinical, whole-genome analysis in cancer. This pilot is being run in conjunction with NHS England. Sequencing will be started at two pathfinder translational sites at Genomic Laboratory hubs located in Leeds and the Royal Marsden, London, before being rolled out to five other sites nationally. In the run up to this pilot, Genomics England has been sequencing large research cohorts of samples at the GEL Sequencing R&D lab. This has led to the optimisation of large-scale sequencing protocols for whole-genome sequencing on the PromethION 48 sequencer, as well as optimisation of data transfer from the machine to enable centralised storage and analysis. Structural variant calling has been optimised following the benchmarking of several algorithms. Significant process has been made with copy number variant calling, methylation calling, and small variant calling. Several case studies have been made of complex variants not called by short-read sequencing but which are able to be resolved using long-read sequencing.

 

Biography

Helen is currently the Group Product Manager for the Bioinformatics Pipelines at Genomics England. She began her career in genetics before moving on to become a data scientist in the natural language processing space and then later a product manager of data analysis products. She has worked across various industries, including education and finance, and now considers herself extremely fortunate to be working on products that serve clinical researchers, clinical scientists, and ultimately rare disease and cancer patients.

 

Keywords

Bioinformatics, Cancer research, Clinical research, Whole-genome sequencing

 

Products

PromethION P24/P48

Auditorium
Cancer research
10:45 - 11:10 BST 11:45 - 12:10 CEST 05:45 - 06:10 EDT 02:45 - 03:10 PDT 19:45 - 20:10 AEST
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PLENARY 2

online onsite
A single-cell approach to cancer mutation discovery and CRISPR phenotypic modelling
Hanlee Ji, Stanford University, USA
Hanlee Ji

Talk title

A single-cell approach to cancer mutation discovery and CRISPR phenotypic modelling

 

Abstract

We developed a new single-cell approach to identify disease-related mutations from individual cells and then genome engineer these mutations into cellular experimental systems for further biological characterization. To identify mutations, we used a targeted, long-read sequencing approach on single cells to identify cancer somatic mutations and even gene fusion rearrangements. This involved leveraging nanopore long-read sequences that covered entire transcripts of cancer genes. Next, we used CRISPR based-editor technology to introduce specific cancer mutations into single cells on a large scale. We directly engineered cancer mutations among different single cells and then determined their transcriptional phenotype with integrated nanopore long- and short-read sequencing. In summary, our work demonstrates a direct and highly scalable method for identifying, modelling, and functionally assessing cancer mutation phenotype at single-cell resolution.

 

Biography

Dr. Ji is a Physician Scientist and Professor at Stanford University. His research addresses basic and translational questions about cancer genetics and genomics. Dr. Ji’s research group has developed numerous DNA sequencing technologies for the characterization of cancer genomes, several of which have been used for clinical diagnostics. Currently, he is applying new single-molecule and single-cell sequencing strategies to identify clinically relevant features and cancer drug targets.

 

Recent publications

Kim, H.S. et al. Single-cell characterization of CRISPR-modified transcript isoforms with nanopore sequencing. Genome biol. 22(1):331 (2021). DOI: 10.1186/s13059-021-02554-1

 

Keywords

Human genomics

 

Products

Midnight

Auditorium
Cancer research
11:10 - 11:20 BST 12:10 - 12:20 CEST 06:10 - 06:20 EDT 03:10 - 03:20 PDT 20:10 - 20:20 AEST
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SPOTLIGHT SESSION: HOW NANOPORE SEQUENCING IS CHANGING MY FIELD OF RESEARCH

online onsite
Fantastic methanotrophs and where to find them
Kalinka Sand Knudsen, Aalborg University, Denmark
Kalinka Sand Knudsen

Talk title

Fantastic methanotrophs and where to find them 

 

Abstract

Methane is a potent greenhouse gas with a global warming potential 27–30 times higher than that of carbon dioxide on a 100-year timescale. The concentration of atmospheric methane has doubled over the last century, largely due to anthropogenic activities. To address this issue, it is essential to understand the diversity and biogeography of methanotrophs — the microorganisms responsible for mitigating emissions. Shallow metagenomes from 10,000 samples taken across Denmark were screened for methane monooxygenase genes. To improve the resolution of this nationwide study, it is crucial to uncover the novelty found within complex environmental samples. The discovery of novel methanotrophs relies on the ability to extract full-length sequences and generate high-quality metagenome-assembled genomes. Preliminary results show promise in capturing and incorporating novel contig-based full-length sequences. The low indel rate of the R10.4 Oxford Nanopore chemistry enables comprehensive searches in raw data prior to assembly, dramatically increasing the usefulness of nanopore sequencing in complex samples.

 

Biography

Kalinka Sand Knudsen is a Master's student at Aalborg University's Center of Microbial Communities. She strives to pursue a career in environmental bioscience, with a special focus on bioinformatics and genomics. Her work is fuelled by an interest in exploring how microbes can contribute to a sustainable future and she is eager to discover the possibilities of this exciting field.

 

Keywords

Assembly, Bioinformatics, Environmental research and conservation, Identification, Metagenomics, Microbiology, Whole-genome sequencing

 

Products

PromethION P24/P48, R10 Flow Cells

Revolutionizing biodiversity research: Oxford Nanopore sequencing for the rapid and accurate identification of endangered species
Mariana Corrales Orozco, EAFIT University, Colombia
Mariana Corrales Orozco

Talk title

Revolutionizing biodiversity research: Oxford Nanopore sequencing for the rapid and accurate identification of endangered species 

 

Abstract

The Neotropics have a high species richness and endemism; however, identifying its diversity is a formidable task. Traditionally, DNA sequencing and morphological characters have been used to recognize and describe species, but this approach is often challenging, requiring euthanizing individuals and the expertise of a taxonomist. Molecular data, such as mitochondrial DNA markers, have been used to identify species, but this method requires specific primers that are not always available for non-model organisms. Oxford Nanopore and the portable MinION sequencer allow on-site shotgun sequencing without the need for specific primers. This technology could provide a quick, accurate, and cost-efficient way of identifying and characterizing biodiversity, particularly in groups that lack diagnostic characters and in scenarios, such as wildlife trafficking, where only incomplete specimens are available. By enabling researchers to identify species rapidly and accurately, Oxford Nanopore sequencing may revolutionize the field of biodiversity research, especially in institutions with limited budgets, such as universities and governmental entities in developing countries.

 

Biography

Mariana Corrales Orozco is a Colombian biologist who has been fascinated by the biodiversity present in her country since she was very young. Her main interests are focused on the use of molecular tools for species identification, establishing a baseline to develop conservation strategies. In the last year, she has participated in research projects that seek to study the cryptic diversity. The use of Oxford Nanopore sequencing to overcome the limitations of traditional molecular and morphological species identification methods has enabled a more efficient and accurate recognition and description of the unknown portion of neotropical biodiversity.

 

Recent Publications

Velásquez-Restrepo, S. et al. Towards onsite and real-time small mammal’s cryptic species identification using the MinION sequencer. (in prep). Molecular Ecology Resources.

 

Keywords

Animal genomics, Assembly, Bioinformatics, Data analysis tool, Education, Environmental research and conservation, Whole-genome sequencing

 

Products

MinION Mk1B, Flongle, R10 Flow Cells, R9 Flow Cells

Unraveling chromosomal evolution in marsupials: comparative genomics and methylomics with telomere-to-telomere precision
Patrick G.S. Grady, University of Connecticut, USA
Patrick G.S. Grady

Talk title

Unraveling chromosomal evolution in marsupials: comparative genomics and methylomics with telomere-to-telomere precision

 

Abstract

Advances in Oxford Nanopore duplex sequencing have pushed the capabilities of genome assembly to new heights and allowed us to address decades-long questions about chromosomal evolution. Marsupials such as the Tammar wallaby have long served as models for chromosomal study, reproductive biology, and drug discovery. The latest sequencing technology has allowed us to rapidly expand to wide-scale comparative genomics of marsupials at large. Here, we present comparisons of telomere-to-telomere genomes and epigenomes across multiple marsupial orders (including Diprotodontia and Dasyuromorphia). These genomes were assembled with Q20+ PromethION long reads and ultra-long reads, resulting in extremely accurate and contiguous assemblies including the elusive centromeres, telomeres, and miniscule Y chromosomes. These analyses reveal a multitude of interesting patterns throughout the marsupial genome, such as marsupial-specific centromere and repetitive element structures. We address the significant differences between sex chromosomes, potential mechanisms of karyotypic instability, and what we have learned from the epigenome.

 

Biography

Patrick Grady, a 5th year PhD candidate in Rachel O’Neill’s lab at the University of Connecticut, is currently engaged in research focused on telomere-to-telomere genomics of marsupials, with a particular emphasis on repetitive elements in the karyotypic evolution of Macropods. He worked with the T2T CHM13 Project on the evolution of repetitive elements and has recently joined the Ruminant T2T Consortium to expand this work. Additionally, he assembles Oxford Nanopore-based T2T genomes for the Tasmanian Tiger Project with Colossal Biosciences.

 

Keywords

Animal genomics, Bioinformatics, Chromatin conformation, Environmental research and conservation, Epigenetics, Gene expression, Phasing, SNVs, Ultra-long reads, Whole-genome sequencing

 

Products

PromethION P24/P48, Q20+, R10 Flow Cells, R9 Flow Cells, Duplex reads

Auditorium
11:20 - 11:45 BST 12:20 - 12:45 CEST 06:20 - 06:45 EDT 03:20 - 03:45 PDT 20:20 - 20:45 AEST
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PLENARY 3

online onsite
Real-time genomics for One Health
Lara Urban, Helmholtz AI Institute, Helmholtz Pioneer Campus, & Technical University of Munich, Germany
Lara Urban

Talk title

Real-time genomics for One Health

 

Abstract

The COVID-19 pandemic catapulted the concept of One Health into the center of public attention, showcasing how environmental, animal, and human health are inextricably linked. I will showcase how nanopore sequencing, as the only disruptive technology that currently allows for portable real-time genomic analyses, can enable timely, in-depth ecosystem health assessments, thereby empowering efficient intervention strategies. I will highlight previous and ongoing nanopore-based studies on diverse topics, such as emerging pathogens, food security, the environmental microbiome, as well as wildlife conservation and trafficking. I will then present my own research group’s latest results in the realm of environmental monitoring for disease detection and classification as examples of One Health applications and will discuss our first steps towards exploring the utility of nanopore squiggle data for pathogen viability and virulence assessments.

 

Biography

Lara obtained her PhD in 2019 in statistical genomics from EMBL-EBI, EMBL, and the University of Cambridge, UK. As an independent Humboldt Research Fellow in New Zealand, Lara then combined this expertise with her background in ecology and applied genomics and machine learning in the context of nature conservation. In 2022, Lara obtained a Helmholtz Principal Investigator Grant to start her own research group at the Helmholtz AI Institute, the Helmholtz Pioneer Campus, and the Technical University of Munich, Germany.

 

Recent Publications

Urban, L. et al. Freshwater monitoring by nanopore sequencing. Elife. 10:e61504 (2021). DOI: https://doi.org/10.7554/eLife.61504 Urban, L. et al. Non-invasive real-time genomic monitoring of the critically endangered kākāpō. bioRxiv 2022.11.14.516431 (2022). DOI: https://doi.org/10.1101/2022.11.14.516431 West, A.G. et al. Capturing species-wide diversity of the gut microbiota and its relationship with genomic variation in the critically endangered kākāpō. bioRxiv 2022.10.31.514450 (2022). DOI: https://doi.org/10.1101/2022.10.31.514450 Digby, A. et al. Hidden impacts of conservation management on fertility of the critically endangered kākāpō. PeerJ. 11:e14675 (2023). DOI: 10.7717/peerj.14675 van Oosterhout, C. et al. Genomic erosion in the assessment of species extinction risk and recovery potential. bioRxiv 2022.09.13.507768 (2022). DOI: https://doi.org/10.1101/2022.09.13.507768

 

Keywords

Animal genomics, Bioinformatics, Environmental research and conservation, Epigenetics, Infectious disease, Metagenomics, Microbiology, Microbiome, Population genomics, Targeted sequencing, Transcriptomics, Whole-genome sequencing

 

Products

MinION Mk1B, MinION Mk1C, GridION, EPI2ME, Automation, Q20+, R10 Flow Cells, R9 Flow Cells, Adaptive sampling, Short fragment mode, Direct RNA

Auditorium
Microbiology & infectious disease
12:15 - 12:35 BST 13:15 - 13:35 CEST 07:15 - 07:35 EDT 04:15 - 04:35 PDT 21:15 - 21:35 AEST
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MINI THEATRE ON-DEMAND

onsite ondemand
Pathogen and species identification using a mobile suitcase laboratory
Ahmed Abd El Wahed, Leipzig University, Germany
Ahmed Abd El Wahed

Talk title

Pathogen and species identification using a mobile suitcase laboratory

 

Abstract

Johann Wolfgang von Goethe said “We only see what we know”; however, sequencing has taught us to start seeing what we did not see before. This can be achieved by applying various methods to analyse the same sets of sequence data. In my presentation, I will discuss the development of the mobile suitcase lab to operate Oxford Nanopore sequencing in low-resource settings in India, Bangladesh, Sudan, Uganda, Egypt, and Senegal. The mobile setup was used for the rapid identification of infectious agents (pathogen ID) from blood (septicaemia) and faecal (diarrheal diseases) samples. To tackle the infectivity of vectors, pathogen ID and the identification of human or animal species in blood meals of mosquito (species ID) were developed. A reverse purification extraction protocol, Oxford Nanopore sequencing, and offline BLAST facilitated the whole procedure in a mobile suitcase lab in less than 150 minutes.

 

Biography

Dr. Ahmed Abd El Wahed studied veterinary medicine at Mansoura University, Egypt. He received his PhD in biology from Goettingen University, Germany in 2011. He is the head of the laboratory at the Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, Germany and established a mobile suitcase laboratory for the rapid detection of viruses, bacteria, and parasites. His model has been deployed in several African and Asian countries.

 

Recent Publications

Khan M. A. A. et al. Feasibility of MinION nanopore rapid sequencing in the detection of common diarrhoea pathogens in fecal specimen. Anal. Chem. 94(48):16658–16666 (2022). DOI: 10.1021/acs.analchem.2c02771

 

Keywords

Clinical research, Education, Infectious disease, Metagenomics, Microbiology

 

Products

MinION Mk1B, MinION Mk1C, Flongle, EPI2ME, R9 Flow Cells, Direct RNA

Antimicrobial wastewater epidemiology in low-resource communities
William Strike, University of Kentucky, USA
William Strike

Talk title

Antimicrobial wastewater epidemiology in low-resource communities

 

Abstract

Antimicrobial resistance (AMR) is an emerging public health threat that disproportionately affects rural areas and low-to-middle-income countries. Environmental pressures, such as overuse and over-reliance on clinically important antimicrobials, has led to an annual increase in multi-AMR pathogens. We developed a wastewater-based surveillance method to identify circulating AMR biomarkers in underserved areas that currently lack comprehensive AMR surveillance. This method leverages new methods developed during the SARS-CoV-2 pandemic, which comprise simple-yet-effective genomic extraction/analysis techniques without the use of conventional laboratory space. Specifically, we developed workflows that have been implemented inside wastewater treatment plants and inside of a cargo van-based laboratory, thereby demonstrating a “decentralized” model for environmental AMR testing. Using this model, we are able to concentrate wastewater on site and begin sequencing data analysis within five hours of collection from clinically relevant sites in Lexington, Kentucky.

 

Biography

William Strike completed a BS degree in chemical engineering from the University of Tennessee at Chattanooga, USA, with an honor’s thesis on cholera fatty acid uptake. He is currently pursuing a PhD in biomedical engineering at the University of Kentucky, in Dr. Scott Berry’s lab, with a focus on low-resource pandemic surveillance. William was awarded the Max Steckler Fellowship award in fall 2021 and enjoys baking sourdough bread in his free time.

 

Recent publications

Strike, W. et al. Development and validation of a simplified method for analysis of SARS-CoV-2 RNA in university dormitories. ACS ES&T Water 2(11):1984–1991 (2022). DOI: 10.1021/acsestwater.2c00044

 

Keywords

Environmental research and conservation, Genomic epidemiology, Infectious disease, Metagenomics, SARS-CoV-2/COVID-19

 

Products

MinION Mk1B, Flongle, EPI2ME, EPI2ME Labs, R10 Flow Cells, R9 Flow Cells

Secret cinema
Microbiology & infectious disease
12:15 - 12:40 BST 13:15 - 13:40 CEST 07:15 - 07:40 EDT 04:15 - 04:40 PDT 21:15 - 21:40 AEST
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SHOWCASE STAGE: TARGETED SEQUENCING

onsite
Dynamic, adaptive sampling during nanopore sequencing using Bayesian experimental design
Lukas Weilguny, EMBL-EBI, UK
Lukas Weilguny

Talk title

Dynamic, adaptive sampling during nanopore sequencing using Bayesian experimental design

 

Abstract

Nanopore sequencers can reject molecules after analysis of a small initial part. Until now, selection has been based on predetermined regions of interest, which inhibits re-focusing on molecules that may contribute most to experimental success. We present a new method to generate dynamically updated targets by quantifying remaining uncertainty by streaming data to decide whether the expected information of a newly observed molecule warrants fully sequencing it. We illustrate this by mitigating coverage bias in a microbial community, improving variant calling. Further, we expand our method for true de novo enrichment, that is, without prior information about sample composition. We achieve this by constructing and incrementally updating assemblies in real time, which are then used to reject over-represented sequences, thus mitigating abundance bias without requiring input genomes. Overall, these data-driven updates are applicable to many scenarios, such as enriching regions with increased divergence or low coverage, or unknown species in mixtures.

 

Biography

Lukas Weilguny is a PhD student at EMBL-EBI and the University of Cambridge, UK in Nick Goldman’s group and collaborating with the Loose lab at the University of Nottingham. He is fascinated by how new methods and algorithms for sequencing technologies help us understand nature's past and present and is motivated to find out how these can be used to positively impact planetary health.

 

Recent Publications

Weilguny, L. et al. Dynamic, adaptive sampling during nanopore sequencing using Bayesian experimental design. Nat. Biotechnol. (2023). DOI: https://doi.org/10.1038/s41587-022-01580-z

 

Keywords

Assembly, Bioinformatics, Metagenomics, Targeted sequencing

 

Products

MinION Mk1B, GridION, R10 Flow Cells, Adaptive sampling

The potential use of nanopore sequencing for routine molecular diagnosis of germline cancer predisposition
Romain Boidot, Centre Georges-François Leclerc, France
Romain Boidot

Talk title

The potential use of nanopore sequencing for routine molecular diagnosis of germline cancer predisposition

 

Abstract

Recently, we have started to explore nanopore sequencing using GridION. We are performing technological assessments on 24 clinical germline cancer samples carrying abnormalities on BRCA1, BRCA2, PALB2, and MLH1 to test methylation status, large-scale rearrangements (LSR), and singlenucleotide variants. We have used adaptive sampling to enrich our target region of more than 150 cancer predisposition genes and used R10.4.1 Flow Cells and Q20+ chemistry for this experiment. After setting up the critical pre-analytical processes (DNA extraction and library prep) and optimizing the experimental workflow, the initial results are promising. We have been able to enrich our region of interest and show that adaptive sampling did not induce any bias in the read depth among the different chromosomes.

 

Biography

Romain Boidot, PhD, has been a Molecular Biologist at the Centre Georges-François Leclerc, France, for 12 years. He is in charge of the Molecular Biology unit dedicated to routine molecular diagnosis related to solid cancer. He is also responsible for a next-generation sequencing service platform. His research activity is focused on technology innovation and biomarker discovery.

 

Keywords

Cancer research

 

Products

GridION, R10 Flow Cells, Adaptive sampling

Rapid identification of bacterial invasion in the amniotic cavity: full-length 16S or adaptive sampling?
Thidathip Wongsurawat, Siriraj Long-read Lab, Mahidol University, Thailand
Thidathip Wongsurawat

Talk title

Rapid identification of bacterial invasion in the amniotic cavity: full-length 16S or adaptive sampling?

 

Abstract

Amniotic infections can cause preterm birth and serious complications for both mother and baby. Early detection and diagnosis are crucial, but traditional methods can be slow and miss some cases. Using two different nanopore technology targeted sequencing approaches, we amplified full-length 16S rRNA and applied adaptive sampling to detect bacteria directly from clinical research specimens. The full-length 16S rRNA method enriched any bacteria that 16S primers could capture and allowed us to identify species and report polymicrobial species that the Sanger method could not. We also tried adaptive sampling to deplete host DNA and identified Prevotella sp. within 15 minutes of sequencing. In the same day, we obtained the complete genome of the bacteria and identified antimicrobial resistance genes using the sequence data. Our research demonstrates the potential use of nanopore-based bacterial identification methods to diagnose amniotic infections.

 

Biography

Dr. Thidathip Wongsurawat (Tip) received her PhD from Nanyang Technological Singapore. She is currently the Group Leader of Siriraj Long-read Lab in the Faculty of Medicine at Siriraj Hospital, Mahidol University, Thailand. Tip's research interest focuses on utilizing nanopore sequencing technology combined with bioinformatics data analysis in pathogen detection as well as cancer research, with the primary goal of translating novel ideas and approaches into clinical reality. She has trained students, researchers, and physicians to use nanopore technology to sequence the genomes and transcriptomes of viruses, bacteria, fungi, plants, mice, and human cell lines, clinical samples, as well as the metagenome from different types of clinical samples.

 

Recent publications

Chaemsaithong, P. et al. Rapid diagnosis of intra-amniotic infection using nanopore-based sequencing. J. Perinat. Med. (2022). https://doi.org/10.1515/jpm-2022-0504

Kruasuwan, K. et al. Nanopore sequencing discloses compositional quality of commercial probiotic feed supplements. Scientific Reports 13(4540) (2023). DOI: https://doi.org/10.1038/s41598-023-31626-4

 

Keywords

Cancer research, Education, Infectious disease, Metagenomics, Microbiology, Microbiome

 

Products

MinION Mk1B, MinION Mk1C, GridION, PromethION P2/P2 Solo, Flongle, Q20+, R10 Flow Cells, R9 Flow Cells, Adaptive sampling, Cas9 targeted sequencing, Short fragment mode

Live lounge
Human & clinical research Cancer research Bioinformatics
12:45 - 13:05 BST 13:45 - 14:05 CEST 07:45 - 08:05 EDT 04:45 - 05:05 PDT 21:45 - 22:05 AEST
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PRODUCT DEMO

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Human genomics — from targeted to whole-genome sequencing
Rachel Rubinstein & Danny E. Miller, Technical Product Manager, Software, Oxford Nanopore Technologies & University of Washington, USA
Danny E. Miller Rachel Rubinstein

Talk title

Human genomics — from targeted to whole-genome sequencing

 

Biographies

Rachel Rubinstein is a technical product manager with a background in molecular biology and microbiology. At Oxford Nanopore, she works with the MinKNOW team to help incorporate customer feedback and make the software more powerful and user friendly. She is passionate about improving user experience, robustness, and stability of the MinKNOW software. In her free time, you can catch her running, swimming, or cycling around the Boston, MA, area.

Danny E. Miller is an Assistant Professor at the University of Washington in the Department of Pediatrics, Division of Genetic Medicine, and the Department of Laboratory Medicine and Pathology. His laboratory focuses on using new technologies, such as long-read DNA and RNA sequencing, to increase the rate of genetic diagnosis, reduce the time required to make a genetic diagnosis, characterize novel disease-causing genetic variation, and reduce barriers to accessing a comprehensive genetic evaluation

 

Keywords

Assembly, Bioinformatics, Clinical research, Epigenetics, Human genomics, Structural variation, Whole-genome sequencing

 

Products

PromethION P2/P2 Solo, PromethION 24/48, EPI2ME Labs, Q20+, R10 Flow Cells, R9 Flow Cells, Adaptive sampling, Duplex reads

Live lounge
Human & clinical research Methods & techniques
12:50 - 13:10 BST 13:50 - 14:10 CEST 07:50 - 08:10 EDT 04:50 - 05:10 PDT 21:50 - 22:10 AEST
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PRODUCT DEMO

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Analysing bacterial genomes – from species identification to AMR
Stephen Rudd, Matt Parker & Natalia Garcia, Director, Bioinformatics Product; Associate Director, Clinical Bioinformatics; & Bioinformatics Workflow Developer. Oxford Nanopore Technologies
Natalia Garcia Matt Parker

Talk title

Analysing bacterial genomes – from species identification to AMR

 

Biography

Stephen works in the Product Management team and is responsible for customer-facing bioinformatics offerings. With the customer workflow team, we are developing EPI2ME Labs to provide solutions for common research problems. Our bioinformatics workflows are implemented using Nextflow and are open source and can be run from a sequencing device, in the cloud, or on other available computer hardware.

Matt is a member of the Customer Workflows team and leads development of analysis solutions that are destined for clinical applications. He is a registered clinical scientist and has >10 years of experience applying genomics and bioinformatics to problems in human health. He is passionate about facilitating the transition of Oxford Nanopore’s game changing sequencing technology to the clinic through easy-to-use and robust analysis workflows.

As a Bioinformatics Workflow Developer in the Customer Workflow team, Natalia creates and maintains workflows that help non-expert users to reliably analyse their data with minimal training. Our open-source workflows, implemented using Nextflow, allow life science researchers to go from raw reads to informative reports designed to help them make the most of their data. In particular, she is focused on the analysis of microbial communities through metagenomics data. 

 

Keywords

Assembly, Bioinformatics, Data analysis tools, Epigenetics, Fusion genes, Gene expression, Human genomics, Infectious disease, Microbiology, Metagenomics, Microbiome, Phasing, Plant genomics, Population genomics, Single cell and spatial

 

Products

EPI2ME, EPI2ME Labs

Data analysis lounge
Microbiology & infectious disease
13:20 - 14:20 BST 14:20 - 15:20 CEST 08:20 - 09:20 EDT 05:20 - 06:20 PDT 22:20 - 23:20 AEST
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CANCER RESEARCH

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The potential of nanopore sequencing for personalised oncogenomics
Kieran O’Neill, Canada’s Michael Smith Genome Sciences Centre at BC Cancer, Canada
Kieran O’Neill

Talk title

The potential of nanopore sequencing for personalised oncogenomics

 

Abstract

Since 2012, our centre has run a successful personalised oncogenomics (POG) trial for patients with advanced cancers using short-read sequencing technology for whole-genome and transcriptome analysis of tumours to inform clinical decisions. Nanopore sequencing offers improved structural variant (SV) resolution, phasing, and methylation information. We have sequenced 187 cases from the POG trial on a PromethION, including 39 with matching normal tissue. We were able to detect clinically relevant structural variants previously known from Illumina, despite lower coverage, and to decipher complex SVs. Phasing allowed us to detect allele-specific expression and methylation, as well as whether multiple hits to the same gene were cis or trans. Methylation allowed us to cluster tumours by type and extract a coarse-level view of the tumour microenvironment using MethylCIBERSORT. We will release our data via the European Genomics Archive to serve as a test bed for tool development in tumour characterization.

 

Biography

Kieran is a staff scientist at one of Canada’s largest sequencing centres, attached to the provincial cancer agency. He works primarily on providing bioinformatics support, guidance, and TechD to projects using new sequencing platforms, especially Oxford Nanopore sequencing. This has included several publications on structural variant calling and characterization of imprinting. In the past, he has developed software for genome scaffolding, ontology browsing, flow cytometry analysis, and others, and has performed research into aspects of leukemia using a range of biological data.

 

Recent publications

Akbari, V. et al. Parent-of-origin detection and chromosome-scale haplotyping using long-read DNA methylation sequencing and Strand-seq. Cell Genom. 3(1) (2023). DOI: https://doi.org/10.1016/j.xgen.2022.100233

Chin, H. L. et al. An approach to rapid characterization of DMD copy number variants for prenatal risk assessment. Am. J. Med. Genet. A. 185(8):2541–2545 (2021). DOI: https://doi.org/10.1002/ajmg.a.62349

Akbari, V. et al. Megabase-scale methylation phasing using nanopore long reads and NanoMethPhase Genome Biol. 22(68) (2021). DOI: https://doi.org/10.1186/s13059-021-02283-5

 

Keywords

Animal genomics, Assembly, Bioinformatics, Cancer research, Chromatin conformation, Data analysis tool, Epigenetics, Fusion genes, Gene expression, Human genomics, Phasing, Structural variation, Targeted sequencing, Transcriptomics, Whole-genome sequencing

 

Products

PromethION P24/P48, R9 Flow Cells

Potential clinical utility of long-read sequencing in myeloid neoplasms
Cecilia C.S. Yeung & Olga Sala-Torra, Fred Hutchinson Cancer Center, USA
Olga Sala-Torra Cecilia C.S. Yeung

Talk title

Potential clinical utility of long-read sequencing in myeloid neoplasms

 

Abstract

Recurrent gene fusions are known drivers of disease pathophysiology in acute and chronic myeloid leukemia. Rapid identification of these fusion genes helps stratify disease by risk and assists with therapy choice. Precise molecular diagnosis in low-and-middle-income countries is challenging given the complexity of assays, need for trained technical support, and availability of reliable electricity. Even in developed countries, fusion detection requires a 7–10-day turnaround. We developed a long-read sequencing DNA assay designed using CRISPR guides to enrich for single molecules of long genomic DNA for nanopore sequencing and successfully detected fusion genes in cell lines and primary research specimens (e.g. BCR–ABL1, PML–RARA, CBFB–MYH11, KMT2A–AF4). We also successfully developed a cloud-based bioinformatics workflow with novel custom fusion finder software, Biodepot Fusion Finder. We detected fusion genes or confirmed the absence of fusions in 95% of cell lines and primary patient samples with the expected breakpoints. With optimized wet bench chemistry, sequencing workflow, and cloud-based bioinformatics data analytics, fusion detection in patient samples could be performed in under eight hours from sample draw to fusion confirmation.

 

Biography

Dr. Cecilia Yeung is an Associate Professor at the Fred Hutchinson Cancer Center and the University of Washington, USA. She serves as the Medical Director of the Fred Hutch Clinical Testing Laboratories. In her clinical appointment, she focuses her diagnostic skills in immunotherapy, transplant, and hematopathology. Her research interests focus on engineering innovative molecular technologies and bioinformatic tools, which strive to improve health care throughout the world with more effective molecular diagnostics — tests that are rapid, precise, and affordable.

Dr. Sala-Torra graduated from the school of Medicine at the University of Navarra, Spain, in 1996 and completed her hematology residency in the Bellvitge Hospital, in Barcelona, in 2002. She has worked at the Fred Hutchinson Cancer Center in Seattle, USA, since 2002. Her research interest focuses on developing novel molecular diagnostics for leukemias.

 

Keywords

Cancer research, Clinical research, Data analysis tool, Epigenetics, Fusion genes, Human genomics, Targeted sequencing, Whole-genome sequencing

 

Products

MinION Mk1C, Flongle, VolTRAX, Automation, R10 Flow Cells, Cas9 targeted sequencing, Duplex reads

Low-cost nanopore transcriptomics enables robust characterisation of diverse tumour types in low-resource settings
Jeremy Wang, University of North Carolina at Chapel Hill, USA
Jeremy Wang

Talk title

Low-cost nanopore transcriptomics enables robust characterisation of diverse tumour types in low-resource settings

 

Abstract

Our aim is to apply low-coverage nanopore transcriptome sequencing to address cancer outcome disparities in low/middle-income countries (LMIC), particularly for children. We performed cDNA sequencing of over 700 pediatric cancer specimens, including acute leukemias, lymphomas, non-central nervous system solid tumors, and brain tumors. We developed a machine-learning classification model that is able to robustly classify these samples according to their primary tumour type and clinically relevant genomic subtypes, despite huge variation in sequencing depth (over three orders of magnitude), sample and RNA quality (e.g. fresh-frozen and formalin-fixed paraffin-embedded), and processing. In collaboration with St. Jude Children’s Research Hospital, USA and collaborators in Malawi, Pakistan, India, Brazil, and Guatemala, we have demonstrated the technical feasibility of this approach in diverse LMIC settings.

 

Biography

Dr. Wang is an Assistant Professor of Genetics at the University of North Carolina at Chapel Hill, USA. The Wang lab develops and applies novel molecular approaches — predominantly nanopore sequencing — and computational genomics approaches to better characterise genetic variation contribution to human disease, including host transcriptomics, pathogen genomics, and the commensal microbiome.

 

Keywords

Cancer research, Clinical research, Gene expression, Transcript

 

Products

MinION Mk1B, MinION Mk1C, PromethION P2/P2 Solo, R9 Flow Cells, Short fragment mode, Direct RNA

Live Lounge networking area
Cancer research
13:20 - 14:20 BST 14:20 - 15:20 CEST 08:20 - 09:20 EDT 05:20 - 06:20 PDT 22:20 - 23:20 AEST
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RARE DISEASE

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Solving genetically undiagnosed inherited neuropathy families: long-read sequencing to the rescue
Marina Kennerson, The ANZAC Research Institute, Australia
Marina Kennerson

Talk title

Solving genetically undiagnosed inherited neuropathy families: long-read sequencing to the rescue

 

Abstract

Inherited peripheral neuropathies (IPNs) are a group of diseases causing axonal degeneration of peripheral motor and/or sensory nerves resulting in lifelong chronic disability. Despite the advances in gene discovery (over 100 causative genes reported), up to 40% of families remain genetically unsolved. The recent discovery of sorbitol dehydrogenase (SORD) and replication factor C subunit 1 (RFC1) has contributed to increasing the diagnostic rate for IPN families. However, due to the genomic organisation of SORD and the intronic pentanucleotide repeat expansion in RFC1, identifying mutations in these genes has been challenging. For this talk several vignettes for unsolved families will be presented in which we have undertaken both Oxford Nanopore Technologies whole-genome sequencing (WGS) and targeted (Read Until) sequencing to solve and identify promising candidate variants for some of our more challenging families.

 

Biography

Professor Marina Kennerson is Director of the Northcott Neuroscience Laboratory, ANZAC Research Institute, and heads the Gene Discovery and Translational Functional Genomics Hereditary Neuropathy (HN) Program. The program uses multi-omics, iPSC derived motor neurons, and C. elegans pre-clinical models, to discover HN gene targets for therapy development. Marina is Chair of the Asian Oceanic Inherited Neuropathy Consortium (AOINC), a member of the International Charcot-Marie-Tooth and Related Neuropathies Consortium (CMTR) board, and serves on the CMT Research Foundation Scientific Advisory Board.

 

Keywords

Human genomics, Structural variation, Whole-genome sequencing

Nanopore sequencing reveals retrotransposon insertions or complex genetic mechanisms in four rare disorders
Belén de la Morena-Barrio, University of Murcia, Spain
Belén de la Morena-Barrio

Talk title

Nanopore sequencing reveals retrotransposon insertions or complex genetic mechanisms in four rare disorders

 

Abstract

Up to 50% of cases with rare diseases lack a molecular diagnosis due to the limitations of current sequencing methods. Oxford Nanopore sequencing has emerged as a promising tool to overcome this gap and improve our understanding of the molecular mechanisms of rare diseases. We used Oxford Nanopore sequencing in 17 unresolved cases with four different rare disorders using PromethION or MinION with enrichment of targeted genes using adaptive sampling. Nanopore sequencing identified the molecular mechanisms in six cases, detecting retrotransposon insertions (three SVA elements and one LINE element) affecting SERPINC1, PEX1, and GYS2, which are responsible for antithrombin deficiency, peroxisomal disease, and glycogen storage disease. A complex structural variant in ITGB3 was detected in two cases with Glanzmann thrombasthenia. These results support that Oxford Nanopore sequencing is a suitable method to facilitate the molecular diagnosis of rare diseases and retrotransposon insertions may be underestimated due to the use of previous molecular methods.

 

Biography

Belén graduated in Pharmacy in 2015. In 2021, she obtained an International PhD in Medicine and received an Extraordinary Doctorate Award from the University of Murcia, Spain. She has published 20 articles, including six as first author. Currently, she has a postdoctoral contract at the University of Murcia/CIBERER, Spain. Her research is focused on the use of nanopore sequencing to identify new molecular mechanisms involved in rare diseases. She has also launched a company, Longseq, offering nanopore sequencing services.

 

Recent publications

de la Morena-Barrio, B. et al. Molecular dissection of structural variations involved in antithrombin deficiency. J. Mol. Diagn. 24(5):462–475 (2022).

Cuenca-Guardiola, J. et al. Improvement of large copy number variant detection by whole genome nanopore sequencing. J. Adv. Res. 30:S2090-1232(22)00241–7 (2022). DOI: 10.1016/j.jare.2022.10.012

de la Morena-Barrio, B. et al. Long-read sequencing identifies the first retrotransposon insertion and resolves structural variants causing antithrombin deficiency. Thromb. Haemost. 122(8):1369–1378 (2022).

 

Keywords

Clinical research, Human genomics, Structural variation, Targeted sequencing, Whole-genome sequencing

 

Products

MinION Mk1B, PromethION P24/P48, R9 Flow Cells, Adaptive sampling

The potential clinical utility of amplicon and targeted nanopore sequencing for rare disease diagnosis
Gavin Arno, University College London Institute of Ophthalmology, Moorfields Eye Hospital & North Thames Regional Genomics Laboratory Hub, UK
Gavin Arno

Talk title

The potential clinical utility of amplicon and targeted nanopore sequencing for rare disease diagnosis

 

Abstract

Next-generation sequencing has driven research into rare diseases and molecular diagnostics for over a decade. Up to 45% of inherited retinal disease patients remain unsolved after clinical testing, with variants of uncertain significance (VUS), non-coding variants, whole-genome sequencing (WGS) intractable genes, and structural rearrangements thought to contribute.

We investigated the potential clinical utility of nanopore sequencing in a case-driven study to improve the detection and characterisation of variants in WGS unsolved patients recruited from the Inherited Eye Disease clinics at Moorfields Eye Hospital. Amplicon sequencing of retinal gene transcripts from patient blood demonstrated the previously undetectable splicing effect of coding and non-coding VUS. Targeted nanopore sequencing enabled read-through of the WGS-intractable OPN1LW/OPN1MW gene array, distant variant phasing, and detection of structural rearrangement.

Nanopore sequencing is effective where traditional methods have failed to conclude diagnostic odysseys and may be an effective tool in the battery of molecular diagnostic tests.

 

Biography

Dr. Arno is a principal investigator at the University College London Institute of Ophthalmology and senior scientist for the Genetics department at Moorfields Eye Hospital, UK. His research interests are in the genomics of rare disease with a focus on inherited eye diseases and the application of novel methods to improve molecular diagnostic pipelines.

 

Keywords

Clinical research, Human genomics, Splice variation, Structural variation, Targeted sequencing, Ultra-long reads

 

Products

MinION Mk1B, MinION Mk1C, Flongle, R9 Flow Cells, Cas9 targeted sequencing

The Jam networking area
Human & clinical research
13:20 - 14:20 BST 14:20 - 15:20 CEST 08:20 - 09:20 EDT 05:20 - 06:20 PDT 22:20 - 23:20 AEST
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ENVIRONMENTAL MICROBIOLOGY

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Confirmation of Borg extrachromosomal genomes: analysis of their methylation patterns, metabolism, and tandem repeats
Marie Charlotte Schoelmerich, University of California, Berkeley, USA
Marie Charlotte Schoelmerich

Talk title

Confirmation of Borg extrachromosomal genomes: analysis of their methylation patterns, metabolism, and tandem repeats

 

Abstract

Huge novel extrachromosomal elements termed Borgs were recently associated with anaerobic methane-oxidizing archaea of the genus "Candidatus Methanoperedens". Oxford Nanopore assemblies yielded large fragments of previously partially sampled genomes and brought to light nine new Borg genomes, two of which were fully curated into the terminal inverted repeat regions. Nanopore sequencing reads also enabled identification of the native methylation patterns of Borg genomes and their hosts. An essentially complete, circularized nanopore-based 4.0 Mbp Methanoperedens genome was also recovered, polished to completion using Illumina reads, and used to compare its metabolic capacities with those provided by the associated Borgs. Overall, the findings confirm all key features of Borg genomes and substantially expand the genomic sampling of these enigmatic extrachromosomal elements of methane-oxidizing archaea.

 

Biography

Marie Schoelmerich is a postdoctoral research fellow in Jill Banfield’s lab at the Innovative Genomics Institute of the University of California, Berkeley, USA. She uses metagenomics to discover and investigate extrachromosomal elements linked to methane-consuming archaea. She is fascinated by anaerobic bacteria and archaea that are key in carbon cycling.

 

Recent publications

Al-Shayeb, B. et al. Borgs are giant genetic elements with potential to expand metabolic capacity. Nature 610(7933):731–736 (2022). DOI: 10.1038/s41586-022-05256-1

Schoelmerich, M.C. et al. Tandem repeats in giant archaeal Borg elements undergo rapid evolution and create new intrinsically disordered regions in proteins. PLoS. Biol. 26;21(1):e3001980 (2023). DOI: 10.1371/journal.pbio.3001980

 

Keywords

Bioinformatics, Metagenomics, Microbiology, Whole-genome sequencing

 

Products

GridION, PromethION P24/P48, R10 Flow Cells, R9 Flow

Nanopore sequencing of wild virus particles reveals previously undetected phage and phage-parasitizing elements
Ed DeLong, University of Hawai’i at Mānoa, USA
Ed DeLong

Talk title

Nanopore sequencing of wild virus particles reveals previously undetected phage and phage-parasitizing elements

 

Abstract

Phage satellites are mobile genetic elements that propagate by parasitizing bacteriophage replication. Nanopore sequencing of wild marine virus particle DNA recovered entire virus genomes in single-molecule reads, as well as phage satellites packaged in viral particles as concatemeric repeat elements. These diverse virus genomes and phage satellite concatemers could not be detected via short-read sequencing alone. The novel phage-parasitizing mobile elements were also found integrated within the genomes of dominant cellular hosts from the same habitats. Marine phage satellites were widespread in global oceanic virioplankton populations, suggesting their ubiquity, abundance, and temporal persistence worldwide. Their gene content and putative life cycles suggest that they exert significant impacts on host-cell phage immunity and defense, lateral gene transfer, and virus productivity. Similar phage parasites are predicted to thrive in virtually any habitat that also harbors bacteriophages.

 

Biography

Edward DeLong is a Professor of Oceanography at the University of Hawai‘i, Manoa. He received his BSc in Bacteriology at the University of California Davis and his PhD in Marine Biology at Scripps Institution of Oceanography, UC San Diego. He is an elected Fellow in the American Academy of Microbiology, the American Academy of Arts and Sciences, the European Molecular Biology Organization, and the American Association for the Advancement of Science.

 

Recent Publications

Beaulaurier J. et al. Assembly-free single-molecule nanopore sequencing recovers complete virus genomes from natural microbial communities. Genome Res. 30:437–446 (2020). doi: 10.1101/gr.251686.119

Eppley J. M. et al. Marine viral particles reveal an expansive repertoire of phage-parasitizing mobile elements. Proc. Natl. Acad. Sci. USA. 119: e2212722119 (2022).

Hackl et al. Novel integrative elements and genomic plasticity in ocean ecosystems. Cell 186:47–62 e16 (2023).

 

Keywords

Environmental research and conservation, Metagenomics, Microbiology, Microbiome, Population genomics 

 

Products

GridION 

 

Unlocking the microbiome of the International Space Station
Sarah Stahl-Rommel, NASA Health and Human Performance Contract & JES Tech, USA
Sarah Stahl-Rommel

Talk title

Unlocking the microbiome of the International Space Station

 

Abstract

The microbiome of the International Space Station (ISS) has been monitored to assess risk to spacecraft and crew for 22 years. This monitoring has been achieved through onboard culture and ground-based analyses with bias toward the detection of culturable organisms depicting generally low biodiversity. The implementation of culture-independent, nanopore-based studies, both onboard the ISS and with returned samples, is revealing a more thorough depiction of the microbiome. There is a common core microbiome across time and location, but key distinct areas of greater diversity exist. Through further investigation, these areas are emerging as unique ecological niches, potentially resulting in environmentally driven microbial selection. Moreover, the presence of some noted taxa has implications for crew health, planetary protection, and controls in future spacecraft systems. The ability to perform in situ profiling of the microbiome is transforming how NASA assesses risk.

 

Biography

Sarah Stahl-Rommel is the research lead for microbial monitoring technology development at the NASA Johnson Space Center. Toward that goal, she has driven the development of a complete sample-to-sequencer process for microbiome assessments and oversaw its successful implementation during analog and spaceflight missions. With her ultimate goal of sequencing-based microbial monitoring in any setting by any crew, Sarah is currently validating new methods to remove temperature constraints on reagents and working to provide enhanced crew autonomy for future NASA missions.

 

Keywords

Microbiology, Microbiome, Targeted sequencing

 

Products

MinION Mk1B, MinION Mk1C

Blondie networking area
Microbiology & infectious disease
13:20 - 14:20 BST 14:20 - 15:20 CEST 08:20 - 09:20 EDT 05:20 - 06:20 PDT 22:20 - 23:20 AEST
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METHYLATION & PHASING

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Nanomix: methylation-based cell-type deconvolution for low-pass nanopore sequencing
Jonathan Broadbent, Ontario Institute for Cancer Research & University of Toronto, Canada
Jonathan Broadbent

Talk title

Nanomix: methylation-based cell-type deconvolution for low-pass nanopore sequencing

 

Abstract

Deconvoluting heterogeneous DNA mixtures is typically accomplished using non-negative least squares (NNLS) when working with methylation arrays and short-read bisulfite sequencing. However, it is unclear how to best deconvolute mixtures using single-molecule base modification measurements. To address this, we developed Nanomix — a suite of tools designed for methylation deconvolution of nanopore sequencing data. Nanomix can simulate in silico mixtures of purified reference cell methylomes. We simulated lung and blood cell mixtures to benchmark deconvolution algorithms and reference cell atlases. We introduce new likelihood-based algorithms that demonstrate higher resilience to sequencing error and perform well at low coverage. Unlike previous methods, our tool can assign individual reads to cell types. Our results show how nanopore sequencing can leverage native methylation calling to deconvolute a complex mixture of DNA, which has applications to tumour purity testing and cell-free DNA analysis of liquid biopsies.

 

Biography

Jonathan Broadbent is a Master’s student of computer science at the University of Toronto and Ontario Institute for Cancer Research, Canada. He received his Bachelor’s degree in Computer Science and Biology from McGill University. He is a member of Jared Simpson’s lab, who specialise in developing bioinformatic tools for long-read sequencing.

 

Recent Publications

Vincent, M. et al. RNAglib: a python package for RNA 2.5 D graphs. Bioinformatics 38(5):1458–1459 (2022). DOI: https://doi.org/10.1093/bioinformatics/btab844

 

Keywords

Bioinformatics, Cancer research, Data analysis tool, Epigenetics, Whole-genome sequencing

 

Products

MinION Mk1B, R10 Flow Cells, R9 Flow Cells, Short fragment mode

Genome-wide single-molecule analysis of DNA methylation by nanopore sequencing reveals heterogeneous patterns at heterochromatin
Lyndsay Kerr, The University of Edinburgh, UK
Lyndsay Kerr

Talk title

Genome-wide single-molecule analysis of DNA methylation by nanopore sequencing reveals heterogeneous patterns at heterochromatin

 

Abstract

DNA methylation patterns are primarily studied at the bulk level, where information is averaged over a cellular population. While some studies have examined methylation patterns within single molecules, the short-read nature of the data used has restricted these analyses to short patterns. However, the ability of nanopore sequencing to generate megabase-scale reads provides the opportunity to study single-molecule patterns up to four orders of magnitude longer than those previously considered. Here, we analyse methylation within single nanopore reads with a mean length of 24.6 kb. Using the correlation in methylation state between neighbouring sites, we quantify heterogeneity within single reads and find that the most heterogeneous single-molecule methylation patterns are observed in heterochromatin and partially methylated domains. Moreover, by analysing single-molecule patterns in more detail, we observe a 185 bp periodicity in DNA methylation that sheds light on the nature of the patterns observed within single molecules.

 

Biography

Lyndsay Kerr has a PhD in mathematics from Strathclyde University, UK, and is now an MRC-funded cross-disciplinary postdoctoral fellow at the Institute of Genetics and Cancer within the University of Edinburgh, UK. Her research focuses on the use of mathematical models and the analysis of sequencing data to study DNA methylation patterns. In particular, while previous studies have paid limited attention to short patterns, she is interested in developing mathematical models and data analysis pipelines that allow long patterns to be studied.

 

Recent publications

Kerr, L., Grima, R., and Sproul, D. Genome-wide single-molecule analysis of long-read DNA methylation reveals heterogeneous patterns at heterochromatin bioRxiv 2022.11.15.516549 (2022). DOI: https://doi.org/10.1101/2022.11.15.516549

 

Keywords

Bioinformatics, Epigenetics, Whole-genome sequencing

MeOW: genome-wide identification of differentially methylated regions using Oxford nanopore long-read sequencing data
Miranda Galey, University of Washington, USA
Miranda Galey

Talk title

MeOW: genome-wide identification of differentially methylated regions using Oxford nanopore long-read sequencing data

 

Abstract

Despite significant improvements in clinical genetic testing, nearly half of individuals with suspected genetic disorders remain undiagnosed. Oxford Nanopore long-read sequencing can identify disease-causing variants missed by other methods. We developed MeOW, a program that quickly identifies genome-wide differentially methylated regions (DMRs) that may contribute to disease. MeOW successfully identified 100% of DMRs in individuals with known imprinting disorders, such as Prader–Willi syndrome, Angelman syndrome, and Beckwith–Wiedemann syndrome. When applied to a research cohort of individuals who remained undiagnosed after comprehensive clinical testing, MeOW revealed high-priority DMRs for further evaluation. Our research shows that MeOW simplifies genome-wide analysis of challenging cases and enables the identification of novel DMRs associated with human disease.

 

Biography

Miranda is a computational biologist specializing in nanopore sequencing and has a proven track record of developing in-house software to make genomic analysis more accessible. With an MSc in Integrated Biosciences from the University of Minnesota, USA, she currently manages the University of Washington’s Nanopore Sequencing Core. Miranda is passionate about the real-world applications of psychedelic mathematics and continually seeks new ways to apply her knowledge and skills.

 

Recent publications

Galey, M. et al. 3-hour genome sequencing and targeted analysis to rapidly assess genetic risk. medRxiv, 2022-09 (2022).

Miller, D.E. et al. Targeted long-read sequencing identifies missing pathogenic variants in unsolved Werner syndrome cases. J. Med. Genet. 59(11):1087–1094 (2022).

Miller, D.E. et al. Targeted long-read sequencing identifies a retrotransposon insertion as a cause of altered GNAS exon A/B methylation in a family with autosomal dominant pseudohypoparathyroidism type 1b (PHP1B). JMBR. 37(9):1711–1719 (2022).

 

Keywords

Bioinformatics, Clinical research, Data analysis tool, Epigenetics, Whole-genome sequencing

 

Products

PromethION P24/P48, R9 Flow Cells

MethPhaser: automated methylation-based haplotype phasing of human genomes with Oxford Nanopore sequencing
Fritz Sedlazeck, Baylor College of Medicine & Rice University, USA
Fritz Sedlazeck

Talk title

MethPhaser: automated methylation-based haplotype phasing of human genomes with Oxford Nanopore sequencing

 

Abstract

Long-read sequencing was declared the method of the year in 2022, and indeed, has fully arrived on the computational biology scene. Specifically, Oxford Nanopore sequencing technology has enabled computational approaches to assemble accurate and complete human genome haplotypes, while providing unprecedented methylation profiling. Nevertheless, homozygous regions and variability in read lengths limit traditional single-nucleotide polymorphism (SNP)-based haplotype phasing methods. To address this, we developed MethPhaser, a computational method for automated methylation-based haplotype phasing of the human genome. MethPhaser is the first in the long-read era to utilize SNP and methylation signals for human genome phasing. We show MethPhaser improves upon widely used SNP-based human genome phasing approaches by bridging the SNP-phased blocks to resolve the ambiguity in homozygous regions. MethPhaser is also able to rescue previously un-haplotagged reads from SNP-based methods. We will conclude with future directions and the next steps. MethPhaser is available at: https://gitlab.com/treangenlab/MethPhaser.

 

Biography

Dr. Fritz Sedlazeck is an Associate Professor at Baylor College of Medicine and an Adjunct Associate Professor at Rice University, USA. He has led a research group at the Human Genome Sequencing Centre at Baylor College of Medicine since 2017. His research focuses on developing computational methods to detect and analyze genomic variations with a focus on structural variations (SVs). SVs are genomic events that manipulate multiple positions in a genome, which impact evolution, genomic disorders, and regulation, and also play an important role in explaining multiple phenotypes. Dr. Sedlazeck’s groups focus on the mechanisms of the formation of SVs across multiple species, to improve our understanding how these complex alleles evolve and impact phenotypes. Over the past years, Dr. Sedlazeck has led multiple efforts from large-scale short reads (e.g. Topmed, CCDG) to long reads (CARD, All of US) to study the occurrence, impact, and mechanisms of SVs.

 

Keywords

Bioinformatics, Epigenetics, Human genomics, Phasing, Whole-genome sequencing

 

Products

PromethION P24/P48, Q20+, R10 Flow Cells

Data analysis lounge
Bioinformatics
14:35 - 14:55 BST 15:35 - 15:55 CEST 09:35 - 09:55 EDT 06:35 - 06:55 PDT 23:35 - 23:55 AEST
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MINI THEATRE ON-DEMAND

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Identifying m6A RNA modifications in neuroblastoma cell lines using nanopore sequencing
Jade Forster, University of Southampton, UK
Jade Forster

Talk title

Identifying m6A RNA modifications in neuroblastoma cell lines using nanopore sequencing

 

Abstract

Neuroblastoma is a childhood cancer in which half of patients are classified as high risk and are already in advanced disease, which is associated with poor outcome despite intensive treatment. This project aimed to use direct RNA sequencing to identify and characterise N6-methyladenosine (m6A) RNA modifications in human neuroblastoma cell lines. There is evidence to suggest m6A modifications are involved in neuroblastoma biology, susceptibility, and prognosis. Using the bioinformatic tool, m6Anet, we identified m6A modifications and characterised target genes in the cell lines analysed. Many of the genes identified as being m6A modified have been implicated in neuroblastoma and more broadly in cancer previously; and a gene ontology analysis showed significant enrichment in important biological processes. Further analysis is needed to understand the significance of these RNA modifications in neuroblastoma.

 

Biography

Dr. Jade Forster is an early career researcher at the University of Southampton, UK. Her expertise and research is based in translational and personalised genomic medicine in primarily cancer and rare disease genomics. Jade’s current research is focused at present on using nanopore sequencing to better understand and characterise RNA modifications and splicing events at bulk and single-cell transcriptomic levels, in neuroblastoma and in response to immunotherapy drugs.

 

Keywords

Cancer research, Epigenetics, Gene expression, Transcriptomics

 

Products

GridION, R9 Flow Cells, Direct RNA

Investigating RNA isoform expression using the IsoMix toolkit
Michael Clark, The University of Melbourne, Australia
Michael Clark

Talk title

Investigating RNA isoform expression using the IsoMix toolkit

 

Abstract

Accurate quantification of genes and their mRNA products is essential to understanding health and disease. In humans, processes such as alternative splicing cause almost all genes to express multiple mRNA products (isoforms), which can have different functions. Long-read RNA sequencing can cover an entire mRNA sequence in a single read and so identify and quantify the isoforms present. Therefore, we have developed the IsoMix toolkit to enable the discovery, quantification, and characterization of RNA isoforms in both bulk and single-cell samples. With these tools we have discovered hundreds of novel isoforms of disease-risk genes and their likely proteomic consequences; tracked cell-type specific expression of isoforms during neuronal development; and quantified differential expression of isoforms between regions of the human brain. The characterisation of RNA isoforms with the IsoMix toolkit will enable a vastly improved understanding of gene isoforms and their biological and pathophysiological functions.

 

Biography

Dr Mike Clark is a researcher at the University of Melbourne, Australia. His research sits at the intersection of genomics and neuroscience, developing and utilizing a number of transcriptomic approaches to investigate gene expression and function in the human brain and in neurological disorders. We are particularly interested in risk genes for mental health disorders and how they act to make some individuals more likely to develop conditions such as schizophrenia, depression, and bipolar disorder.

 

Recent publications

You, Y. et al. Identification of cell barcodes from long-read single-cell RNA-seq with BLAZE. Genome Biol. (2023) In press.

You, Y., Clark, M.B., and Shim, H. NanoSplicer: accurate identification of splice junctions using Oxford Nanopore sequencing. Bioinformatics. 38(15):3741–3748 (2022). DOI: https://doi.org/10.1093/bioinformatics/btac359

Gleeson, J. et al. Accurate expression quantification from nanopore direct RNA sequencing with NanoCount. Nucleic Acids Res. 50(4): e19 (2022). DOI: https://doi.org/10.1093/nar/gkab1129

Tian, L., et al. Comprehensive characterization of single cell full-length isoforms in human and mouse with long-read sequencing. Genome Biol. 22(1):310 (2021). DOI: https://doi.org/10.1186/s13059-021-02525-6

De Paoli-Iseppi, R., Gleeson, J., and Clark, M.B. Isoform Age — splice isoform profiling using long-read technologies. Front Mol Biosci. 8:711733 (2021). DOI: https://doi.org/10.3389/fmolb.2021.711733

 

Keywords

Bioinformatics, Data analysis tool, Gene expression, Human genomics, Single cell and spatial, Splice variation, Transcriptomics

 

Products

GridION, PromethION P24/P48, Q20+, R10 Flow Cells, R9 Flow Cells, Direct RNA

Secret cinema
Cancer research Bioinformatics
14:55 - 15:20 BST 15:55 - 16:20 CEST 09:55 - 10:20 EDT 06:55 - 07:20 PDT 23:55 - 00:20 AEST
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SHOWCASE STAGE: LIQUID BIOPSY

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Nanopore sequencing of cell-free DNA for methylation-based breast cancer detection in a case-control research cohort
Billy Lau, Stanford University School of Medicine, USA
Billy Lau

Talk title

Nanopore sequencing of cell-free DNA for methylation-based breast cancer detection in a case-control research cohort

 

Abstract

Liquid biopsies are increasingly being used as a cancer detection modality. Epigenetic characterization of cell-free DNA (cfDNA), specifically DNA methylation, is an emerging approach for the sensitive detection and quantification of tumor burden. Detection of early-stage cancers remains an ongoing challenge due to lower amounts of tumor-specific DNA molecules found in cfDNA. In the context of breast cancer detection, existing cfDNA analysis methods suffer from poor sensitivity, especially at earlier stages of malignancy. To resolve this, we developed a novel approach for single-molecule methylation analysis of cfDNA from cancer patients. Our study included a large cohort (~200 with stage I–II breast cancer and ~400 healthy controls). We successfully distinguished breast cancer cfDNA samples from healthy controls based on separate validation datasets. Overall, our study demonstrated that our nanopore-based cfDNA sequencing method can be an effective and scalable technique for the non-invasive detection of breast cancer from blood.

 

Biography

Dr. Billy Lau is an Instructor in the Division of Oncology at Stanford University School of Medicine, USA. His research focus is on leveraging genome technology for cancer detection and studying human genomic variation. Dr. Lau received his doctorate in Engineering Sciences from Harvard University, USA and completed his postdoctoral training with Dr. Hanlee Ji at Stanford University. He has also received the National Human Genome Research Institution’s Genomic Innovator Award, where he focuses on building tools to maximize information from single molecules and cells.

 

Keywords

Cancer research, Epigenetics, Whole-genome sequencing

 

Products

PromethION P24/P48, Automation, R10 Flow Cells, R9 Flow Cells

The potential application of nanopore sequencing for liquid biopsy analysis in children with cancer
Carolin Sauer, EMBL-EBI, UK
Carolin Sauer

Talk title

The potential application of nanopore sequencing for liquid biopsy analysis in children with cancer

 

Abstract

Paediatric cancers are the leading cause of death in children post infancy. Analysis of cell-free DNA (cfDNA) to detect circulating tumour-derived DNA (ctDNA) may offer a powerful, minimally invasive tool for diagnosis and comprehensive molecular tumour profiling. Current ctDNA approaches are limited in sensitivity, specificity, scalability, turnaround time, and cost, hindering their implementation into standard clinical care. Here, we exploit whole-genome nanopore sequencing for the multi-modal analysis of cfDNA in paediatric cancer patients. Using liquid biopsy samples from the Stratified Medicine Paediatrics study, we demonstrate the utility of nanopore sequencing to detect clinically relevant somatic aberrations, highly concordant with those detected using matched low-pass Illumina whole-genome sequencing. Additionally, nanopore sequencing allowed read-out of methylation profiles from cfDNA, facilitating tissue-of-origin and oncotype characterisation. Finally, longitudinal monitoring using nanopore sequencing correlated with disease burden and was predictive of disease recurrence, illustrating the strong potential of nanopore-based approaches for clinical disease management in children with cancer.

 

Biography

Originally from Germany, Carolin moved to the UK in 2013 to study for her BSc (Hons) degree in Biology at the University of Manchester. Subsequently, Carolin completed her PhD in Medical Sciences at the Cancer Research UK Cambridge Institute, University of Cambridge working in Prof. Brenton’s Functional Genomics of Ovarian Cancer laboratory. In 2022, Carolin joined the Cancer Genomics Group led by Dr. Cortés-Ciriano and is now a postdoctoral research fellow at the EMBL European Bioinformatics Institute (EMBL-EBI).

 

Keywords

Bioinformatics, Cancer research, Clinical research, Whole-genome sequencing

 

Products

MinION Mk1B, MinION Mk1C, PromethION P24/P48, R10 Flow Cells, R9 Flow Cells, Short fragment mode

Nanopore sequencing of ctDNA — better than short read!
Andrew Beggs, University of Birmingham, UK
Andrew Beggs

Talk title

Nanopore sequencing of ctDNA — better than short read!

 

Abstract

In this talk I will discuss the potential applications of nanopore ctDNA sequencing in developing a pan-cancer assay for detection and screening. Through this, I will demonstrate data that shows the detection of MDM2 copy number in sarcoma samples as well as very low input VAF samples. I will also give an overview of some of the technical challenges that have to be overcome with nanopore sequencing of ctDNA. 

 

Biography

Andrew Beggs is a Professor of Cancer Genetics & Surgery at the University of Birmingham and University Hospitals Birmingham, in the UK. He currently holds an MRC Senior Clinical Fellowship and leads the genomic medicine work packages for multiple stratified oncology consortia. He runs a mixed wet/dry lab in oncology, immunogenetics, and organoid models. 

 

Keywords 

Cancer research, Fusion genes, Human genomics, Targeted sequencing 

 

Products 

GridION, PromethION P24/P48, R10 Flow Cells, Duplex reads 

Live lounge
Cancer research
15:30 - 16:00 BST 16:30 - 17:00 CEST 10:30 - 11:00 EDT 07:30 - 08:00 PDT 00:30 - 01:00 AEST
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PLENARY 4

online onsite
Update from the Applications team
Dan Turner, SVP, Applications, Oxford Nanopore Technologies
Dan Turner

Talk title

Update from the Applications team

 

Biography

Dan leads Oxford Nanopore’s Applications Team, who are based in Oxford, New York, San Francisco, Singapore, and Norwich. The Applications team has a wide range of responsibilities, including library and sample prep, developing assays for Oxford Nanopore Diagnostics — the company’s diagnostics arm, biological benchmarking of the technology, and development of genomics applications with external collaborators. The overarching aim of the team is to expand the utility of Oxford Nanopore Technologies’ devices and help bring the benefits of these technologies to the wider world.

 

 

Auditorium
16:00 - 16:30 BST 17:00 - 17:30 CEST 11:00 - 11:30 EDT 08:00 - 08:30 PDT 01:00 - 01:30 AEST
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LIGHTNING TALKS

online onsite
The dark side of carrier screening: illuminating hard-to-decipher genes in common genetic disorders with nanopore sequencing
Bradley Hall, Asuragen, USA
Bradley Hall

Talk title

The dark side of carrier screening: illuminating hard-to-decipher genes in common genetic disorders with nanopore sequencing

 

Abstract

Carrier screening (CS) aims to identify couples at risk for having a child with a severe genetic disorder. Although next-generation sequencing (NGS) is a widely used method, it fails to resolve many problematic genes, such as those with tandem repeats, copy number variation, pseudogenes, and structural variation. These genes require multiple specialized techniques and only cover a fraction of carrier risk. We combined three innovations to address these shortcomings: novel long-range PCR enrichment, nanopore sequencing, and companion bioinformatic software. Using a single workstream, we developed a prototype assay panel of 11 genes critical for CS, including eight “hard-to-decipher” genes, representing ~70% of all pathogenic variants for a severe inherited disorder in at-risk couples compared to gene panels at least 15 times larger. We describe evaluation of this prototype assay for CFTR, SMN1, SMN2, FMR1, HBA1, HBA2, HBB, F8, GBA, CYP21A2, and TNXB across 380 samples.

 

Biography

Bradley Hall, Director of R&D at Asuragen, received a Molecular Biology PhD from the University of Texas in 2008. Here, he developed the Aptamer Stream within the Freshman Research Initiative, the largest undergraduate research program in the country. He transitioned to Altermune Technologies in 2010, founded by Nobel laureate Kary Mullis, focused on immune-redirecting therapies. In 2016, Brad became a Senior Scientist at Asuragen. He has been awarded multiple SBIR grants, patents, and published 15 manuscripts.

 

Keywords

Bioinformatics, Clinical research, Data analysis tool, Human genomics, Phasing, SNVs, Structural variation, Targeted sequencing

 

Products

MinION Mk1B

Unlocking nanopore sequencing for managing food safety in the food industry
Koen Bossers, Leiden Centre for Applied Bioscience, University of Applied Sciences Leiden, Netherlands
Koen Bossers

Talk title

Unlocking nanopore sequencing for managing food safety in the food industry

 

Abstract

Bacterial food contaminants such as Listeria monocytogenes are a major cause of food poisoning. Whole genome sequencing can be a very valuable tool for the food industry to identify potential new targets for food safety interventions. For example, it is very important to know whether a strain of L. monocytogenes found on an end product originates from a particular supplier or from a strain that is persistently present in a plant and re-emerges from time to time. Together with food industry partners, we developed a pipeline that reconstructs complete L. monocytogenes genomes from nanopore sequencing reads. We are also developing an accompanying web application in which food industry partners can interactively cluster and visualize L. monocytogenes genomes to precisely monitor their production chains and pinpoint the origin of a contamination. Our tools can also be applied to other food contaminants such as Salmonella or E. coli.

 

Biography

Koen Bossers obtained a Master’s degree in Chemistry from Radboud University Nijmegen, Netherlands, and completed his PhD training in molecular neuroscience at the Netherlands Institute for Brain Research. Since 2017, he has been working as a bioinformatician at the Leiden Center for Applied Biosciences and lectures in bio-informatics at the Leiden University of Applied Sciences, Netherlands.

 

Keywords

Bioinformatics, Data analysis tool, Infectious disease, Microbiology, Whole-genome sequencing

 

Products

GridION

Isogenomic reference genomes using de novo assembly of experimentally relevant human diploid cell lines
Simona Giunta, Sapienza University of Rome, Italy
Simona Giunta

Talk title

Isogenomic reference genomes using de novo assembly of experimentally relevant human diploid cell lines

 

Abstract

The Giunta Laboratory of Genome Evolution studies some of the most recalcitrant loci in the human genome, namely repetitive DNA. Here, we present for the first time our matched referencing approach using experimentally relevant cell lines. To define our innovative paradigm, I coined the word “isogenomic” referencing. Beyond the current use of reference genomes, we present an example of isogenomic referencing using the de novo assembly of experimentally relevant human diploid retinal epithelial cells RPE1. We combined 40x HiFi reads, 30x nanopore ultra-long reads (>100 kb) with a Q score >20, 70x nanopore reads, and 90x Illumina reads for de novo assembly of the RPE1 genome. RPE1 is a widely used line across fields of research, this serves as a resource for the scientific community. Importantly, we found experiments on RPE1 where matched isogenomic reference provides improved and more faithful alignments, and removes computational biases caused by comparison done across non-matched genomes, especially of polymorphic genomic loci. Thus, we propose to apply isogenomic referencing for future omics analyses of laboratory cell lines.

 

Biography

Simona Giunta is the Associate Professor of Human Genomics and Head of Laboratory of Genome Evolution at Sapienza University of Rome. She obtained a PhD from the University of Cambridge, a UICC Fellowship at CSIRO (Australia), and numerous research funding during her 10 years as a Research Scientist at the Rockefeller University (USA). She received the Rita Levi-Montalcini award, Marie Curie Fellowship, and a Start-Up Grant from AIRC. More recently, Simona was awarded an ERC Starting Grant to continue her pioneering work on instability within human repetitive DNA.

 

Keywords

Cancer research, Human genomics, Ultra-long reads, Whole-genome sequencing

 

Products

PromethION P2/P2 Solo, PromethION P24/P48, Q20+, R10 Flow Cells, R9 Flow Cells, Cas9 targeted sequencing

Squiggle analysis for metagenomic viability inference
Harika Ürel, Helmholtz AI Institute, Helmholtz Pioneer Campus, & Technical University of Munich, Germany
Harika Ürel

Talk title

Squiggle analysis for metagenomic viability inference

 

Abstract

Metagenomic approaches enable unbiased whole microbial community characterizations but cannot differentiate between living and dead microbes, which is crucial for virulent pathogen detection. Traditional methods for identifying living microbes are labor-intensive and time-consuming. This project aims to develop a computer-based framework using nanopore sequencing to predict microorganism viability from raw metagenomic squiggle data. Nanopore sequencing measures ionic current fluctuations in signal traces (“squiggle”) in real-time as single-strand nucleotides pass through membrane-embedded nanopores. Squiggles can detect atomic changes that reveal functionally important genomic characteristics. We hypothesize that DNA from dead microorganisms gets exposed to environmental damage and lacks DNA repair mechanisms, thereby generating squiggle signal that is distinct from DNA in living organisms. We extracted DNA from living and dead bacteria, obtained squiggle data via nanopore sequencing, and trained deep neural networks to explore differences in squiggle data from such AI predictions.

 

Biography

Harika Ürel is a PhD student at the Technical University of Munich, Helmholtz AI, and Helmholtz Pioneer Campus and a member of the Munich School of Data Science. Her MSc in Molecular Bioengineering at the Technical University of Dresden ignited her passion for computational biology. During her internship at the Max Planck Institute of Biophysics, she worked on Bayesian inference for protein simulations. In Dr. Lara Urban's Lab, she develops deep learning models for exploring squiggle data.

 

Keywords

Bioinformatics, Data analysis tool, Environmental research and conservation, Metagenomics, Microbiology

 

Products

MinION Mk1B

Advancing targeted haplotyping in pharmacogenomics using adaptive sampling
Koen Deserranno, Ghent University, Belgium
Koen Deserranno

Talk title

Advancing targeted haplotyping in pharmacogenomics using adaptive sampling

 

Abstract

Pharmacogenomics (PGx) encompasses the personalisation of a patient’s drug therapy based on their genomic blueprint. However, current genotyping techniques are still limited in terms of the relevance of the information they provide. Therefore, we applied the recently unrolled adaptive sampling feature on the PromethION device to characterize relevant PGx genes. We targeted a panel of over 1,056 pharmacogenes, including challenging genes such as CYP2D6, from the Pharmacogenomics Knowledge Base. Using the latest R10.4.1 Flow Cells and Native Barcoding Kit V14, we multiplexed reference DNA standards, including the well-characterized GIAB NA12878 sample and performed PromethION sequencing. After superhigh accuracy basecalling, we evaluated variant calling, structural variant detection, and haplotype phasing with respect to the published references and earlier Oxford Nanopore sequencing data from R9.4.1 Flow Cells. Our results confirm the potential added value of the latest Oxford Nanopore sequencing chemistry to inform haplotype-guided pharmacological treatment.

 

Biography

Koen Deserranno graduated as a Pharmacist in Drug Development in 2021 at Ghent University, Belgium. Currently, he is pursuing a PhD at the Ghent University Lab of Pharmaceutical Biotechnology at the Faculty of Pharmaceutical Sciences. His Master’s thesis focused on long-read sequencing in pharmacogenetics. Last year, he contributed to this field by publishing a Cas9 targeted nanopore sequencing strategy to result in enhanced variant calling and improve CYP2D6–CYP2D7 hybrid allele genotyping.

 

Recent publications

Rubben, K.F. et al. Cas9 targeted nanopore sequencing with enhanced variant calling improves CYP2D6–CYP2D7 hybrid allele genotyping. PLOS Genet. 18(9):e1010176 (2022).

 

Keywords

Bioinformatics, Human genomics, Phasing, Structural variation, Targeted sequencing

 

Products

PromethION P24/P48, Q20+, R10 Flow Cells, R9 Flow Cells, Adaptive sampling, Duplex reads

Auditorium
Human & clinical research Microbiology & infectious disease Bioinformatics
16:30 - 16:50 BST 17:30 - 17:50 CEST 11:30 - 11:50 EDT 08:30 - 08:50 PDT 01:30 - 01:50 AEST
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PLENARY 5

online onsite
The Emirati Genome Project: where long reads became an integral part of large genome projects (a first!)
Tiago R. Magalhães, G42 Healthcare, United Arab Emirates
Tiago R. Magalhães

Talk title

The Emirati Genome Project: where long reads became an integral part of large genome projects (a first!)

 

Abstract

The Emirati Genome Program (EGP) is using genomics to ensure the best healthcare and quality of life for the Emirati population. It will also be an engine for science and knowledge, a key driver of the UAE's development. The EGP will sequence one million Emiratis, the entire population.

The UAE has one of the highest rates of birth defects and the impact of the EGP can already be measured in programs, such as pre-marital screening.

Since its inception, the EGP has used long reads at scale, because of the increased power in structural variants, phasing, methylation, and accuracy. The EGP has sequenced over 80,000 samples with nanopore sequencing, the largest long-read cohort in the world.

This has provided G42 with extensive knowledge on how to use Oxford Nanopore technology at scale, which we will present at London Calling, including the implementation of Dorado (joint work with AWS and Oxford Nanopore Technologies). G42 has recently started analysis on the EGP, and we will present preliminary results on HLA calling, and a population characterization of the Emirati population.

 

Biography

Tiago Magalhães is currently the Director of Bioinformatics at G42, Abu Dhabi, where he oversees the bioinformatics team to produce and analyze one of the largest population cohorts in the world. Previously, Tiago was the VP for Bioinformatics at GMI, Genomics Medicine Ireland. He has a PhD from UC Berkeley, USA, and an EMBA from Bicocca University, Italy. Tiago has worked and published on autism, multiple sclerosis, cancer, and ancestry. He was the Executive Director at CCMAR, a marine research institute in the Algarve, Portugal. Tiago was involved in several European Regional Innovation plans and he is a reviewer for the European and other funding bodies in genomics.

 

Keywords

Bioinformatics, Cancer research, Clinical research, Data analysis tool, Gene expression, Genomic epidemiology, Human genomics

 

Products

PromethION P24/P48

Auditorium
Human & clinical research
16:50 - 17:10 BST 17:50 - 18:10 CEST 11:50 - 12:10 EDT 08:50 - 09:10 PDT 01:50 - 02:10 AEST
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RNA UPDATE

online onsite
Direct RNA sequencing update (SQK-RNA004): initial impressions of RNA004 and its application for functional profiling of cancer-associated long non-coding RNAs
Libby Snell & Martin Smith, Principal Scientist, Applications, Oxford Nanopore Technologies & Sainte-Justine University-Hospital Research Centre, Canada
Martin Smith Libby Snell

Talk title

Direct RNA sequencing update (SQK-RNA004): initial impressions of RNA004 and its application for functional profiling of cancer-associated long non-coding RNAs

 

Abstract

Oxford Nanopore Technologies’ direct RNA sequencing chemistry is unique as it determines the sequence of long-read RNA transcripts, capturing full-length isoforms, UTRs, and poly(A) tail lengths, without the requirement of first converting to DNA, nor PCR amplification. Here, we present our new, improved direct RNA sequencing chemistry (SQK-RNA004). Recent chemistry upgrades include a new nanopore optimized for RNA base discrimination and improvements to the basecaller architecture, providing increased raw-read accuracy. Furthermore, through the development of a faster motor protein and sequencing software upgrades, we have boosted sequencing output. Combined, these augmentations provide the ability to generate rich transcriptome information.

The capacity to sequence native RNAs is one of the unique features of nanopore sequencing and a revolution for RNA biology. However, the low yield and high input requirement have hindered the widespread adoption of this sequencing chemistry. I will first present our initial impressions of the updated RNA004 kit, comparing yields from poly(A) enriched and total RNA input, quality scores, and various observations on synthetic spike-in standards. I will then present preliminary results from over 18 RNA004 PromethION Flow Cells applied to functional cancer genomics. Specifically, we generated native transcriptomes from CRISPR-Cas13 knockdowns of four cancer-associated long non-coding RNAs identified through a CRISPR-Cas9 screen, seeking to characterise the biological functions of these non-coding genes.

 

Biographies

Libby Snell, PhD, is the lead scientist overseeing Oxford Nanopore Technologies’ RNA-based sequencing. She is an original designer and developer of direct RNA and novel cDNA sequencing methods. She is a Principal Scientist in the Applications group and has been with the company for over eleven years. She has a broad background in transcriptomics, molecular genetics, comparative genomics, and evolution and developmental biology from her MS, PhD, and postdoctoral research (USA and UK) prior to her time at the company.

Martin Smith is a computational biologist at the University of Montreal and the Sainte-Justine University-Hospital Research Centre with an interest in RNA, cancer, and immunology. His laboratory develops biomedical and bioinformatics solutions for real-time genomics and nanopore signal analysis, with an emphasis on clinical translation. A nanopore user since 2014, he has established certified nanopore services at CHU Sainte Justine in Montreal and the Kinghorn Centre for Clinical Genomics in Sydney.

 

Keywords

Bioinformatics, Cancer research, Gene expression, Human genomics, Splice variation, Transcriptomics

 

Products

PromethION P24/P48, Direct RNA

Auditorium
Methods & techniques
17:45 - 18:05 BST 18:45 - 19:05 CEST 12:45 - 13:05 EDT 09:45 - 10:05 PDT 02:45 - 03:05 AEST
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SECRET CINEMA

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A complete analysis of human genomes and transcriptomes using nanopore sequencing
Miten Jain, Northeastern University, USA
Miten Jain

Talk title

A complete analysis of human genomes and transcriptomes using nanopore sequencing

 

Abstract

We will share updates on human genome analyses using duplex DNA and RNA004 chemistries.

 

Biography

Miten is an Assistant Professor of Bioengineering and Physics and leads the Genome Technology Laboratory at Northeastern University. He did his PhD at the University of California, Santa Cruz, in the Nanopore Group. His long-term goals include developing applications at the intersection of technology, engineering, and biology, and translating them to the clinic.

 

Keywords

Animal genomics, Assembly, Bioinformatics, Cancer research, Chromatin conformation, Clinical research, Data analysis tool, Education, Environmental research and conservation, Epigenetics, Fusion genes, Gene expression, Genomic epidemiology, Human genomics, Identification, Immunology, Infectious disease, Metagenomics, Microbiology, Microbiome, Phasing, Population genomics, Single cell and spatial, SNVs, Splice variation, Structural variation, Targeted sequencing, Transcriptomics, Ultra-long reads, Whole-genome sequencing

 

Products

MinION Mk1B, GridION, PromethION P2/P2 Solo, PromethION P24/P48, Q20+, R10 Flow Cells, R9 Flow Cells, Adaptive sampling, Duplex reads, Direct RNA, Pore-C

Nanopore sequencing of tRNA modifications
Tsutomu Suzuki, University of Tokyo, Japan
Tsutomu Suzuki

Talk title

Nanopore sequencing of tRNA modifications

 

Abstract

Transfer (t) RNAs are extensively decorated with a wide variety of post-translational modifications. The steady-state level of each tRNA and its modification status are dynamically regulated in different cells and tissues in a spatiotemporal manner. To explore the physiological importance of tRNAs in various biological contexts, it is necessary to establish an innovative technology to profile and analyze cellular tRNAs with their modification status. Although next-generation sequencing (NGS)-based methods are highly sensitive and widely available for profiling tRNAs and detecting several tRNA modifications from limited specimens, they are applied only to specific tRNA modifications, because most of the information on RNA modifications is eliminated during cDNA conversion. Nanopore-based sequencing is a unique method capable of directly analyzing RNA molecules without cDNA conversion. We have been developing a handy and practical method for classifying cellular tRNAs with their modification status using nanopore sequencing.

 

Biography

Tom Suzuki's research centres on RNA biochemistry, especially on biogenesis and function of RNA modifications, and molecular mechanisms of protein synthesis. His group developed their platform technologies for isolating individual RNAs and for highly sensitive analysis of RNA modifications by mass spectrometry. His group discovered several novel modifications and dozens of RNA-modifying enzymes, and reported the first instance of human disease caused by deficient RNA modification. He is now a research director of the JST ERATO project on RNA modification.

 

Keywords

Clinical research, Gene expression, Transcriptomics, Data analysis tool

 

Products

MinION Mk1B, R9 Flow Cells, Direct RNA

Secret cinema
Human & clinical research Methods & techniques
17:50 - 18:15 BST 18:50 - 19:15 CEST 12:50 - 13:15 EDT 09:50 - 10:15 PDT 02:50 - 03:15 AEST
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SHOWCASE STAGE: CONSERVATION

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From genome assembly to epigenome characterisation: a nanopore journey in the footsteps of an endangered tortoise
Luca Pandolfini, Italian Institute of Technology, Italy
Luca Pandolfini

Talk title

From genome assembly to epigenome characterisation: a nanopore journey in the footsteps of an endangered tortoise

 

Abstract

Pyxis arachnoides is a critically endangered tortoise that lives in a narrow coastal ecoregion of Madagascar. Investigating the genetic structure of its population and identifying the sex of individuals in a fast and non-invasive way is of pivotal importance to monitoring the conservation status of the species. Furthermore, like most Testudines, this species undergoes temperature-dependent sex determination, representing an interesting subject to dissect the molecular and evolutionary aspects of this developmental process. In this study, we obtained a high-quality, chromosome-level P. arachnoides reference genome by combining Q30+ shotgun sequencing and Pore-C scaffolding. Then, we characterised its sex-related methylome dimorphisms and highlighted biologically relevant, differentially methylated CpG islands. This project demonstrates the feasibility of an end-to-end approach relying solely on Oxford Nanopore long-read sequencing for both de novo genome assembly and functional exploration of a novel species.

 

Biography

Luca Pandolfini got his Ph.D. in Scuola Normale Superiore di Pisa, Italy, then moved to the UK to conduct his post-doctoral studies at the Gurdon Institute in Cambridge. Since 2020 he has been working as an independent researcher at Istituto Italiano di Tecnologia, Italy, focusing on nervous system development and regeneration. Luca’s lab strongly relies on multiple nanopore sequencing approaches to dissect non-canonical model organisms from a developmental functional genomics point of view.

 

Keywords

Animal genomics, Assembly, Environmental research and conservation, Epigenetics, Whole-genome sequencing

 

Products

PromethION P24/P48, R10 Flow Cells, Duplex reads, Pore-C

How much is enough? A low-cost, rapid approach to generate non-model genomes for biodiversity and conservation genomics
Matthew Miller, Reneco International Wildlife Consultants, United Arab Emirates
Matthew Miller

Talk title

How much is enough? A low-cost, rapid approach to generate non-model genomes for biodiversity and conservation genomics

 

Abstract

We present high-quality de novo reference genomes for four flagship conservation species from Middle Eastern ecosystems, demonstrating how a small research team can generate high-quality reference genomes in less than two weeks, using just Oxford Nanopore long-read sequences. Although our genomes are not technically classified as chromosomal assemblies, they are vastly more contiguous to most chromosome-level genomes on NCBI. For example, only 6% of avian chromosome-level genomes have ungapped contig N50 > 30 Mb, and only 19% of fish genomes have ungapped contig N50 > 15 Mb. Most applications in biodiversity and conservation genomics rely on the analysis of large ungapped genome regions rather than chromosomes per se. Collectively, the approach presented here demonstrate that de novo reference genomes can be generated quickly in low-resource settings without the need for costly capital investment in sequencing and computation.

 

Biography

Matthew completed his PhD on the comparative genomics of Neotropical birds at the University of Alaska Museum. Subsequently he was a Research Fellow at the Smithsonian Tropical Research Institute in Panama, and Curator of Birds and Professor of Biology at the University of Oklahoma. Matthew joined Reneco International Wildlife Consultants in 2021 where he oversees the genomics lab and develops new tools for biodiversity genomics with special emphasis on the fauna of the Middle East, Africa, and Asia.

 

Keywords

Animal genomics, Assembly, Environmental research and conservation, Population genomics, Whole-genome sequencing

 

Products

MinION Mk1C, GridION, PromethION P2/P2 Solo

Building a comprehensive knowledge graph of novel proteins with long-read metagenomic sequencing and global partnerships
Phoebe Oldach, Basecamp Research, UK
Phoebe Oldach

Talk title

Building a comprehensive knowledge graph of novel proteins with long-read metagenomic sequencing and global partnerships

 

Abstract

Basecamp Research is built on the belief that nature has already designed solutions to our planet's greatest challenges. We have developed partnerships with over 50 public, private, and governmental biodiversity guardians in 65 expeditions across 18 countries to map unexplored microbial biodiversity. In doing so, we build bioliteracy and molecular biology capacity, and create a sustainable and ethical route to the biotechnology industry for biodiversity assets.

Our protein knowledge graph and bespoke analysis suite open the route to the biotechnology industry. We use long-read and polishing platforms for metagenome sequencing, which yield assemblies with longer contigs and more high-confidence annotations than available in public databases. Along with the detailed and standardized environmental and sample metadata, this facilitates cutting-edge protein characterization approaches. We leverage our uniquely contextualized data and novel analytical suite to find biological solutions to previously intractable problems across a range of biotechnology industries.

 

Biography

Phoebe Oldach is leading the Field Science team at Basecamp Research, a London-based startup, which is building a bridge between biodiversity and biotechnology by finding proteins with commercial applications in novel genomes sequenced around the world. She has a PhD in genome stability from Oxford University.

 

Keywords

Assembly, Bioinformatics, Education, Environmental research and conservation, Metagenomics, Microbiology, Microbiome, Whole-genome sequencing

 

Products

MinION Mk1B, GridION, PromethION P24/P48

Live lounge
Microbiology & infectious disease Plant & animal
18:15 - 18:25 BST 19:15 - 19:25 CEST 13:15 - 13:25 EDT 10:15 - 10:25 PDT 03:15 - 03:25 AEST
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PRODUCT DEMO

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ORG.one — the butterfly effect
Dan Fordham, Director, Strategic Product Management EMEA, Oxford Nanopore Technologies
Dan Fordham

Talk title

ORG.one — the butterfly effect

 

Biography

Dan started with Oxford Nanopore 13 years ago in applications and advanced research. He then moved into a commercial role, where his expertise was utilised on a project focusing on population-scale sequencing in large cohorts. He has recently joined the Strategic Product Management Team to continue and build on this important work. Dan also leads the ORG.one programme. 

 

 

Live lounge
Plant & animal
08:15 - 09:20 BST 09:15 - 10:20 CEST 03:15 - 04:20 EDT 00:15 - 01:20 PDT 17:15 - 18:20 AEST
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DATA FOR BREAKFAST

online onsite
Dorado — the future of basecalling
Mark Bicknell, Realtime Analysis Fellow, Oxford Nanopore Technologies
Mark Bicknell

Talk title

Dorado — the future of basecalling

 

Abstract

Mark will be giving an update on the current status of the Dorado standalone basecaller, talking about the motivations and going through some of the great new features that are available. He will also discuss how Dorado is being integrated into the MinKNOW ecosystem and how live basecalling features will be provided in future MinKNOW releases.

 

Biography

Mark joined Oxford Nanopore Technologies in 2017 after a previous life working in video game graphics and animation. Mark has spent the last few years working on the Guppy and Dorado basecallers.

 

Keywords

Bioinformatics, Data analysis tool

 

Products

MinION Mk1B, MinION Mk1C, GridION, PromethION P2/P2 Solo, PromethION P24/P48

 

How we get the most out of GPUs (for sequencing)
Georg Kolling, Principal Algorithms Scientist, Oxford Nanopore Technologies
Georg Kolling

Talk title

How we get the most out of GPUs (for sequencing)

 

Abstract

This talk will cover why GPUs are especially suited to processing the large amounts of data Oxford Nanopore sequencers generate in real time, and the approaches we take to get the best performance out of the hardware.

 

Biography

An interest in video games and graphics from an early age led Georg to start his career at GPU maker Imagination Technologies, where he supported developers, created demos, and helped design GPUs. After a brief stint in the games industry, he joined Oxford Nanopore Technologies in 2015, taking his GPU expertise beyond graphics. He has been working on making basecalling faster and better ever since.

 

Keywords

Bioinformatics, Data analysis tool

 

Products

MinION Mk1B, MinION Mk1C, GridION, PromethION P2/P2 Solo, PromethION P24/P48, Q20+, Duplex reads

Leveraging Nextflow for the analysis of anything, anywhere, by anyone
Chris Wright, Senior Director, Customer Bioinformatics, Oxford Nanopore Technologies
Chris Wright

Talk title

Leveraging Nextflow for the analysis of anything, anywhere, by anyone

 

Abstract

We will take a whirlwind tour of the activities of the Customer Analysis Workflows group at Oxford Nanopore. Starting with a discussion of why Nextflow is our workflow manager of choice and how we author workflows for it, we will progress to why it’s uniquely suited to the analysis of nanopore sequencing data. We’ll discuss the choices we’ve made, and how these choices lead us to rapidly develop, deploy, and support workflows for customers. We will end with thoughts around how the Nanopore Community can work together to share analyses.

 

Biography

Chris has worked at Oxford Nanopore for over 10 years. He started as a data analyst helping laboratory scientists develop the core technologies with MinION and PromethION Flow Cells. Chris was one of the primary authors for the first publicly released basecaller: Nanonet, as well as earlier HMM-based methods. He is also the lead developer of Medaka. More recently, Chris oversees the Customer Workflows group, responsible for creating bioinformatics resources for customers of Oxford Nanopore.

 

Keywords

Bioinformatics, Data analysis tool, Education

 

Products

EPI2ME, EPI2ME Labs

Advances in basecalling research and development
Katherine Lawrence, Machine Learning Bioinformatician, Oxford Nanopore Technologies
Katherine Lawrence

Talk title

Advances in basecalling research and development

 

Abstract

This presentation will explore recent progress in basecalling models and techniques, focusing on the cutting-edge research carried out by Oxford Nanopore Technologies’ Machine Learning team. The talk will cover topics such as stereo duplex and discuss the wider impact of these developments on the field.

 

Biography

Dr. Katherine Lawrence is a member of the Machine Learning Operations team at Oxford Nanopore Technologies, where she has made substantial contributions to improving duplex sequencing basecalling methods. Prior to joining the team, she earned her PhD in Physics and Evolutionary Biology from MIT.

 

Keywords

Bioinformatics, Whole-genome sequencing

 

Products

PromethION P2/P2 Solo, PromethION P24/P48, Q20+, R10 Flow Cells, Duplex reads

The Jam
Bioinformatics
09:30 - 09:50 BST 10:30 - 10:50 CEST 04:30 - 04:50 EDT 01:30 - 01:50 PDT 18:30 - 18:50 AEST
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WELCOME BACK TO LONDON CALLING 2023

online onsite
Rosemary Sinclair Dokos, Senior VP, Product & Programme Management, Oxford Nanopore Technologies
Rosemary Sinclair Dokos

Talk Title 

Welcome back to London Calling 2023 

 

Biography 

Rosemary Sinclair Dokos, Senior VP of Product and Programme Management, joined Oxford Nanopore in January 2014. Her initial role included the implementation of product management, release, and distribution framework around the MinION Access Programme. 

Rosemary is responsible for the management and release of all Oxford Nanopore devices, chemistry, and software products. Part of this role is to ensure that teams across R&D, production, commercial, and operations work together to accelerate innovation from our research teams into the hands of the customer and scale our offering to our growing user base. 

Rosemary has over 15 years’ experience in the life science industry. 

Rosemary and her team maintain a close connection with our user community, ensuring their experiences of using Oxford Nanopore devices inform our product development cycle. 

Auditorium
09:50 - 10:15 BST 10:50 - 11:15 CEST 04:50 - 05:15 EDT 01:50 - 02:15 PDT 18:50 - 19:15 AEST
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PLENARY 6

online onsite
scNanoATAC-seq: a long-read single-cell assay to simultaneously detect chromatin accessibility and genetic variants
Fuchou Tang, Biomedical Pioneering Innovation Center, Peking University, China
Fuchou Tang

Talk title

scNanoATAC-seq: a long-read single-cell assay to simultaneously detect chromatin accessibility and genetic variants

 

Abstract

Single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) on the next-generation sequencing (NGS) platform is a powerful tool to decode chromatin states. However, it is difficult to detect structural variations (SVs) simultaneously with short-read sequencing. We developed scNanoATAC-seq, an scATAC-seq method based on a nanopore sequencing platform. The ability of scNanoATAC-seq to reveal chromatin accessibility features was comparable to that of the NGS-based scATAC-seq. Using scNanoATAC-seq, we discriminated parental alleles for each peak in GM12878 using genetic polymorphisms flanking the peak, which cannot be achieved by NGS-based scATAC-seq. Moreover, we simultaneously identified SVs and copy number variations using scNanoATAC-seq data. Finally, we provided the direct evidence of co-accessibility between neighboring peaks from scNanoATAC-seq, where the chromatin accessibility of two sites in the same single cell was detected simultaneously by a long read. We will also discuss other third-generation sequencing platform-based single-cell epigenome sequencing technologies.

 

Biography

Fuchou Tang is a Full Professor at Biomedical Pioneering Innovation Center, College of Life Sciences, Peking University, China. He is also Associate Director of Beijing Advanced Innovation Center for Genomics. His lab focuses on the epigenetic regulation of gene expression networks during human early embryonic development and germline development. His lab pioneered the single-cell sequencing field and systematically developed a serial of single-cell functional genomic sequencing technologies. He has been invited to give presentations at AGBT, ISSCR, ICHG, Gordon Conference, and HCA.

 

Recent publications

Hu Y. et al. scNanoATAC-seq: a long-read single-cell ATAC sequencing method to detect chromatin accessibility and genetic variants simultaneously within an individual cell. Cell Res. 33:83–86 (2023).

 

Keywords

Bioinformatics, Epigenetics, Single cell and spatial

 

Products

PromethION P24/P48

Auditorium
Methods & techniques
10:15 - 10:40 BST 11:15 - 11:40 CEST 05:15 - 05:40 EDT 02:15 - 02:40 PDT 19:15 - 19:40 AEST
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PLENARY 7

online onsite
Single-cell long-read RNA sequencing reveals complex heterogeneity in leukaemia
Rachel Thijssen, Walter and Eliza Hall Institute of Medical Research, Australia & Amsterdam University Medical Centers, Netherlands
Rachel Thijssen

Talk title

Single-cell long-read RNA sequencing reveals complex heterogeneity in leukaemia

 

Abstract

While introduction of novel targeted inhibitors has markedly altered the therapeutic options for treating patients with blood cancers, relapses due to acquired resistance after initial response remain a major problem. To delineate drug resistance, we applied a novel single-cell omics approach on samples from patients with progressive leukaemia who failed therapy with a targeted agent. Combining short-read with long-read targeted and whole-transcriptome sequencing identified mutations and alternative transcripts in specific sub-clones of the tumour at relapse. Thus, our single-cell integration of short-read and full-length RNA-seq provides novel insights into how complex tumour heterogeneity evolves upon acquisition of drug resistance.

 

Biography

Dr. Rachel Thijssen is an Assistant Professor at the Amsterdam UMC, Netherlands and is an expert in targeted therapy resistance in blood cancer. She completed her PhD at the Academic Medical Center, Amsterdam and performed her postdoctoral studies at the Walter & Eliza Hall Institute (WEHI), Melbourne, Australia. Her research focuses on unravelling how haematopoietic cancer cells evade cell death, with a focus on venetoclax relapse in leukaemias using single-cell RNA-seq (CITE-seq) and single-cell long-read nanopore sequencing.

 

Recent Publications

Thijssen, R. et al. Single-cell multiomics reveal the scale of multilayered adaptations enabling CLL relapse during venetoclax therapy. Blood 140(20): 2127–2141 (2022). DOI: https://doi.org/10.1182/blood.2022016040

 

Keywords

Cancer research, Single cell and spatial, Targeted sequencing, Transcriptomics

 

Products

PromethION P2/P2 Solo, PromethION P24/P48, R9 Flow Cells

Auditorium
Cancer research
10:55 - 11:20 BST 11:55 - 12:20 CEST 05:55 - 06:20 EDT 02:55 - 03:20 PDT 19:55 - 20:20 AEST
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PLENARY 8

online onsite
Population-scale nanopore sequencing to further understand the genetics of Alzheimer’s disease and related dementias
Kimberley Billingsley, NIH Center for Alzheimer’s and Related Dementias, USA
Kimberley Billingsley

Talk title

Population-scale nanopore sequencing to further understand the genetics of Alzheimer’s disease and related dementias

 

Abstract

Previous large-scale genetic sequencing efforts for Alzheimer's disease and related dementias have been performed using short-read sequencing, which is not optimized to identify structural variation or repeat expansions. While long-read sequencing technologies substantially overcome this limitation, they have previously not been considered as a feasible replacement at scale due to being too expensive, not scalable enough, or too error-prone. We developed an efficient and scalable wet lab and computational pipeline for nanopore long-read sequencing. We applied our pipeline to ~300 human brain samples from the North American Brain Expression cohort and demonstrate that this data can be used to phase small and structural variants at megabase scales, better resolve disease-relevant haplotypes, and produce highly accurate haplotype-specific methylation calls. As part of the NIH Center for Alzheimer’s and Related Dementias (CARD) long-read sequencing initiative, we are currently applying this framework to thousands of human brain samples to generate a new long-read resource for the wider research community.

 

Biography

Kimberley Billingsley is a Postdoctoral Research Fellow at NIH, leading the Long-Read Sequencing team at the Center for Alzheimer’s and Related Dementias. Her work focuses on generating large-scale high value datasets to study the impact of structural variants in neurodegenerative disease. Kimberley obtained her PhD from the University of Liverpool, UK, studying the role of transposable elements in Parkinson's disease.

 

Recent Publications

Billingsley, K.J. et al. Genome-wide analysis of structural variants in Parkinson disease [published online ahead of print, 2023 Jan 25]. Ann. Neurol.10.1002/ana.26608 (2023). DOI: 10.1002/ana.26608

Kolmogorov, M. et al. Scalable nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation. bioRxiv 2023.01.12.523790 (2023). DOI: 10.1101/2023.01.12.523790

 

Keywords

Human genomics, Structural variation, Whole-genome sequencing

 

Products

PromethION P24/P48

Auditorium
Human & clinical research
11:50 - 12:10 BST 12:50 - 13:10 CEST 06:50 - 07:10 EDT 03:50 - 04:10 PDT 20:50 - 21:10 AEST
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SECRET CINEMA

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Zootails: implementing nanopore sequencing for veterinary diagnostics
Natalie Ring, The Roslin Institute, UK
Natalie Ring

Talk title

Zootails: implementing nanopore sequencing for veterinary diagnostics

 

Abstract

We are developing methods using nanopore sequencing to rapidly identify the species and predict antimicrobial resistance in veterinary infections without the need for culture. We recently described the metagenomic approach we developed for use with canine urine and skin swab samples. Now, we are adapting this approach to different types of samples, from different animal species and types of infection. In this talk, I will describe the optimisation to date, including a strategy for reusing flow cells, testing of adaptive sampling, and our current analysis pipeline, as well as discussing our plans and considerations as we prepare to launch this protocol for cage-side, same-day use with veterinary patients in a university animal hospital.

 

Biography

Natalie is a Postdoctoral Research Fellow and Senior Clinical Researcher at the Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh. Her main interest is the application of long-read sequencing in a veterinary setting. She has a variety of current projects, primarily the use of MinION for the rapid identification of pathogens in veterinary infections. She also wrote a chapter on the genetics of regeneration for a book about Doctor Who!

 

Recent Publications

Ring, N. et al. Rapid metagenomic sequencing for diagnosis and antimicrobial sensitivity prediction of canine bacterial infections bioRxiv 2023.01.30.526267 (2023). DOI: https://doi.org/10.1101/2023.01.30.526267

Ring, N. et al. Comparative genomics of Bordetella pertussis isolates from New Zealand, a country with an uncommonly high incidence of whooping cough. Microb. Genom. 8(1):000756 (2022).

Ring, N. Resolving the complex Bordetella pertussis genome using barcoded nanopore sequencing. Microb. Genom. 4(11):e000234 (2018).

 

Keywords

Animal genomics, Assembly, Bioinformatics, Clinical research, Genomic epidemiology, Identification, Infectious disease, Metagenomics, Microbiology, Microbiome, Whole-genome sequencing

 

Products

MinION Mk1B, MinION Mk1C, GridION, Flongle, EPI2ME, R10 Flow Cells, R9 Flow Cells, Adaptive sampling

Coinfection in endemic influenza A virus-infected herds using nanopore metagenomic sequencing of tracheobronchial swabs
Nick Vereecke, PathoSense BV, Belgium
Nick Vereecke

Talk title

Coinfection in endemic influenza A virus-infected herds using nanopore metagenomic sequencing of tracheobronchial swabs

 

Abstract

Respiratory disease in swine results in lowered animal health, welfare, and economic losses. Influenza A plays an important role in respiratory infections, but the problem is multifactorial. To date, there are no complete diagnostics available to study these complexes. Hence, practitioners rely on targeted diagnostics, including RT-qPCR, antigen detection, and serology. This hampers effective preventive and therapeutic actions. A metagenomic diagnostic platform was applied to study respiratory disease across four age groups on 25 German farms. The detection of swine influenza A virus (swIAV) was assessed using RT-qPCR on tracheobronchial swabs, along with metagenomic characterization. This revealed the age-dependent interplay of known viral and bacterial agents. Also, some lesser-known microbes were identified. The effect of swIAV detection and associated clinical symptoms could also be studied. In conclusion, nanopore metagenomics was shown as promising tool to facilitate more complete routine diagnostics. The results contribute to the understanding of pathogen dynamics within the disease complex.

 

Biography

Dr. Nick Vereecke is a Belgian R&D scientist at PathoSense BV (Belgium) who is a Baekeland-supported PhD Fellow (Flanders Innovation and Entrepreneurship). At the new Ghent university spin-off, he performs state-of-the-art research on viral and bacterial diagnostics in veterinary medicine in collaboration with various laboratories at Ghent University. With a great interest for various applications of (long-read) sequencing, his aim is to revolutionize current identification, (virulence) typing, and antimicrobial resistance of infectious diseases in veterinary (and human) medicine.

 

Recent publications

Vereecke, N. et al. Viral and bacterial profiles in endemic influenza A virus infected swine herds using nanopore metagenomic sequencing on tracheobronchial swabs. Microbiol. Spectr. e0009823 (2023). DOI:10.1128/spectrum.00098-23

Vereecke, N. et al. Successful whole genome nanopore sequencing of swine influenza A virus (swIAV) directly from oral fluids collected in Polish pig herds. Viruses 15(2):435 (2023). DOI:10.3390/v15020435

Vereecke, N. et al. High quality genome assemblies of Mycoplasma bovis using a taxon-specific Bonito basecaller for MinION and Flongle long-read nanopore sequencing. BMC Bioinform. 21(1):517 (2020). DOI:10.1186/s12859-020-03856-0

 

Keywords

Animal genomics, Bioinformatics, Identification, Infectious disease, Metagenomics, Microbiology, Microbiome

 

Products

MinION Mk1B, GridION, R9 Flow Cells

Secret cinema
Microbiology & infectious disease Plant & animal
12:10 - 12:30 BST 13:10 - 13:30 CEST 07:10 - 07:30 EDT 04:10 - 04:30 PDT 21:10 - 21:30 AEST
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PRODUCT DEMO

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Metagenomics and isolate genome sequencing
Rachel Rubinstein & Natalie Ring, Technical Product Manager, Software, Oxford Nanopore Technologies & The Roslin Institute, UK
Natalie Ring Rachel Rubinstein

Talk title

Metagenomics and isolate genome sequencing

 

Biographies

Rachel is a technical product manager with a background in molecular biology and microbiology. At Oxford Nanopore, she works with the MinKNOW team to help incorporate customer feedback and make the software more powerful and user friendly. She is passionate about improving user experience, robustness, and stability of the MinKNOW software. In her free time, you can catch her running, swimming, or cycling around the Boston, MA, area.

Natalie is a Postdoctoral Research Fellow and Senior Clinical Researcher at the Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh. Her main interest is the application of long-read sequencing in a veterinary setting. She has a variety of current projects, primarily the use of MinION for the rapid identification of pathogens in veterinary infections. She also wrote a chapter on the genetics of regeneration for a book about Doctor Who!

 

Keywords

Identification Metagenomics, Microbiology, Microbiome

 

Products

MinION Mk1B, MinION Mk1C, EPI2ME Labs, R10 Flow cells

Live lounge
Microbiology & infectious disease Methods & techniques
12:40 - 13:40 BST 13:40 - 14:40 CEST 07:40 - 08:40 EDT 04:40 - 05:40 PDT 21:40 - 22:40 AEST
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DATA ANALYSIS TOOLS: VARIANT ANALYSIS

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The long and short of structural variants using Oxford Nanopore sequencing
Luis Paulin, Baylor College of Medicine, USA
Luis Paulin

Talk title

The long and short of structural variants using Oxford Nanopore sequencing

 

Abstract

Structural variant (SV) calling, which is the identification of small and simultaneously large SVs, remains challenging. Long-read sequencing is a highly accurate way to identify simple and complex genomic alterations. Additionally, copy number variations (CNVs), large genomic amplifications, or deletions of Mbp, remain challenging using long-read sequencing, but are important determinants in cardiovascular diseases, Mendelian diseases, and cancer research. To address these challenges, we improved Sniffles2 (v2.2), a successor to the SV-detection method Sniffles, and developed Spectre — a novel CNV caller for Oxford Nanopore long-read sequencing. Sniffles2 increases both accuracy and speed, and has more advanced functionality, which includes population-level SV calling and the detection of somatic/mosaic SVs across bulk long-read data. While Sniffles2 accurately detects small and mid-size SVs, Spectre, a CNV caller designed for long-read sequencing, specializes in detecting large CNVs that may not have precise breakpoints. This is the case if a CNV impacts a telomeric or centromeric region, or a highly duplicated large segmental duplication.

 

Biography

Luis Paulin studied Genome Sciences and Biochemistry at the National Autonomous University of Mexico (UNAM). He then moved to Vienna, where he joined Arndt von Haeseler’s lab, which is a bioinformatic group in the Max F. Perutz Laboratories, to pursue a PhD. After his PhD, he worked for two years in IT for a governmental institution. In 2021, Luis joined Fritz Sedlazeck’s lab in the Human Genome Sequencing Center working on structural and CNV detection with long reads.

 

Recent Publications

Paulin, L.F. SVhound: detection of regions that harbor yet undetected structural variation. BMC Bioinformatics 24(23) (2023). DOI: https://doi.org/10.1186/s12859-022-05046-6

Smolka, M. et al. Comprehensive structural variant detection: from mosaic to population-level. bioRxiv 2022.04.04.487055 (2022). DOI: https://doi.org/10.1101/2022.04.04.487055

 

Keywords

Bioinformatics, Human genomics, Structural variation

 

Products

PromethION P24/P48

SAVANA: a computational method to characterise structural variation in human cancer genomes using nanopore sequencing Hillary Elrick | EMBL-EBI
Hillary Elrick, EMBL-EBI, UK
Hillary Elrick

Talk title

SAVANA: a computational method to characterise structural variation in human cancer genomes using nanopore sequencing 

 

Abstract

To date, the study of cancer genomes has relied on the analysis of short-read whole-genome sequencing, which generates short, highly accurate 100–300-bp reads. However, the detection of structural variants (SVs) using short reads is limited. As a result, our understanding of the patterns and mechanisms underpinning structural variation in cancer genomes remains incomplete.

SAVANA is a novel structural variant caller for long-read sequencing data specifically designed to detect somatic SVs. Extensively validated against a multi-platform truth set, we show that SAVANA identifies a range of somatic rearrangements with high recall and precision, outperforming existing tools while maintaining a low execution time. In tumour samples, SAVANA can identify clinically relevant SVs with high accuracy. Additionally, SAVANA permits the reconstruction of double minutes, multi-chromosomal chromothripsis events, and SVs mapping to highly repetitive regions. In summary, SAVANA permits the characterization of complex structural variants and can uncover clinically relevant mutations across diverse cancer types with high accuracy.

 

Biography

Hillary is working towards a PhD in cancer genomics at EMBL-EBI, UK, in Isidro Cortes-Ciriano’s group. Previously, she worked as a bioinformatician at SickKids Hospital in Toronto, Canada and completed undergraduate training in biomedical computing at Queen’s University in Kingston, Canada.

 

Keywords

Bioinformatics, Cancer research, Data analysis tool, Structural variation, Whole-genome sequencing 

 

Products

R10 Flow Cells, R9 Flow Cells

Precise characterization of somatic complex structural variations from paired long-read sequencing data using nanomonsv
Yuichi Shiraishi, National Cancer Center, Japan
Yuichi Shiraishi

Talk title

Precise characterization of somatic complex structural variations from paired long-read sequencing data using nanomonsv

 

Abstract

We present our novel software, nanomonsv, for the detection of somatic structural variations (SVs) using tumour and matched control long-read sequencing data. The current version of nanomonsv includes two detection modules: the Canonical SV module and the Single Breakend SV module. The Canonical SV module can identify somatic SVs that can be captured by short-read technologies with higher precision and recall than existing methods. In addition, the Single Breakend SV module enables the detection of complex SVs that can only be identified by long-read technologies, such as SVs with highly repetitive centromeric sequences, and LINE1 and virus-mediated rearrangements. Our approaches can be applied to cancer long-read sequencing data and may reveal different characteristics of somatic SVs, leading to a better understanding of the mutational processes and functional consequences of somatic SVs.

 

Biography

Yuichi Shiraishi received his PhD in statistical science from the Graduate University for Advanced Studies, Japan (2008), and then joined the Cellular Systems Modelling Team at RIKEN, Japan (2010–2011). In 2010, he joined the Institute of Medical Science at the University of Tokyo, Japan, where he developed algorithms and software for cancer genome sequencing data. In 2018, he moved to the National Cancer Center, where he continues to develop the genome sequencing analysis pipeline while expanding its scope to longread sequencing data.

 

Keywords

Bioinformatics, Cancer research, Data analysis tool, Human genomics, Structural variation

 

Products

PromethION P24/P48

Ultra-rapid nanopore sequencing: computational pipeline 2.0
Sneha Goenka, Stanford University, USA
Sneha Goenka

Talk title

Ultra-rapid nanopore sequencing: computational pipeline 2.0

 

Abstract

In 2021, the ultra-rapid nanopore sequencing pipeline set the world record for the fastest diagnosis using DNA sequencing in 7 hours 28 minutes. With further improvements to basecalling and nanopore chemistry, we further improved the pipeline in terms of accuracy, speed, and cost. While leveraging the improvement in basecalling accuracy with newer versions of Guppy, the pipeline now consists of autoscaling of the resource in the high-performance cloud computing infrastructure using Ray. Autoscaling of resources based on the rate of sequencing data generation and fine-grained control over resource-scheduling improves cost efficiency while maintaining the speed of basecalling and alignment. Additionally, a suite of tools associate compute performance across batches of sequencing data. The pipeline can now call small variants, structural variants, and copy number variants within 30 minutes of alignment. The variant curation stage is now automated using the GEM software from Fabric Genomics. As a result, we can generate a curated list of variants within two hours of completing sequencing, for almost 180 GB of data.

 

Biography

Sneha Goenka is a PhD candidate in the Electrical Engineering Department at Stanford University, where she is supervised by Prof. Mark Horowitz. Her research centers on designing efficient computer systems for advancing genomic pipelines for clinical and research applications, with a focus on improving speed and cost. She is a 2023 Forbes 30 Under 30 Honoree in the Science category, 2022 NVIDIA Graduate Fellow, and 2021 Cadence Women in Technology Scholar. She has a BTech and MTech (Microelectronics) in Electrical Engineering from the Indian Institute of Technology, Bombay, where she received the Akshay Dhoke Memorial Award for the most outstanding student in the program.

 

Keywords

Bioinformatics, Clinical research, Data analysis tool, Human genomics, SNVs, Structural variation, Whole-genome sequencing

 

Products

PromethION P24/P48, R10 Flow Cells, R9 Flow Cells

DAT Cave
Bioinformatics
12:40 - 13:40 BST 13:40 - 14:40 CEST 07:40 - 08:40 EDT 04:40 - 05:40 PDT 21:40 - 22:40 AEST
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INFECTIOUS DISEASE

online onsite
Detection and differentiation of respiratory viral pathogens using near real-time sequencing
Lukasz Rabalski, University of Gdańsk & Military Institute of Hygiene and Epidemiology, Poland
Lukasz Rabalski

Talk title

Detection and differentiation of respiratory viral pathogens using near real-time sequencing

 

Abstract

In the recent respiratory disease season, we observed increased instances of multiple infections in single patients. Coinfection of influenza and COVID-19 can exacerbate illness severity and clinical impact. Our research aimed to develop a rapid detection and differentiation method for viral infections. We focused on detecting and characterizing co-infections, analyzing both historical and current patient samples. Our real-time Oxford Nanopore sequencing procedure enabled the detection of coexisting viral infections within hours of obtaining samples. We amplified genetic material from respiratory pathogens in collected samples and identified respiratory infections. Over 30 different pathogens were distinguished during multiplex reactions. Using a Flongle Flow Cell, 90 individuals could be analysed at a reduced cost. The ability to distinguish so many pathogens is not achievable using classical or other molecular methods.

 

Biography

Lukasz Rabalski is Assistant Professor at the Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, Poland. He recently started working at the Biological Threats Identification and Countermeasure Centre of the Military Institute of Hygiene and Epidemiology. He is also CEO and founder of Vaxican Ltd. Lukasz has been interested in viruses and preventing viral diseases since the beginning of his scientific career. He is Project Manager/Principal Investigator of six research projects that focus on virus genomics, molecular diagnostics for human pathogens, and recombinant vaccines.

 

Keywords

Assembly, Bioinformatics, Infectious disease, Microbiology, Microbiome, SARS-CoV-2/COVID-19, SNVs, Structural variation, Targeted sequencing

 

Products

MinION Mk1B, MinION Mk1C, GridION, Flongle, VolTRAX, EPI2ME, EPI2ME Labs, Midnight

Tuberculosis drug resistance profiling from native sputum using nanopore targeted sequencing: a field application study
Tiana Schwab, Institute of Social and Preventative Medicine, University of Bern, Switzerland
Tiana Schwab

Talk title

Tuberculosis drug resistance profiling from native sputum using nanopore targeted sequencing: a field application study

 

Abstract

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), and drug-resistant tuberculosis (DR-TB) remain global public-health threats. Drug susceptibility testing is essential for diagnosing and treating DR-TB effectively, but current molecular diagnostic assays are limited. We tested Oxford Nanopore’s targeted next-generation sequencing (tNGS) assay at two clinics in Southern Africa as part of an ongoing prospective TB cohort research study to evaluate its feasibility and performance in profiling DR-TB in a near-patient setting. Sequencing results were compared with local routine drug susceptibility testing results. Our initial findings suggest that Oxford Nanopore tNGS can detect Mtb and drug resistance associated mutations using native sputum samples and is a promising and feasible rapid sequencing approach for comprehensive genotypic drug resistance profiling in high TB burden countries.

 

Biography

Tiana is a PhD student at the Institute of Social and Preventative Medicine at the University of Bern. She has a BSc in Biochemistry, Genetics, and Bioinformatics from the University of Cape Town, South Africa and an MSc in Chemical Biology from the University of Geneva, Switzerland. For her doctoral work, she is working with medical diagnostic laboratories and HIV/TB clinics in Southern Africa to implement and evaluate a targeted sequencing assay for the rapid detection and characterisation of drug-resistant tuberculosis.

 

Keywords

Clinical research, Infectious disease, Microbiology, Targeted sequencing

 

Products

MinION Mk1B, EPI2ME Labs

The value of real-time, long-read sequencing for public health
Joep de Ligt, Institute of Environmental Science and Research Limited (ESR), New Zealand
Joep de Ligt

Talk title

The value of real-time, long-read sequencing for public health

 

Abstract

Real-time, whole-genome sequencing using the Oxford Nanopore Midnight protocol was used to support the COVID-19 response in Aotearoa New Zealand by providing an additional line of evidence to contact tracers and policy officials. The data were successfully used to demonstrate the airborne nature of SARS-CoV-2 and enhance mitigation measures in quarantine settings. In addition to the real-time nature of Oxford Nanopore long-read sequencing, it also offers further public health value as demonstrated by the generation of local reference genomes and their use in pan-genome graphs for reliable outbreak detection without reference bias. We demonstrate that using a pangenome graph, instead of a single linear reference genome, improves the mapping rates and variant calling (of both simple and complex variants) for simulated and real datasets of Neisseria meningitidis.

 

Biography

Dr. de Ligt is the Senior Science Lead — Genomics & Bioinformatics, at ESR, covering both the Human and Pathogen disease space. He has worked extensively on unlocking health benefits through implementation and innovation of genomics in both research and clinical settings. The team (ranging from bench to high-performance computing) demonstrated the value of rapid sequencing in New Zealand’s COVID-19 response. The group works on unlocking the potential of real-time long-read genomics technologies for future health systems.

 

Recent Publications

Fox-Lewis, A. et al. Airborne transmission of SARS-CoV-2 delta variant within tightly monitored isolation facility, New Zealand (Aotearoa). Emerg. Infect. Dis. 28(3):501–509 (2022). DOI: https://doi.org/10.3201/eid2803.212318

Swadi, T. et al. Genomic evidence of in-flight transmission of SARS-CoV-2 despite predeparture testing. Emerg. Infect. Dis. 27(3):687–693 (2021). DOI: https://doi.org/10.3201/eid2703.204714

 

Keywords

Assembly, Bioinformatics, Data analysis tool, Infectious disease, Metagenomics, Microbiology, Structural variation, Whole-genome sequencing

 

Products

MinION Mk1B, GridION, R10 Flow Cells, R9 Flow Cells, Duplex reads

Blondie
Microbiology & infectious disease
12:40 - 13:40 BST 13:40 - 14:40 CEST 07:40 - 08:40 EDT 04:40 - 05:40 PDT 21:40 - 22:40 AEST
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AGRIGENOMICS

online onsite
Automated telomere-to-telomere crop genome assembly using only Oxford Nanopore sequencing
Sergey Koren, National Institutes of Health, USA
Sergey Koren

Talk title

Automated telomere-to-telomere crop genome assembly using only Oxford Nanopore sequencing

 

Abstract

Recently, the combination of ultra-long Oxford Nanopore sequencing reads with long, accurate PacBio HiFi reads has enabled the completion of the human genome and spurred similar efforts for many other species. However, the current recipe for telomere-to-telomere genome assembly relies on sequencing data from two different instruments, limiting its adoption. We generated Oxford Nanopore simplex and duplex data for two important crop species, Zea mays B73 and Solanum lycopersicum Heinz 1706. Assembling the Solanum lycopersicum Heinz 1706 data using Verkko followed by manual analysis, resulted in a complete, telomere-to-telomere genome assembly with only one gap, corresponding to the rDNA, remaining. Duplex data quality is similar to PacBio HiFi, although read lengths are tens of kilobases longer. The assembly has a base-accuracy exceeding 99.999% (Q50). We conclude that Oxford Nanopore duplex sequencing reads are a viable substitute for PacBio HiFi reads, and, in combination with simplex sequencing, have the potential to provide a single-instrument solution for complete genome assembly.

 

Biography

Sergey Koren pioneered the use of newer noisy long-read data for high-quality assembly. To assemble diploid genomes, he led the development of an approach, which uses parental genomic information to generate two complete sequences for a single individual. His work has enabled the study of previously invisible human genomic regions, corrected errors in the current reference, and led to the first truly complete human genomic sequence. Dr. Koren’s work continues to build on this success, so that complete and accurate genomes become routine.

 

Recent publications

Rautiainen, M. et al. Telomere-to-telomere assembly of diploid chromosomes with Verkko. Nat. Biotechnol. (2023). https://doi.org/10.1038/s41587-023-01662-6

Nurk, S. et al. The complete sequence of a human genome. Science 376(6588):44–53 (2022). doi:10.1126/science.abj6987

 

Keywords

Animal genomics, Assembly, Bioinformatics, Data analysis tool, Human genomics, Metagenomics

 

Products

GridION, PromethION P24/P48, Q20+, R10 Flow Cells, R9 Flow Cells

(Epi)genotyping by low-pass sequencing using nanopore technologies
Oscar Gonzalez-Recio, National Institute for Agricultural and Food Research and Technology, Spanish National Research Council, Spain
Oscar Gonzalez-Recio

Talk title

(Epi)genotyping by low-pass sequencing using nanopore technologies

 

Abstract

We proposed an (epi)genotype-by-sequencing using Oxford Nanopore sequencing as an alternative to SNP genotyping arrays in genomic selection and polygenic risk score estimation. Genotype-by-sequencing requires a low sequencing depth to be cost effective, which may increase the error at the genotype assignment. The latest nanopore chemistry (LSK114 and Q20+) achieved a modal basecalling accuracy of 99.55% and allowed estimating direct genomic value with an accuracy ranging between 0.79 and 0.99. Simultaneously, we were able to detect more than one million high reliable methylated sites, even at low sequencing depth.

 

Biography

Oscar González-Recio is a senior research scientist at the National Institute for Agricultural and Food Research — CSIC, Spain. His research mainly focuses on genomic and metagenomic applications to breed for more sustainable livestock with lower carbon footprint and better adapted to expected global warming conditions.

 

Recent publications

González-Recio, O. et al. Invited review: Novel methods and perspectives for modulating the rumen microbiome through selective breeding as a means to improve complex traits: Implications for methane emissions in cattle. Livest. Sci. 269:105171 (2023). DOI: https://doi.org/10.1016/j.livsci.2023.105171

González-Recio, O. Accuracy of direct genomic values and methylation profile through genotype-by-LowPass sequencing using nanopore technology. bioRxiv 2023.01.15.523960 (2023). DOI: https://doi.org/10.1101/2023.01.15.523960

 

Keywords

Animal genomics, Epigenetics

 

Products

GridION, PromethION P2/P2 Solo, Q20+, R10 Flow Cells, R9 Flow Cells

Exploring the genetic and functional diversity of the NLRome/resistome in melon using nanopore adaptive sampling
Javier Belinchon-Moreno, INRAE-EPGV, France
Javier Belinchon-Moreno

Talk title

Exploring the genetic and functional diversity of the NLRome/resistome in melon using nanopore adaptive sampling

 

Abstract

Nucleotide-binding-site-leucine-rich-repeat (NLR) disease resistance genes encode the most important family of plant resistance proteins. They are usually arranged in clusters that commonly present a high level of presence–absence polymorphisms. Therefore, long-read sequencing methods, such as Oxford Nanopore sequencing, may provide valuable information. Nanopore adaptive sampling (NAS) is presumed to be a good approach, since sequencing of the entire genome is not necessary. Our project explores the implementation of NAS for the sequencing and characterization of the complete NLR-like resistance genes (or NLRome) in melon, using around 140 melon varieties. In a first step, we demonstrated the performance of NAS against whole-genome sequencing for the sequencing and assembly of previously defined NLR clusters in a well-studied melon variety. We also assessed the transferability of our design to other melon varieties and plan to continue exploring the possibilities of this promising targeted sequencing approach.

 

Biography

Javier Belinchon-Moreno obtained his BSc in Biotechnology from the Polytechnic University of Valencia, Spain. In 2020, he was granted an Erasmus Mundus scholarship to complete his Master’s degree in Plant Breeding at UniLaSalle Beauvais, France. During his Master’s internship, he joined the French Institute of Agricultural Research (INRAE) to work on QTL discovery and association genetics. After this, he began his PhD at INRAE, investigating the structural and functional characterisation of the NLRome in melon.

 

Recent Publications

Belinchón-Moreno, J. Identification of QTLs and candidate genes involved in nitrogen stress response through QTL mapping in a multi-parent MAGIC tomato population (Master's thesis, Universitat Politècnica de València). RiuNet UPV. (2022). http://hdl.handle.net/10251/187927

Seguí-Simarro, J.M. et al. Species with haploid or doubled haploid protocols. In Segui-Simarro, J.M. (Ed.). Doubled haploid technology volume 1: general topics, Alliaceae, cereals (pp 41–103). United States, Springer US (2021).

Belinchón-Moreno, J. Evaluación del efecto de la micorrización en plantas de berenjena y pimiento crecidas en condiciones de estrés abiótico (Bachelor's thesis, Universitat Politècnica de València). RiuNet UPV. (2020). http://hdl.handle.net/10251/147815 

 

Keywords

Assembly, Bioinformatics, Data analysis tool, Environmental research and conservation, Plant genomics, Structural variation, Targeted sequencing

 

Products

GridION, PromethION P24/P48, Q20+, Adaptive sampli

The Clash
Plant & animal
12:40 - 13:40 BST 13:40 - 14:40 CEST 07:40 - 08:40 EDT 04:40 - 05:40 PDT 21:40 - 22:40 AEST
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HUMAN TRANSCRIPTOMICS RESEARCH

online onsite
Oxford Nanopore long-read RNA sequencing enables precise RNA isoform discovery and quantification in human brains
Bernardo Aguzzoli Heberle, University of Kentucky, USA
Bernardo Aguzzoli Heberle

Talk title

Oxford Nanopore long-read RNA sequencing enables precise RNA isoform discovery and quantification in human brains

 

Abstract

Nanopore long-read sequencing technologies can sequence entire RNA molecules in a single read, allowing researchers to accurately quantify expression for the complete set of RNA isoform species. This is a major improvement over past studies where, due to the limitations of short-read sequencing, researchers condensed all RNA isoforms into a single gene measurement. Here, we sequenced 12 aged human frontal cortex samples (six controls and six with Alzheimer’s disease) from post-mortem autopsy tissue. We discovered 245 new gene bodies and 428 new RNA isoforms in annotated gene bodies. Among these 428 new isoforms, 49 were from medically relevant genes, such as MAOB. Lastly, we identified 3,309 gene bodies expressing multiple RNA isoforms in a human frontal cortex, including genes implicated in Alzheimer’s disease, such as MAPT(4), CLU(4), APP(5), PSEN1(5), and BIN1(7). These results highlight the importance of accurately quantifying all RNA isoforms within a gene, as any of them could be differentially expressed in disease tissue.

 

Biography

Bernardo is a second year PhD student in the Department of Neuroscience at the University of Kentucky, USA. Under the guidance of his advisor, Mark Ebbert, PhD, he is using nanopore sequencing to identify RNA isoform expression patterns associated with Alzheimer’s disease in frontal cortex samples from postmortem autopsy brain tissue.

 

Keywords

Bioinformatics, Gene expression, Human genomics, Splice variation, Transcriptomics

 

Products

PromethION P24/P48, R9 Flow Cells

Integrating the transcriptome and epitranscriptome of the human brain using direct RNA sequencing
Josie Gleeson, The University of Melbourne, Australia
Josie Gleeson

Talk title

Integrating the transcriptome and epitranscriptome of the human brain using direct RNA sequencing

 

Abstract

The human brain is subject to complex regulation of gene expression, with high levels of splicing and RNA modification N6-methyladenosine (m6A). Investigating how these different biological mechanisms interact and contribute to the brain's function is critical for our understanding of brain development and disease. Long-read direct RNA sequencing (DRS) from Oxford Nanopore Technologies allows for simultaneous investigation of the human brain transcriptome and epitranscriptome. Here, we applied DRS to three brain regions and identified thousands of differentially expressed isoforms and 1,658 isoforms with differential m6A modification levels between brain regions. Highly methylated isoforms were associated with synaptic function, whereas lowly modified isoforms were associated with DNA binding. We also found a subpopulation of highly methylated long non-coding RNAs. Our results reveal new insights into brain region specificity and functioning, providing new avenues for further investigation into neurological development and disease.

 

Biography

Josie Gleeson is a PhD candidate at the University of Melbourne, specialising in long-read sequencing methods to study the human brain. Her research mainly utilises direct RNA sequencing from Oxford Nanopore Technologies to investigate the complex mechanisms that regulate gene expression, such as RNA splicing and modification. Through her work, she also contributes to tool development for long-read sequencing data analysis.

 

Keywords

Bioinformatics, Gene expression, Splice variation, Transcriptomics

 

Products

PromethION P24/P48, Direct RNA

Discovery of novel neuropsychiatric disorder risk-gene transcripts in the human brain
Ricardo De Paoli-Iseppi, The University of Melbourne, Australia
Ricardo De Paoli-Iseppi

Talk title

Discovery of novel neuropsychiatric disorder risk-gene transcripts in the human brain

 

Abstract

Disruptions to alternative RNA splicing are associated with human diseases, including neuropsychiatric disorders. Genome-wide association studies have recently identified hundreds of risk loci for these disorders. However, how these genes contribute to disease risk through altered gene expression and RNA splicing remains poorly understood. We reveal the precise RNA isoform profiles of 32 neuropsychiatric risk genes using post-mortem brain samples from healthy individuals. We reveal highly expressed novel isoforms in the schizophrenia risk gene ATG13, and two isoforms including novel exons in the depression gene NEGR1. Overall, we identified 765 novel isoforms and 22 novel exons, of which most (16/22) appear to be “poison exons”. Our results show that current gene transcript annotations are incomplete and supports the use of long-read sequencing to identify novel RNA isoforms. Uncovering the splicing repertoire for neuropsychiatric risk genes will inform future analyses of the functional impact these isoforms have on neuropsychiatric disorder development.

 

Biography

Ricardo De Paoli-Iseppi is an early career researcher and expert in the field of long-read sequencing and transcriptomics. His doctoral research has led him from studying DNA methylation in seabirds to profiling RNA isoforms in the human brain. Ricardo is now a Postdoctoral Fellow studying neurogenomics and joined the lab of Dr. Mike Clark at the University of Melbourne, Australia in 2019.

 

Keywords

Gene expression, Splice variation, Targeted sequencing

 

Products

Keywords

The Jam
Human & clinical research
13:50 - 14:10 BST 14:50 - 15:10 CEST 08:50 - 09:10 EDT 05:50 - 06:10 PDT 22:50 - 23:10 AEST
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MINI THEATRE ON-DEMAND

onsite ondemand
Identification of viral contamination of a biopharmaceutical product using nanopore sequencing
Hans-Peter Fasching, ViruSure, Austria
Hans-Peter Fasching

Talk title

Identification of viral contamination of a biopharmaceutical product using nanopore sequencing

 

Abstract

Contamination events in cell culture-derived biopharmaceuticals are very rare due to the implementation of strict testing procedures for the characterization of cell banks. However, they occurred regularly over the last decades and some of the more famous events included the detection of porcine circovirus in a rotavirus vaccine and simian virus 40 found in a poliovirus vaccine. This talk will describe the detection of contamination in a cell culture-derived biopharmaceutical observed at ViruSure. This contamination event was discovered using a cell-based in vitro adventitious agent testing approach, which is highly sensitive for the detection of virus present in underlying samples but is unable to identify the virus. Therefore, this sample was subjected to nanopore sequencing, which, after optimization of the sample preparation protocol, led to the identification of the contaminant as the epizootic haemorrhagic disease virus.

 

Biography

After finishing his studies in Molecular Biology at the University of Vienna, Austria, Hans-Peter joined ViruSure as Scientific Assistant in the Molecular Biology Group. He is currently a GLP Study Director for Sanger Sequencing projects and working on the establishment of nanopore sequencing for the detection of adventitious agents in biopharmaceuticals.

 

Keywords

Identification, Infectious disease

 

Products

MinION Mk1B, EPI2ME, R9 Flow Cells

Using nanopore sequencing to understand the manufacture, delivery, and action of mRNA vaccines
Helen Gunter, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Australia
Helen Gunter

Talk title

Using nanopore sequencing to understand the manufacture, delivery, and action of mRNA vaccines

 

Abstract

The lifecycle of an mRNA vaccine begins with its manufacture and formulation into lipid nanoparticles. The mRNA is then delivered to patients, where it is taken up by recipient cells and translated into the encoded protein. This study uses Oxford Nanopore cDNA and direct RNA sequencing to analyze each step in the mRNA vaccine lifecycle. We first show that Oxford Nanopore sequencing can be used during mRNA manufacturing to monitor mRNA quality and integrity, and detect contaminating RNA species that can induce unwanted inflammatory responses. Then, we directly measure the impact of different degradation pathways on mRNA integrity during formulation and storage. Finally, we describe the uptake, expression, and final degradation of mRNA vaccines within cells. Together, this study uses Oxford Nanopore sequencing to trace the lifecycle of an mRNA vaccine, providing quality data throughout the manufacturing process and insight into its mode of action within the cell.

 

Biography

Helen Gunter is a Senior Scientist at the Australian Institute for Bioengineering and Nanotechnology at the University of Queensland, Australia. Working with Tim Mercer, her research aims to develop tools that improve mRNA vaccine quality and efficacy. Helen has diverse industry and research experience in genomics, with 16 years in genomics research, and experience as a Project Manager at the second largest genomics facility in the UK.

 

Recent Publications

Gunter, H.M. et al. Library adaptors with integrated reference controls improve the accuracy and reliability of nanopore sequencing. Nat. Commun. 13(6437) (2022). https://doi.org/10.1038/s41467-022-34028-8

 

Keywords

Bioinformatics, Data analysis tool, Gene expression, Transcriptomics

 

Products

GridION, Flongle, R10 Flow Cells, R9 Flow Cells, Direct RNA

Secret cinema
Microbiology & infectious disease
14:20 - 14:45 BST 15:20 - 15:45 CEST 09:20 - 09:45 EDT 06:20 - 06:45 PDT 23:20 - 23:45 AEST
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SHOWCASE STAGE: RAPID SEQUENCING

onsite
High-resolution HLA typing for deceased donor organ transplantation within six hours from blood sample to analysis result
Sarah J. Reiling, McGill University Health Centre, Canada
Sarah J. Reiling

Talk title

High-resolution HLA typing for deceased donor organ transplantation within six hours from blood sample to analysis result

 

Abstract

Chronic kidney disease affects about 10% of the population and is fatal if not treated when the disease advances to end stage. The only treatment options are life-long hemodialysis or a kidney transplant. While transplant is preferred, the immunogenetic matching of the human leukocyte antigens (HLA) influences post-transplant graft function, and the deceased donor’s HLA needs to be typed prior to transplantation. The current practices in clinical HLA typing laboratories have two main drawbacks: (1) long organ allocation time of deceased donors, resulting in delayed graft function and (2) suboptimal matching due to the low-resolution qPCR typing, resulting in premature graft rejection. A rapid nanopore sequencing based high-resolution typing method is a promising solution for better matching of deceased organ donors with potential transplant recipients. Our data using MinION Flow Cells show the feasibility to obtain accurate high-resolution HLA typing results within an acceptable turnaround time after sample reception.

 

Biography

Sarah Reiling is a Clinical Specialist in Molecular Biology at the HLA lab of the McGill University Health Centre in Montreal, Canada. In her previous career, Sarah was the program manager of the nanopore platforms at the McGill Genome Centre Advanced Genomic Technologies Group. She now focuses on educating the HLA community about the potential use of rapid nanopore sequencing for deceased organ donors.

 

Keywords

Clinical research, Immunology, Targeted sequencing

 

Products

MinION Mk1B, MinION Mk1C, R10 Flow Cells, R9 Flow Cells

Ultra-rapid nanopore whole-genome sequencing in a critical care setting
John Gorzynski, Stanford University, USA
John Gorzynski

Talk title

Ultra-rapid nanopore whole-genome sequencing in a critical care setting

 

Abstract

In 2021, the launch of the Ultra-Rapid Whole-Genome Sequencing (ur-WGS) project at Stanford University demonstrated its ability to identify genetic etiologies of disease in a critically ill patient in as little as seven hours and 18 minutes. The project's first phase focused on the infant and pediatric population and identified a pathogenic or likely pathogenic variant in five out of 12 patients (42%). After confirmation in a clinical laboratory, the findings guided patient management in every case.

Over the past year, the team has optimized all components of the ur-WGS pipeline to further reduce the turnaround time. Replacement of the Ligation Sequencing Kit (LSK)-based library preparation to a modified rapid library preparation, a transition from high-accuracy (HAC) to super-accuracy (SUP) basecalling, and modifications to the variant identification process are among many changes made to the protocol.

In 2023, we launched the second phase of the study with the newly optimized pipeline. During this presentation, we will provide the Oxford Nanopore Technologies community with an ur-WGS progress report focused on current implementations of the protocol and its clinical utility.

 

Biography

John studied at the University of London’s Royal Veterinary College where he earned a degree in veterinary medicine, and continued his education at Stanford University where he obtained a PhD in genetics. John is now a postdoc in the Euan Ashley lab at Stanford University and is interested in utilizing long-read (nanopore) genome sequencing to improve the health of human and non-human patients.

 

Keywords

Human genomics, Whole-genome sequencing

 

Products

PromethION P24/P48, R10 Flow Cells, R9 Flow Cells

gMendel® Test-SCAN: a novel decision-supporting tool for mass screening of genetic disorders based on Oxford Nanopore technology
Anne Kristine Schack, gMendel & University of Copenhagen, Denmark
Anne Kristine Schack

Talk title

gMendel® Test-SCAN: a novel decision-supporting tool for mass screening of genetic disorders based on Oxford Nanopore technology

 

Abstract

Sex chromosome aneuploidies (SCAs) are the most undiagnosed, yet most common, chromosomal abnormalities. With a variety of clinical features, common features include reproductive abnormalities and neurocognitive features. While several studies suggest early diagnosis benefits life qualities, SCAs are not included in standard postnatal screening programs. Here, we present research demonstrating a cost-effective, end-to-end assay, gMendel® Test-SCAN, a novel decision-supporting tool for potential mass screening of aneuploidies (Turner syndrome and Triple X Syndrome), based on Oxford Nanopore sequencing technology. The data analysis process, which is part of the Phivea® decision-supporting platform, is fully automated and performs in real-time using a cutting-edge machine-learning approach. We demonstrate the high sensitivity and specificity of the gMendel Test-SCAN, and show it can act as a decision-supporting tool in the field of clinical research, and that it has the potential to equip practitioners with more accurate information for proper counselling.

 

Biography

Anne Kristine Schack has an MSc in microbiology from the University of Copenhagen focusing on phage-host interactions. She is currently a researcher at gMendel ApS, completing her PhD program with a focus on development and optimization of protocols for Oxford Nanopore Technologies with applications in the diagnostics of genetic disorders.

 

Keywords

Bioinformatics, Clinical research, Data analysis tool, Human genomics, Targeted sequencing

 

Products

MinION Mk1B, GridION, Flongle, R10 Flow Cells, R9 Flow Cells

Live lounge
Human & clinical research
14:55 - 15:20 BST 15:55 - 16:20 CEST 09:55 - 10:20 EDT 06:55 - 07:20 PDT 23:55 - 00:20 AEST
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PLENARY 9

online onsite
Galapagos Genetic Barcode: a model for island economic resilience during the COVID-19 pandemic
Jaime A. Chaves, San Francisco State University, USA & Universidad San Francisco de Quito, Ecuador
Jaime A. Chaves

Talk title

Galapagos Genetic Barcode: a model for island economic resilience during the COVID-19 pandemic

 

Abstract

The Galapagos Islands have been key in inspiring great scientific breakthroughs in history. Today, the islands continue to be internationally recognized as a model for science and conservation; however, their extreme reliance on tourism put the islands in dire conditions in 2020. The hard ban on travel and tourism at the onset of the COVID-19 pandemic deprived locals of income and left the archipelago’s vulnerable ecosystems at high risk due to the trafficking of protected species and loss of funding for conservation. We present the Galapagos Genetic Barcode, a citizen science model applied to the Galapagos Islands between 2020 and 2022 to confront this situation by providing employment in an ambitious scientific project using genetic barcoding techniques and creating economic resilience through capacity building. Ultimately, this approach was designed to serve as a model to improve the islands’ resilience and create independence from future uncertainties in tourism and transport

 

Biography

Jaime A. Chaves is an Evolutionary Biologist from Ecuador investigating how biodiversity is generated and maintained in the Neotropics, with a special emphasis on understanding the link between molecules (genetics) and phenotypes. His projects are based on international multidisciplinary collaborations involving local students and communities in the Galapagos Islands. He is currently an Assistant Professor at San Francisco State University, California and Researcher at the Galapagos Science Center — Universidad San Francisco de Quito.

 

Recent Publications

Chaves, J. A. et al. Evolutionary history of the Galápagos rail revealed by ancient mitogenomes and modern samples. Diversity 12(11):425 (2020). DOI: https://doi.org/10.3390/d12110425

Michel A. J. et al. The gut of the finch: uniqueness of the gut microbiome of the Galápagos vampire finch. Microbiome 6(1):167 (2018). DOI: https://doi.org/10.1186/s40168-018-0555-8

Chaves J.A. et al. Genomic variation at the tips of the adaptive radiation of Darwin’s finches. Mol. Ecol. 25(21):5282–5295 (2016). DOI: https://doi.org/10.1111/mec.13743

 

Keywords

Education, Environmental research and conservation, Identification, Microbiome

 

Products

MinION Mk1C, R9 Flow Cells

Auditorium
Plant & animal
15:20 - 16:15 BST 16:20 - 17:15 CEST 10:20 - 11:15 EDT 07:20 - 08:15 PDT 00:20 - 01:15 AEST
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PANEL PLENARY: THE FUTURE OF CLINICAL GENOMICS

online onsite
Empowering NHS rapid diagnostic testing with long-read DNA sequencing
Emma Baple, Royal Devon University Healthcare NHS Foundation Trust & University of Exeter
Emma Baple

Talk title

Empowering NHS rapid diagnostic testing with long-read DNA sequencing

 

Abstract

The Exeter NHS Genomics Laboratory delivers the national rapid whole-genome sequencing service for children in England. Currently, this ground-breaking service provides a diagnosis for 41% of the 1,200 babies and children tested each year, with a turn-around time of less than 10 days. This national success story demonstrates the power of genomic medicine to transform clinical care and improve healthcare outcomes.

Recently, the Exeter NHS Laboratory became the first centre to embed a PromethION 24 within an NHS laboratory. Learn about how our project is investigating the power of long-read sequencing to phase genetic variants increasing diagnostic yield for children in whom only one or neither parent is available for testing, reducing time to diagnosis and the need for parallel genetic testing.

Utilising analysis approaches developed in the research setting, we will illustrate with clinical case examples the potential for Oxford Nanopore technology to revolutionise the approach to rapid diagnostic practice in the critical care setting.

 

Biography

Emma is Professor of Genomic Medicine at the University of Exeter, a Consultant Clinical Geneticist at the Royal Devon University Healthcare NHS Trust, Medical Director for the South West Genomic Laboratory Hub, and Medical Lead for the NHS National Rapid Genome Sequencing Service for Acutely Unwell Children in England. Emma is also co-chair of the NHS England Rare Disease Test Evaluation Working Group. Between 2015 and 2020, Emma was the Clinical Lead for Rare Disease Validation and Feedback at Genomics England. Her principal area of interest is in the use of new and emerging genomic technologies to identify the cause of rare genetic disorders and the translation of that knowledge into improved clinical diagnostic testing and treatment strategies.

 

Keywords

Clinical research, Human genomics, Structural variation, Whole-genome sequencing

 

Products

PromethION P24/P48, Flongle

Nanopore sequencing as a potential diagnostic tool for genetic diseases in the Middle East
Ahmad Abou Tayoun, Al Jalila Children’s Specialty Hospital, United Arab Emirates
Ahmad Abou Tayoun

Talk title

Nanopore sequencing as a potential diagnostic tool for genetic diseases in the Middle East

 

Abstract

Despite a comprehensive suite of diagnostic tools — including short-read, whole-exome, and whole-genome sequencing, chromosomal microarrays, targeted methylation, and repeat testing — the cumulative diagnostic yield in a Middle Eastern cohort with rare diseases (n = 1,000) was 32.5%, leaving two-thirds of patients without diagnoses and likely missing possible personalized treatment and/or management plans. This incomplete diagnostic yield may be due to the inherent limitations of current technologies in accurately and comprehensively querying complete sets of all possible disease-causing variants in our genomes.

Here, we demonstrate the potential utility of Oxford Nanopore sequencing as a single comprehensive tool in routine clinical practice. Using previously characterized clinical samples, we optimized a long-read, whole-genome sequencing pipeline, which we then applied to a cohort of patients with negative results using current technologies and demonstrated the additional value of nanopore sequencing.

We also optimized a targeted Oxford Nanopore assay to analyse SMN1 and SMN2 and demonstrated its potential feasibility in clinical settings.

 

Biography

Ahmad is currently the director of the Al Jalila Genomics Center and Associate Professor of Genetics at Mohammed Bin Rashid University of Medicine and Health Sciences, United Arab Emirates. He received his PhD in genetics from Dartmouth Medical School, followed by a clinical molecular genetics fellowship at Harvard Medical School. Prior to moving to Dubai, he was a director of genomic diagnostics and Assistant Professor at the Children's Hospital of Philadelphia, University of Pennsylvania, USA. Ahmad has coauthored over 100 peer-reviewed publications and his main interests include characterizing the genomic landscape of rare diseases in the Middle East, developing/translating new diagnostic tools and assays for clinical use, and establishing guidelines for variant interpretation in collaboration with various expert groups, mainly ClinGen, ACMG, AMP, and CAP.

 

Recent publications

El Naofal, M. et al. The genomic landscape of rare disorders in the Middle East. Genome Med. 15(1):5 (2023). DOI: https://doi.org/10.1186/s13073-023-01157-8

 

Keywords

Clinical research, Data analysis tool, Human genomics, Whole-genome sequencing

 

Products

MinION Mk1B, MinION Mk1C, PromethION P24/P48

Potential use of nanopore sequencing in clinical cancer genomics
Janessa Laskin, Canada's Michael Smith Genome Sciences Centre at BC Cancer, Canada
Janessa Laskin

Talk title

Potential use of nanopore sequencing in clinical cancer genomics

 

Abstract

Advances in sequencing technologies have transformed our understanding of cancer and ushered in a new era for cancer research. The Personalized OncoGenomics (POG) program, is a prospective precision medicine initiative integrating whole-genome and transcriptome analysis (WGTA) into the clinical care of people with advanced cancers in British Columbia, Canada. In a sub-study of our larger cohort, we performed long-read Oxford Nanopore sequencing on 178 patient’s samples, in order to address some limitations we have noted with short-read sequencing. Comparison of these data sets has demonstrated situations where we now plan to apply nanopore sequencing prospectively within POG.

 

Biography

Dr. Laskin is a Clinical Associate Professor in the Department of Medicine at the University of British Columbia, an Associate Member in Canada’s Michael Smith Genome Sciences Centre, and a Medical Oncologist at BC Cancer, in Vancouver, Canada. Dr. Laskin’s research is focused on genomic and personalized medicine as the clinical program leader for the Personalized OncoGenomics (POG) Program. POG is a collaborative translational research effort that uses in-depth genomic sequencing to guide chemotherapy decision-making in a clinically relevant timeframe.

 

Keywords

Cancer research, Clinical research, Whole-genome sequencing

 

Products

PromethION, P2/P2 Solo

Filling the gap with long-read sequencing: lessons learned from Genomics Thailand
Manop Pithukpakorn, Siriraj Genomics, Mahidol
Manop Pithukpakorn

Talk title

Filling the gap with long-read sequencing: lessons learned from Genomics Thailand

 

Abstract

Short-read sequencing has been widely used in genomics research and clinical application, with its known limitations in resolving complex genomic regions, such as repetitive sequences and structural variations. Copy number variation (CNV) is a common structural variation in some cancer genes. In this talk, we will discuss the challenges of short-read germline sequencing in detecting CNVs in cancer susceptibility genes and the potential use of long-read sequencing to fill this gap. We will focus on lessons learned from Genomics Thailand's experience in applying long-read sequencing to study CNVs in a cancer research cohort and the potential clinical applications of long-read sequencing in hereditary cancer diagnosis.

 

Biography

Dr. Pithukpakorn is a Professor of Medicine at the Faculty of Medicine, Siriraj Hospital, Mahidol University, Thailand. He received his medical degree from Mahidol University, internal medicine residency from the University of Illinois at Chicago, USA, and Clinical and Molecular Genetics fellowship from the National Human Genome Research Institute, USA. The Genomics Thailand Initiative is a national project aiming to implement genomic medicine in healthcare systems and build a population-level genome database. Dr. Pithukpakorn is the head of the cancer program at Genomics Thailand.

 

Keywords

Cancer research, Clinical research, Education, Human genomics, Population genomics, Targeted sequencing

 

Products

MinION Mk1B, MinION Mk1C, GridION, PromethION P2/P2 Solo, PromethION P24/P48, Flongle

Auditorium
Human & clinical research Cancer research
16:15 - 16:40 BST 17:15 - 17:40 CEST 11:15 - 11:40 EDT 08:15 - 08:40 PDT 01:15 - 01:40 AEST
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PLENARY 10

online onsite
Nanopore sequencing for real-time genomic surveillance of Plasmodium falciparum
William Hamilton, Wellcome Sanger Institute, UK
William Hamilton

Talk title

Nanopore sequencing for real-time genomic surveillance of Plasmodium falciparum

 

Abstract

Malaria is a global public health priority causing over 600,000 deaths annually, mostly in young children living in sub-Saharan Africa. Molecular surveillance can provide key information for malaria control, such as the prevalence and distribution of antimalarial drug resistance. However, genome sequencing capacity in endemic countries can be limited. We implemented an end-to-end workflow for Plasmodium falciparum genomic surveillance in Ghana using Oxford Nanopore sequencing targeting antimalarial resistance markers and the leading vaccine antigen circumsporozoite protein (CSP). The workflow was rapid, robust, accurate, affordable, and straightforward to implement. We found that P. falciparum parasites in Ghana had become largely susceptible to chloroquine, with persistent sulfadoxine-pyrimethamine resistance and no evidence of artemisinin resistance. Multiple single-nucleotide polymorphism differences from the vaccine CSP sequence were identified, although their significance is unclear. This study demonstrates the potential utility and feasibility of malaria genomic surveillance in endemic settings using nanopore sequencing.

 

Biography

William Hamilton is an academic clinician based in Cambridge, UK, specialising in infectious diseases and microbiology. Clinically, he is a Specialist Registrar at Addenbrooke’s Hospital and a Clinical Lecturer in medical microbiology at Cambridge University. In his research, he aims to use the latest technology in genomics to explore pathogen evolution, transmission dynamics, and host–pathogen interaction, and inform clinical and public health decision making. He particularly focuses on the malaria parasite Plasmodium falciparum, antimicrobial resistance, and global health.

 

Recent publications

Girgis, S.T. et al. Nanopore sequencing for real-time genomic surveillance of Plasmodium falciparum. bioRxiv 2022.12.20.521122 (2022). DOI: https://doi.org/10.1101/2022.12.20.521122

 

Keywords

Genomic epidemiology, Infectious disease, Microbiology

 

Products

MinION Mk1B, Q20+, R10 Flow Cells

Auditorium
Microbiology & infectious disease
16:40 - 16:45 BST 17:40 - 17:45 CEST 11:40 - 11:45 EDT 08:40 - 08:45 PDT 01:40 - 01:45 AEST
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CLOSING REMARKS

online onsite
Gordon Sanghera, CEO, Oxford Nanopore Technologies
Gordon Sanghera

Talk Title 

Closing remarks 

 

Biography

Gordon Sanghera is co-founder of Oxford Nanopore with Spike Willcocks and Hagan Bayley. He was appointed CEO in May 2005 and has led the company through multiple finance rounds, and in 2021, a listing on the London Stock Exchange. The company has developed a new generation of nanopore-based sensing technology. The first products enable the real-time, high-performance, accessible, and scalable analysis of DNA and RNA, and this new class of sensing has the potential to expand into proteomics and metabolomics.

Fully bespoke manufacturing capability has been built from the ground up, integrating state-of-the-art electronics with silicon fab technology, combining the chemistry and biology. The company has been commercially distributing sequencing platforms since 2015, including the handheld and portable MinION and Flongle, and the high-throughput benchtop devices, GridION and PromethION. These platforms are used in more than 100 countries to understand the biology of humans and diseases such as cancer, plants, animals, bacteria, viruses, and whole environments.

Dr. Sanghera’s PhD in bioelectronic technology was followed by a career at MediSense — an Oxford spin-out that delivered a new generation glucose technology to the market — where he held positions including VP World Wide Marketing, Research Director, and Manufacturing Process Development Director. During this time, he was instrumental in the launch of several generations of blood glucose bio-electronic systems for the consumer and hospital medical markets.

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