London Calling 2023 Agenda

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.

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. 

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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 

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

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

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

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

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

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

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

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

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

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

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

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

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 

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.

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

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

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

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

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

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

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

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

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

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

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

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

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.