Open a chat to talk to our sales team
Day 1 - Monday, 5th Dec Day 2 - Tuesday, 6th Dec Day 3 - Wednesday, 7th Dec
10:00 - 10:30 EST 07:00 - 07:30 PST 15:00 - 15:30 GMT 16:00 - 16:30 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

HOW TO GET STARTED WITH NANOPORE SEQUENCING AND PLAN YOUR EXPERIMENT

online
Anupama Chandramouli, Field Application Scientist, North East Region, Americas
Anupama Chandramouli

Talk title

How to get started with nanopore sequencing and plan your experiment

Biography

Anupama received her PhD at The University of Arizona in Cancer Biology and moved to New York City for a postdoc at NYU Langone Medical Center. Here, she worked on mouse breast cancer models focusing on key nodes of mammary developmental in mice. In 2018, she joined Oxford Nanopore Technologies as part of the Technical Services team and is now a Field Application Scientist serving the Northeast region in the Americas.

Abstract

Summary:

Learn how nanopore sequencing works, the benefits of the technology for your area of research, and how to set up your first nanopore sequencing experiment.

Learning objectives:

This masterclass provides an introduction to nanopore sequencing and guides you through planning your first experiment with Oxford Nanopore technology. In this session, you will learn:

• How nanopore sequencing works

• The key benefits of using nanopore sequencing

• How to plan and get started with your first nanopore sequencing experiment, step by step

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

10:35 - 11:15 EST 07:35 - 08:15 PST 15:35 - 16:15 GMT 16:35 - 17:15 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

HOW TO EXTRACT HIGH-QUALITY DNA AND RNA

online
Vânia Costa, Technical Applications Scientist
Vânia Costa

Talk title

How to extract high-quality DNA and RNA

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 using nanopore devices.

Abstract 

Summary:

Find out how to get the best from your DNA and RNA samples to optimise sequencing performance.

Learning objectives:

This masterclass will describe how to get the best from your DNA and RNA samples.

In this session, you will learn:

• 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 storing nucleic acids for optimal sequencing performance

11:20 - 11:50 EST 08:20 - 08:50 PST 16:20 - 16:50 GMT 17:20 - 17:50 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

HOW TO SELECT THE RIGHT LIBRARY PREPARATION WORKFLOW FOR YOUR EXPERIMENT

online
Yan Yang, Team Lead — Technical Services, North America West Coast
Yan Yang

Talk title

How to select the right library preparation workflow for your experiment

Biography

Yan Yang joined Oxford Nanopore Technologies’ US Technical Services team after working as an Applications Scientist for the company. Yan is passionate about leveraging her hands-on nanopore sequencing experience to enable customers to benefit from experimental design to data analysis in a variety of applications. Prior to Oxford Nanopore, Yan’s PhD work used genomics approaches to studying transcriptional regulation by histone modifications and alternative polyadenylation of pre-mRNA.

.

Abstract

Summary:

Learn all about how to prepare libraries for nanopore sequencing, enabling you to select the right kit for your experimental needs.

Learning objectives:

The masterclass will introduce what you need to know to select the right library preparation workflow for your experiment. In this session, you will learn:

• How to prepare a DNA or RNA library for sequencing

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

• The differences between rapid and ligation chemistry

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

11:50 - 12:35 EST 08:50 - 09:35 PST 16:50 - 17:35 GMT 17:50 - 18:35 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

PRODUCT DISPLAY AREA ACTIVITIES

online ondemand

Product tables, Technical services, Oxford Nanopore Technologies Literature, Customer Services, and posters

Product Display Area
11:50 - 12:35 EST 08:50 - 09:35 PST 16:50 - 17:35 GMT 17:50 - 18:35 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

ON DEMAND

ondemand

Please visit the virtual platform to view a host of content from posters, Masterclass tutorials, pre- recorded Mini Theatre presentations, as well as product information in the Product display area. All content will be available until Friday December 16th 2022

12:35 - 13:05 EST 09:35 - 10:05 PST 17:35 - 18:05 GMT 18:35 - 19:05 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

WHICH NANOPORE SEQUENCING DEVICE TO CHOOSE

online
Austin Compton, Technical Applications Scientist
Austin Compton

Talk title

Which nanopore sequencing device to choose

Biography

Austin Compton earned his PhD in the Department of Biochemistry at Virginia Tech. There, he developed a passion for applying cutting-edge biotechnology to solve new and exciting biological questions. As a customer since 2017, he has watched Oxford Nanopore’s technology flourish into what it is today. As a Technical Applications Specialist at Oxford Nanopore, he is excited to help you adopt nanopore sequencing and to help develop your projects to get the most out of your sequencing device.

Abstract

Summary:

Learn about the range of Oxford Nanopore sequencing devices, flow cells, and choosing the best combination for your application.

Learning objectives:

This masterclass will teach you about our range of Oxford Nanopore sequencing devices and the types of flow cells available. In this session, you will learn:

• The types of flow cells available and how they pair with nanopore sequencing devices

• The key features of each nanopore sequencing device, including case studies

• How to select the right flow cell and nanopore sequencing device for your application

• How to perform real-time targeted sequencing with adaptive sampling

13:10 - 14:10 EST 10:10 - 11:10 PST 18:10 - 19:10 GMT 19:10 - 20:10 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

HOW TO LOAD A FLONGLE FLOW CELL

online
Vanessa Michael , Sequencing QC Scientist
Vanessa Michael

Talk title

How to load a Flongle Flow Cell

Biography

Vanessa Michael is a Sequencing QC Scientist at Oxford Nanopore Technologies. She has worked there for just over two years, starting off in 2020 working on Oxford Nanopore Technologies' response to the COVID-19 pandemic. Since transitioning into the Production QC world, she runs the assessment of different kits and flow cells for performance monitoring and quality control of sequencing products.

Abstract

Summary:

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

Learning objectives:

In this practical demonstration masterclass, you will learn:

• How to load a sequencing library on to a Flongle Flow Cell

• The basics of loading MinION and PromethION Flow Cells

 

14:10 - 14:55 EST 11:10 - 11:55 PST 19:10 - 19:55 GMT 20:10 - 20:55 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

PRODUCT DISPLAY AREA ACTIVITIES

online ondemand

Product tables, Technical services, Oxford Nanopore Technologies Literature, Customer Services, and posters

Product Display Area
14:10 - 14:55 EST 11:10 - 11:55 PST 19:10 - 19:55 GMT 20:10 - 20:55 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

ON DEMAND

ondemand

Please visit the virtual platform to view a host of content from posters, Masterclass tutorials, pre- recorded Mini Theatre presentations, as well as product information in the Product display area. All content will be available until Friday December 16th 2022

14:55 - 15:55 EST 11:55 - 12:55 PST 19:55 - 20:55 GMT 20:55 - 21:55 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

HOW TO BASECALL YOUR DATA AND DETECT METHYLATION

online
Jessica Anderson , Field Applications Scientist
Jessica Anderson

Talk title

How to basecall your data and detect methylation

Biography

Prior to working as a Field Applications Scientist with Oxford Nanopore Technologies, Jessica spent time in academia researching cell differentiation by examining the mechanisms by which heterocyst’s develop in cyanobacteria. This was followed by nearly a decade in an industry-leading R&D lab focused on plant genomics, in particular gene discovery and expression, including utilization of Oxford Nanopore Technologies’ PromethION device to sequence large, complex plant genomes for de novo assembly.

Abstract

Summary:

Learn how to basecall your nanopore sequencing data and detect methylation — no previous data analysis experience necessary.

Learning objectives:

This masterclass provides an introduction to basecalling and detecting epigenetic modifications in your nanopore sequencing data. In this session, you will learn:

• The different file formats involved in nanopore sequencing data analysis

• How to perform basecalling, without command line experience

• How to directly detect methylation in PCR-free nanopore sequencing data

• How to use real-time targeted sequencing via adaptive sampling for Reduced-Representation Methylation Sequencing (RRMS)

 

16:00 - 17:00 EST 13:00 - 14:00 PST 21:00 - 22:00 GMT 22:00 - 23:00 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

HOW TO GENERATE ASSEMBLIES AND CALL VARIANTS

online
Matt Attreed, Technical Applications Scientist (Bioinformatics)
Matt Attreed

Talk title

How to generate assemblies and call variants

Biography

Matt Attreed received his doctoral degree in molecular genetics. His thesis project was the engineering of a novel heparan sulfate visualization system in Caenorhabditis elegans. He made dozens of novel constructs using the sequences of synthetic antibodies for expression in live animals. During this time, he gained experience in bioinformatics and next-generation sequencing. After graduating, he worked for four years as a forensic scientist analyzing evidence and testifying in court.

Abstract

Summary:

Discover the approaches available for assembling your nanopore sequencing data and calling variants, including SNVs and structural variants.

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 and SNVs

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

 

 

 

08:15 - 09:20 EST 05:15 - 06:20 PST 13:15 - 14:20 GMT 14:15 - 15:20 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

DATA FOR BREAKFAST

onsite
Mike Vella, Director, Machine Learning Operations, Oxford Nanopore Technologies
Mike Vella

Talk title

The Dorado basecaller — a deep dive

Biography

Mike Vella is a Director of Machine Learning Operations at Oxford Nanopore. He received his PhD in Computational Neuroscience from the University of Cambridge, where he became fascinated with using computers to solve problems in biology. Mike’s work involves developing practical solutions using machine learning to improve the speed and accuracy of bioinformatics software. 

Abstract 

A basecaller maps raw signal, measured from sensors in a flow cell, to sequences of nucleotides. This involves several steps, such as scaling, chunking, encoding, decoding, and stitching, each of which presents computational challenges at the scale of tens of millions of samples per second. This talk will describe these steps and explain some of the computational advances we have achieved in the Dorado basecaller to allow these models to run at high speed. 

Katherine Lawrence, Machine Learning Bioinformatician, Oxford Nanopore Technologies
Katherine Lawrence

Talk title

Advances in duplex basecalling

Biography

Katherine Lawrence is a recent addition to the Machine Learning Operations team at Oxford Nanopore. Previously, she completed her PhD in Physics at MIT, where she mapped fitness landscapes in yeast using a variety of sequencing technologies. 

Abstract 

In Oxford Nanopore devices, duplex sequencing — in which both DNA strands from a single molecule are sequenced back-to-back — provides substantial accuracy benefits over single-strand sequencing. This talk will introduce duplex sequencing, give an overview of joint basecalling methods, and demonstrate the speed and accuracy of a new approach called Stereo Duplex.

Marcus Stoiber, Principle Algorithms Researcher, Oxford Nanopore Technologies
Marcus Stoiber

Talk title

Nanopore modified base update

Biography

Marcus Stoiber has been with Oxford Nanopore Technologies for over five years developing modified base detection and raw signal analysis algorithms. Before joining Oxford Nanopore, Marcus received his bachelor’s degree in Mathematics and Biochemistry at Occidental College, Master’s degree in Bioinformatics from Johns Hopkins University, and PhD in Biostatistics from the University of California, Berkeley. Marcus completed a postdoctoral fellowship at Lawrence Berkeley National Laboratories where his work on nanopore raw signal analysis first began. When not developing modified base algorithms, Marcus enjoys coaching his son’s and daughter’s little league teams and running.  

Abstract 

The nanopore sequencing platform generates a unique, information-rich output capable of detecting various base analogues. The release of the Remora modified base detection algorithm, separating the basecalling and modified base detection tasks, greatly simplified this process while simultaneously improving methylation detection accuracy. This talk will explore the latest developments in the Remora including 5-hydroxymethylation detection and all-context modified base detection training and current performance. Nanopore sequencing is quickly becoming the gold standard platform for methylation, and we aim to expand the catalogue of standard models available and enable the expansion of this catalogue more easily via the incredible nanopore community.  
 

Alex Merry, Instrument Software Fellow, Oxford Nanopore Technologies
Alex Merry

Talk title

Arrow: pointing the way forward for high-performance nanopore signal handling
with POD5

Biography

Alex has been at Oxford Nanopore for over eight years, working on the MinKNOW software. He now leads the team that works on MinKNOW Core, the technology that underpins MinKNOW.

Abstract 

POD5 is the upcoming Apache Arrow-based file format for storing the measured signal data of reads, replacing the existing FAST5 format. It allows reads to be basecalled on other systems or at a later date, as well as supplying training data for new basecalling models. Here, I discuss what it is, why it exists, and what advantages it has over FAST5, as well as touching on the changes that have been made since the initial public preview release.

Innovation Stage
10:00 - 10:25 EST 07:00 - 07:25 PST 15:00 - 15:25 GMT 16:00 - 16:25 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

WELCOME TO THE NANOPORE COMMUNITY MEETING 2022

online onsite
Spike Willcocks, Chief Strategy Officer & Co-founder, Oxford Nanopore Technologies
Spike Willcocks

Biography

After completing an MA in Chemistry and a DPhil in Biochemistry at the University of Oxford, Dr. Willcocks became one of the initial members of IPGroup Plc following its landmark deal with the Chemistry Department at Oxford. Ultimately leading the Life Science team, Dr. Willcocks' role encompassed all aspects of technology commercialisation, including spin-out company formation and business and corporate development, as well as private and public equity financings.

Dr. Willcocks was a key player in the creation of 14 life science businesses based on technology from three universities, leading proposals for the investment of £4m in seed financing from IPGroup and holding positions of Director and Chairman for sixportfolio companies. Working alongside the executive teams of the portfolio companies, Dr. Willcocks played an integral role in out-licensing transactions, co-development deals,and acquisitions. As well as supporting fundraisings for portfolio biotechnology companies, raising an aggregate of £20m, Dr. Willcocks also assisted with IPGroup's own IPO in October 2003 on the LSE, raising £30m and capitalising the company at over £100m. Dr. Willcocks was actively involved in the establishment of Oxford Nanopore Technologies whilst at IPGroup before joining full time in January 2006.

He is also a leading real tennis player and regularly competes in international tournaments.

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

Biography

Emma is Senior Director of Marketing Operations and joined Oxford Nanopore in 2014 as the MinION Access Programme launched. As part of her role, she is responsible for the vision, brand, and organisation of events such as London Calling and the Nanopore Community Meeting, as well as the sharing of information and customer stories both inside and outside of the Nanopore Community. Prior to joining Oxford Nanopore, she spent over 10 years working in various marketing roles for a multi-national life science company.

Auditorium
10:25 - 10:50 EST 07:25 - 07:50 PST 15:25 - 15:50 GMT 16:25 - 16:50 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

Expanding studies of global genomic diversity with complete, telomere-to-telomere assembly of diploid genomes

online onsite
Karen Miga, University of California, Santa Cruz, USA
Karen Miga

Talk title

Expanding studies of global genomic diversity with complete, telomere-to-telomere assembly of diploid genomes  

Biography

Dr. Karen Miga is an Assistant Professor in the Biomolecular Engineering Department at the University of California, Santa Cruz (UCSC) and an Associate Director of the UCSC Genomics Institute. She co-founded the Telomere-to-Telomere (T2T) consortium, an open, community-based effort to generate the first complete assembly of a human genome. Dr. Miga directs the Human Pangenome Project, with the goal to broaden the human reference to represent hundreds of diverse genomes from around the world. 

Abstract 

The Telomere-to-Telomere (T2T) consortium has finished the first truly complete sequence of a human genome, representing gapless assemblies for all 22 autosomes plus chromosomes X and Y. The newly completed regions include all centromeric satellite arrays and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome to variational and functional studies for the first time. Progress made to date has been focused exclusively on a single, effectively haploid cell line of European ancestry and although human in nature, does not represent a natural human diploid genome. Here, we demonstrate the use of a new innovative assembly method, Verkko, to phase and reconstruct complete human chromosomes using a combination of high-coverage highly accurate reads (HiFi or Duplex) and ultra-long nanopore datasets (ONT-UL). In parallel, will discuss new automated workflows to assess base-level accuracy and correct structural reconstruction of repetitive regions.

 

Auditorium
Human & translational research
10:50 - 11:20 EST 07:50 - 08:20 PST 15:50 - 16:20 GMT 16:50 - 17:20 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

Finding the needle: haplotype-resolved discovery and annotation of clinically relevant genetic and epigenetic variants using whole-genome nanopore sequencing

online onsite
Sissel Juul & Philipp Rescheneder, Oxford Nanopore Technologies
Sissel Juul Philipp Rescheneder

Talk title

Finding the needle: haplotype-resolved discovery and annotation of clinically relevant genetic and epigenetic variants using whole-genome nanopore sequencing

Biography 

Sissel Juul joined Oxford Nanopore in 2014 to lead the company’s Genomic Applications group, setting up a lab in New York City and later in San Francisco. The Genomic Applications teams utilize the unique strengths of Oxford Nanopore technologies to showcase high-impact biological applications both independently, as well as with external collaborators and Oxford Nanopore customers.  

Philipp Rescheneder works as a bioinformatician in the Applications team at Oxford Nanopore. In his current role he identifies, benchmarks, and adapts 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 methylation calling. Before joining Oxford Nanopore Technologies, his research focused on developing computational tools for efficiently aligning noisy long and short next-generation sequencing reads. 

Abstract

With the recent completion of the human genome from telomere to telomere, the possibility to leverage genetic information to aid in the understanding of the biology of disease is ever increasing. As whole-genome sequencing is becoming a commonplace method for interrogating the genetic component of disease, the ability to easily generate information-rich data encompassing a wide range of genetic and epigenetic variations is required. Here,we show how a single nanopore dataset enables the haplotype-specific identification of phased genetic and epigenetic variants and how they can be linked to disease phenotype in a disease-agnostic manner. Furthermore, we demonstrate how some of these methods may be utilised in the oncology research space through the sequencing and analysis of varied solid tumour/normal pairs as well as cell-free DNA.

Auditorium
11:20 - 11:30 EST 08:20 - 08:30 PST 16:20 - 16:30 GMT 17:20 - 17:30 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

SPOTLIGHT SESSION

online onsite
Shannon Murphy, Wadsworth Center ⁠— New York State Department of Health, USA
Shannon Murphy

Talk title

Profiling drug-resistant Mycobacterium tuberculosis with targeted nanopore sequencing

Biography

Dr. Shannon Murphy earned her BS in Biochemistry from the State University of New York at Geneseo and her PhD in microbiology from Cornell University. She is currently an Association of Public Health Laboratories Fellow at the Wadsworth Center at the New York State Department of Health, where she is using next-generation sequencing technologies to improve detection and characterization of antimicrobial resistant bacteria. 

Abstract

The time required to characterize Mycobacterium tuberculosis (MTB) infections can be considerable, specifically in cases involving multi-drug or extensively-drug resistant strains. Culture-based antimicrobial susceptibility testing requires weeks to complete due to MTB’s slow growth rate. However, sequencing-based assays can identify antimicrobial resistance in less time. At the Wadsworth Center at the New York State Department of Health, we have developed a targeted Next-Generation Sequencing (tNGS) assay that amplifies loci implicated in antimicrobial resistance direct from respiratory samples. These libraries are sequenced on a MinION Mk1C device from Oxford Nanopore and analyzed with a bioinformatics pipeline developed in-house that generates susceptibility profiles. The ability to sequence and analyze this data in real-time via Oxford Nanopore platforms offers the potential for shorter sequencing runs and improved turnaround times. This assay for profiling MTB antimicrobial susceptibility is currently undergoing validation in a CLEP-compliant laboratory for potential application in New York State by the Wadsworth Center after undergoing validation.  

Danielle Wrenn, Institute of Arctic Biology, University of Alaska Fairbanks, USA
Danielle Wrenn

Talk title

DART: a toolbox for the rapid detection of antibiotic resistance

Biography

Danielle Wrenn is an alumna of the Boston Conservatory where she graduated magna cum laude. Currently a senior at the University of Alaska Fairbanks, she is pursuing a BS in biological sciences with a focus on cell and molecular biology and a minor in statistics. A member of Dr. Devin Drown’s lab at the Institute of Arctic Biology, her research pertains to antibiotic resistance in soil microbial communities.  

Abstract 

Antibiotic resistance is an ongoing public health threat. The surveillance of environmental reservoirs of antibiotic resistance genes (ARGs) can both inform and enhance the way that we combat resistant pathogens. The Oxford Nanopore Technologies MinION sequencer enables streamlined library preparation that reduces the cost and time elapsed between sample collection and sequence analysis. Here, we describe the development of DART (Detection of Antibiotic Resistance Toolbox), a novel toolbox developed for the detection of antibiotic-resistant organisms in soil microbiomes. DART applies adaptive sampling technology to enrich ARG implemented with a combination of low-cost GPUs, Flongle flow cells, and the MinION sequencer. Despite a decrease in total sequencing output, adaptive sampling increased target composition and tended to increase the total number of hits to our ARG panel. Overall, adaptive sampling demonstrated the ability to enrich for ARGs.  

Jasper Verwilt, Ghent University, Belgium
Jasper Verwilt

Talk title

Revealing plasma exRNA’s deepest secrets

Biography

Jasper Verwilt is a 4th-year PhD student at the OncoRNALab at Ghent University. His research is currently focused on the study of RNA in human plasma using short- and long-read RNA sequencing methods. 

Abstract 

Due to the rise in transcriptome profiling of liquid biopsies, the RNAome of human blood plasma is slowly but steadily sharing its secrets. The fragmentation status of the extracellular RNA (exRNA) has remained elusive. Due to the unavailability of full-length RNA sequencing data of human plasma, the current hypothesis remains that most, if not all, exRNA in plasma is highly degraded. Although assumed to be generally intact, it currently remains unclear whether intact, circular RNA (circRNA) circulates in blood plasma. We used nanopore sequencing to obtain full-length exRNA data from low sample input human plasma and its purified EVs. We demonstrated for the first time that human blood plasma does contain full-length mRNA and intact circRNA (e.g., ZC3H6, VAMP3, SMARCA5, etc).Specifically, we show the presence of long RNA transcripts, previously hypothesized to be absent from plasma.

Auditorium
Spotlight
11:35 - 12:45 EST 08:35 - 09:45 PST 16:35 - 17:45 GMT 17:35 - 18:45 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

ON DEMAND

ondemand

Please visit the virtual platform to view a host of content including posters, Masterclass tutorials, pre-recorded Mini Theatre presentations, as well as product information in the Product display area. All content will be available until Friday December 16th 2022

11:40 - 12:30 EST 08:40 - 09:30 PST 16:40 - 17:30 GMT 17:40 - 18:30 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

FLOW CELL LOADING

onsite

Perfect your flow cell loading technique and learn how to load a VolTRAX cartridge for automated sample prep in this hands-on, expert-led demonstration

Product Display Area
11:50 - 12:10 EST 08:50 - 09:10 PST 16:50 - 17:10 GMT 17:50 - 18:10 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

SECRET CINEMA

onsite
Joshua Lee, University of York, UK
Joshua Lee

Talk title

Redefining cancer transcriptomes at single-transcript resolution with long-read sequencing

Biography

Josh obtained his BSc in Biochemistry from the University of Bristol. He completed a placement year in Prof. Venugopal Nair’s lab at the Pirbright Institute where he studied the application of apoptosis-inducing viral proteins in cancer therapy. He then worked at Prof. David Matthews’s lab at Bristol, with a focus on proteomic profiling of host-MERS viral proteins interactomes. He is now a PhD student at the University of York, working with Prof. Dimitris Lagos on probing the cancer transcriptome using nanopore sequencing technologies. 

Abstract 

Cancer progression is associated with aberrant processing of RNA transcripts in both tumour and immune cells. Despite advances, accurate profiling of transcript isoform usage and modifications remain challenging due to the limited read length offered by traditional RNA sequencing technologies. We used long-read Oxford Nanopore direct RNA and cDNA sequencing to explore the transcriptome profiles of clear cell renal cell carcinoma (ccRCC), using archival nephrectomy tumour samples from individuals who experienced disease relapse alongside controls. Differential gene expression and transcript usage analysis identified changes in the abundance and isoform usage associated with ccRCC relapse. Gene expression-based cell type deconvolution showed loss of specific populations of tumour infiltrating immune cells in relapse tumours. Remarkably, thousands of previously unannotated transcript isoforms were identified, including isoforms of clinically important tumour immune checkpoints. Our study demonstrates the feasibility of Oxford Nanopore long-read sequencing in tumour samples that uncovers cancer transcriptomes at unprecedented single-transcript resolution.

 

Rosemary Bamford, University of Exeter, UK
Rosemary Bamford

Talk title

Ultra-deep targeted long-read transcriptome sequencing reveals isoform diversity across human neurodevelopment  

Biography

Rosie works as a Postdoctoral Research Fellow in the Complex Disease Epigenetics Group at the University of Exeter. Her current research focusses on using long-read and single-cell sequencing technologies to advance genomics research into neurological development and medical conditions.

Abstract 

Alternative splicing dramatically increases transcriptomic and proteomic diversity from the coding genome and is an important mechanism in the control of gene expression in the central nervous system. We used Oxford Nanopore Technologies (ONT) whole-transcriptome sequencing to profile transcript diversity across human brain development. In parallel, we performed ultradeep targeted transcriptome sequencing across a panel of >300 genes associated with schizophrenia, autism, and intellectual disability. ONT-barcoded cDNA was pooled and enriched with a panel of 6000 hybridisation probes before ONT library preparation and sequencing. A bespoke data analysis pipeline was used for isoform visualisation and quantification. We identified widespread transcript diversity in the developing cortex with the detection of novel transcripts not previously described in existing genomic annotations. Our data confirm the importance of alternative splicing in the human cortex, dramatically increasing transcriptional diversity and representing an important mechanism underpinning gene regulation in the brain.

Secret Cinema
12:00 - 12:15 EST 09:00 - 09:15 PST 17:00 - 17:15 GMT 18:00 - 18:15 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

MINI THEATRE

online onsite
Amanda Warr, The Roslin Institute, UK
Amanda Warr

Talk title

Attack of the ultra-long chickens: assembling genomes and exploring the methylation patterns of three chicken cancer cell lines 

Biography

Amanda Warr is a BBSRC Discovery Fellow based at The Roslin Institute within the University of Edinburgh. She has experience using long-read sequencing for a range of applications including assembly of vertebrate genomes, metagenomes, and viral genomes from a variety of samples and for a variety of applications. Her current work focuses on understanding interactions between host, gut microbiome, and viruses using nanopore sequencing. Amanda also founded ION_BRU, the Scottish Nanopore User Group.  

Abstract 

Marek’s disease virus (MDV) causes a lymphoproliferative disease in poultry similar to that caused by Epstein–Barr virus in humans and often leads to T-cell lymphomas and a high death rate. MDV’s genome is large for a virus at ~200 kb and it integrates itself into the host’s genome. Cell lines are commonly used to study the virus and as a model for other viruses; however, relatively little is known about these cell lines as they are grown from naturally infected birds, and in some cases the viral strain and structural variants are unknown. Ultra-long-read sequencing was used to assemble the host genome, identify viruses and copy numbers, and explore differences in methylation patterns between the lines. All three chicken genomes assembled from these cell lines were more contiguous than the latest PacBio chicken reference genome and of comparable completeness, despite using a fraction of the coverage.  

Recent publications 

Warr, A. et al. No part gets left behind: tiled nanopore sequencing of whole ASFV genomes stitched together using Lilo. Biorxiv 2021.12.01.470769 (2022). 
https://www.biorxiv.org/content/10.1101/2021.12.01.470769v1

Mini Theatre
Microbiology
12:45 - 13:40 EST 09:45 - 10:40 PST 17:45 - 18:40 GMT 18:45 - 19:40 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

INNOVATIONS IN TARGETED SEQUENCING

onsite
Laurent Mesnard, French Center for Thrombotic Microangiopathies, France
Laurent Mesnard

Talk title

Rapid genomic analysis for thrombotic microangiopathy using nanopore adaptive sampling with EPI2ME SeqOne framework

Biography

Prof. Laurent Mesnard is a national coordinator for the French National plan of sequencing for rare adult kidney diseases and a national co-coordinator of the Thrombotic Microangiopathies 
(TMA) network (CNR-MAT). The team is located in Paris and currently developing applications of long-read sequencing technologies to potentially accelerate clinical diagnosis for rare kidney diseases, whilst at the same time providing new metrics to evaluate the risk of chronic kidney graft failure, which go beyond the information provided by the HLA locus itself.  

Abstract 

Thrombotic microangiopathy (TMA) encompasses various genetically driven diseases. The highly repetitive character of sequences in this region makes it difficult to detect structural variants when using standard short-read sequencing methods. To implement a versatile, fast-track genomics analysis for TMA in adult renal disease at the Sorbonne University, ICU, we developed a framework using nanopore adaptive sampling coupled to the SeqOne platform for analysis. SeqOne provides a centralized cloud-based solution that includes a nanopore-validated pipeline derived from the EPI2ME framework. This new approach maximizes the chance of discovering new descriptions related to SNVs and SVs and could enable precision medicine for complement-mediated TMA in less than three days for targeted therapy. 

Recent publications 

Doreille, A. et al. Diagnostic Utility of exome sequencing for kidney disease. N Engl J Med
380:2079–2080 (2019). https://doi.org/10.1056/NEJMoa1806891

Doreille, A. et al. Exome sequencing as part of a multidisciplinary approach to diagnosis. JAMA 324:2445 (2020). https://doi.org/10.1001/jama.2020.21521

Doreille, A. et al. Nephronophthisis in young adults phenocopying thrombotic microangiopathy and severe nephrosclerosis. Clin J Am Soc. Nephrol. 16:615–617 (2021). 
https://doi.org/10.2215/CJN.11890720

Mesnard, L. et al. Exome sequencing and prediction of long-term kidney allograft function. PLoS Comput Biol. 12:e1005088 (2016). https://doi.org/10.1371/journal.pcbi.1005088  

Rocio Esteban, Applications Support Bioinformatician, Oxford Nanopore Technologies
Rocio Esteban

Talk title

Reduced-Representation Methylation Sequencing (RRMS): real-time targeted methylation sequencing with Oxford Nanopore

Biography

Rocio Esteban is an Applications Support Bioinformatician at Oxford Nanopore. She completed a biotechnology degree in the University of Lleida and a Master’s degree in computational sciences in the University of Vigo. Prior to joining Oxford Nanopore, she worked as a Bioinformatics Specialist for a genomics company, helping to develop various bioinformatics pipelines including genotyping projects for population genomics studies, and genome assembly and annotation. She joined Oxford Nanopore three years ago, starting in the benchmarking team, where her work focused on methylation calling and germ-line and somatic SV calling general benchmarking, and also on adaptive sampling, helping to develop the Reduced-Representation Methylation Sequencing (RRMS) method. Recently, she started a new role, providing support in customer-facing projects

Abstract 

Adaptive sampling (AS) offers a fast, flexible, and precise method to enrich for regions of interest by depleting off-target regions with no need for special library prep. Here, we introduce Reduced Representation Methylation Sequencing (RRMS), an AS method in which we target CpG-rich regions in the human genome including 100% of CpG islands, shores, and shelves, and overlapping promoter regions. We will show how RRMS works and how it compares with other available targeted methods (e.g., RRBS, EPIC). During the talk we will also show relevant results from a tumour/normal clinical research paired experiment. Finally, as a unique feature of any ASbased method, the rejected reads can be considered shallow whole-genome sequencing, which gives a more complete picture of the sample of interest.

Franziska Haarich, University of Lübeck, Germany
Franziska Haarich

Talk title

CRISPRoff as potential treatment strategy for collagen VI congenital muscular dystrophy

Biography

Franziska Haarich studied molecular life sciences at the University of Lübeck. During internships and her Master’s thesis, she strengthened her interest in genetics and discovered her passion for sequencing and CRISPR/Cas9 methods. Since 2019, she has worked on her PhD thesis under the supervision of Prof. Jeanette Erdmann at the Institute for Cardiogenetics at the University of Lübeck. She is investigating the usage of CRISPR knockdown methods for allele-specific knockdown of COL6A2 as a therapeutic approach for ColVI-CMD.

Abstract 

Collagen VI congenital muscular dystrophy (ColVI-CMD) is a rare spectrum disorder for which there is still no treatment. One group of mutations that is often observed is heterozygous dominant-negative glycine substitutions in the triple helix of one of the three ColVI genes. Therapeutic strategies currently under investigation in cell culture aim to knockdown the pathogenic allele, and since many pathogenic variants are very rare, we aim to develop a therapeutic approach that is allele specific but mutation independent. Using Cas9 enrichment, we sequenced a 60-kb region including COL6A2 and its known regulatory elements to identify and phase common variants in this region. The next step was to design allele-specific guide RNAs and test those with CRISPRoff in patient-derived primary fibroblasts. Since the treatment aims to methylate the target, we used Cas9 enrichment again to sequence this region and Remora, Clair3, and methylartist to analyze allele-specific methylation.

Innovation Stage
Human & translational research
12:45 - 13:40 EST 09:45 - 10:40 PST 17:45 - 18:40 GMT 18:45 - 19:40 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

CANCER RESEARCH

online onsite
Mélanie Sagniez, CHU Sainte-Justine Research Centre, Canada
Mélanie Sagniez

Talk title

Rapid leukemia classification using nanopore sequencing

Biography

After obtaining a biological engineering degree, Mélanie gained experience as a biobank manager and clinical trials quality assurance officer in France. In 2020, she decided to pursue a PhD in bioinformatics in Montréal, focusing on the future potential of rapid diagnosis and stratification of pediatric leukemias using nanopore sequencing

Abstract 

Nanopore sequencing technology can generate high-resolution transcriptomic data in real-time and at a low cost, which heralds new opportunities for molecular medicine. We demonstrated the potential clinical utility of real-time transcriptomic profiling by processing RNA sequencing data from childhood acute lymphoblastic leukemia (ALL) clinical research samples on-the-fly with a trained neural network classifier. Our major findings were that the neural network was able to accurately classify 11 out of 12 leukemia samples, with as little as four minutes of sequencing needed to accurately classify ALL. 

Recent publications 

Sagniez, M. et al. Real-time molecular classification of leukemias. medRxiv 2022.06.22.22276550 (2022).https://doi.org/10.1101/2022.06.22.22276550

Sarah Frampton, University of Southampton, UK
Sarah Frampton

Talk title

Shining a light on the FCGRs: deconvoluting their challenging (epi)genomic organisation and consequences in immune oncology research

Biography

Sarah is a Cancer Research UK (CRUK)-funded PhD candidate within Prof. Jonathan Strefford’s Cancer Genomics group in the UK. She is in her final year of the integrated PhD Cell Biology and Immunology of Cancer program at the University of Southampton. Her research interests include FcγRs, B-cell lymphoma genetics, and bioinformatics.

Abstract 

Despite monoclonal antibody (mAb) immunotherapy having revolutionised cancer treatment, resistance is still common. mAb immunotherapies educe their functional response by interacting with the Fc gamma receptors (FcγRs). The low-affinity locus encoding FCGR2A, FCGR2B, FCGR2C, FCGR3A, and FCGR3B contains a 98% homologous 85-kb segmental duplication and is highly polymorphic, harbouring multiple large copy number variations (CNVs) and single nucleotide polymorphisms (SNPs). In the past, this locus has been extremely challenging to study as the standard short-read sequencing technologies often fail to produce reads that can be adequately aligned or assembled. For the first time, an accurate and detailed genomic map of the FCGR locus can be generated. Working on a healthy human cohort (n=22) with different FCGR CNV states and SNPs, and B cell lymphoma samples (n=11), Oxford Nanopore adaptive sampling and Cas9-targeting (tiling of 10 ROIs) resulted in 6.5-and 500-fold increases in FCGR sequencing, respectively. Oxford Nanopore sequencing represents an exciting opportunity to overcome the inherent difficulties with sequence homology, enabling the creation of comprehensive maps providing phased sequence, breakpoint, and methylation information. This in turn will facilitate greater understanding of FcγR regulation and how their function may be manipulated for the benefit of cancer patients.

Melissa Kramer, Cold Spring Harbor Laboratory, USA
Melissa Kramer

Talk title

Long-read sequencing and variant prioritization of unexplained early onset colon cancer trios

Biography

Working in the McCombie lab at CSHL, Melissa has been part of efforts to sequence reference genomes of several model organisms of animals and plants, including human and Arabidopsis. She has worked with data from a variety of sequencing platforms, in an endeavour to investigate genomic variants that contribute to complex traits. 

Abstract 

The underlying cause for the increased prevalence of early onset colorectal cancer in recent years remains elusive, despite investigations of both genetic and environmental factors. Hereditary factors explain only a small proportion of cases, and many cases do not show obvious drivers upon standard testing with short-read sequencing. Long reads provide access to regions of the genome intractable to short reads and uncover thousands of variants that are missed by short-read sequencing technology. We describe the long-read germline sequencing of two early onset colorectal cancer trios, where both probands were diagnosed under age 40 and whose parents had no history of cancer. We have developed a pipeline to survey multiple aspects of genomic variation, including structural variants, SNVs, and methylation changes, and to prioritize variants for further study. These methods provide a framework to aid in identification of events that may contribute to cancer predisposition. 

Mini Theatre
Human & translational research
12:45 - 13:40 EST 09:45 - 10:40 PST 17:45 - 18:40 GMT 18:45 - 19:40 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

CLINICAL MICROBIOLOGY

online onsite
Laurens Lambrechts, Ghent University, Belgium
Laurens Lambrechts

Talk title

Long-read sequencing assay allows accurate characterization of the HIV-1 reservoir

Biography

Laurens graduated with a Master of Bioscience Engineering: Cell and Gene Biotechnology at Ghent University in 2018. He then joined the HIV Cure Research Center and was granted an FWO strategic basic research fellowship. His PhD focuses on the development of a novel assay using third-generation sequencing methods to characterize the latent HIV-1 reservoir. 

Abstract 

The advent of near full-length (NFL) HIV-1 proviral genome sequencing has expanded our understanding of the reservoir composition, revealing that approximately 2–5% of persistent proviruses in antiretroviral therapy-treated individuals can be considered genome-intact. However, current NFL assays are based on labor-intensive and costly principles of repeated PCRs at limiting dilution, restricting their scalability. We developed a long-read sequencing assay that allows for high-throughput amplicon sequencing of NFL HIV-1 genomes. By tagging individual HIV-1 genomes with two distinct UMIs, the step of limiting dilution can be omitted, enabling the amplification of many NFL genomes in a single reaction. We employed our assay to successfully characterize the viral reservoirs of research samples obtained from a chronic cohort of people living with HIV (n=18). We believe that our long-read assay will have a wide future applicability in the field of HIV-1 research and could help to further increase our understanding of HIV-1 reservoir composition and dynamics. 

Levin Joe Klages, CeBiTec — Bielefeld University, Germany
Levin Joe Klages

Talk title

Analysis of clinical research samples by nanopore sequencing with Q20+ chemistry reveals inaccurate classifications within the genus Serratia

Biography

Levin Joe Klages is a PhD student at the Center for Biotechnology in Bielefeld focusing on the analysis of clinical sepsis research samples using nanopore sequencing technology. Levin completed his Master of Science in Genome Based Systems Biology at Bielefeld University. After his Master’s degree, he worked as a research assistant at IIT GmbH (IIT Society for Innovative Information Technologies mbH) sequencing SARS-CoV2 as well as further DNA samples. 

Abstract 

The identification of human pathogens is crucial for clinical diagnostics, and false assignment of species can interfere with treatment and harm the patient. We analyzed human clinical research samples that had been assigned as the pathogen Serratia marcescens by standard clinical methods with nanopore sequencing and found we could assign some to the distinct species Serratia bockelmannii as they displayed a significant distance to all genomes of known Serratia species on the nucleotide level, which indicated that they belonged to a novel species. Other samples in the NCBI database were shown to cluster with our proposed novel species or formed their own clusters, indicating the presence of additional novel species according to a classification with the type strain genome server (TYGS) that could not be discriminated between based on 16S sequences alone. Thus, we propose that whole-genome sequencing with Oxford Nanopore Q20+ chemistry is a superior way for fast and reliable species identification compared to 16S amplicon sequencing for example. 

Katrina Kalantar, Chan Zuckerberg Initiative, USA
Katrina Kalantar

Talk title

CZ ID: an open-source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring

Biography

Katrina Kalantar is a lead computational biologist in the Infectious Diseases team at the Chan Zuckerberg Initiative, leading research and computational biology in service of tool development across CZ ID and CZ Gen Epi. As part of a partnership with CZ Biohub and the Gates Foundation, she has also developed and led computational biology training efforts to support scientists interested in applying metagenomic NGS to their research and public health questions of interest. 

Abstract 

Metagenomic next-generation sequencing (mNGS) has transformed disease surveillance by enabling the rapid, unbiased detection and identification of microbes without pathogen-specific reagents, culturing, or a priori knowledge of the microbial landscape. While Oxford Nanopore sequencers have transformed the ability to track diseases during outbreaks by providing compact and portable sequencing technology, long-read methods offer specific challenges for successful implementation of metagenomics within the context of disease surveillance. mNGS data analysis requires a series of computationally intensive processing steps to accurately determine the microbial composition of a sample. Most mNGS data analysis tools require bioinformatics expertise and access to local server-class hardware resources which presents an obstacle for many research laboratories, especially in resource-limited environments. Here, we describe the CZ ID portal, which is an open-source cloud-based metagenomics pipeline and web application that overcomes these barriers and provides a service for global pathogen detection and monitoring (https://czid.org/). 

 

Nanopore Community Theatre
Microbiology
13:40 - 14:45 EST 10:40 - 11:45 PST 18:40 - 19:45 GMT 19:40 - 20:45 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

ON DEMAND

ondemand

Please visit the virtual platform to view a host of content including posters, Masterclass tutorials, pre-recorded Mini Theatre presentations, as well as product information in the Product display area. All content will be available until Friday December 16th 2022

13:45 - 14:35 EST 10:45 - 11:35 PST 18:45 - 19:35 GMT 19:45 - 20:35 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

FLOW CELL LOADING

onsite

Perfect your flow cell loading technique and learn how to load a VolTRAX cartridge for automated sample prep in this hands-on, expert-led demonstration

Product Display Area
13:50 - 14:10 EST 10:50 - 11:10 PST 18:50 - 19:10 GMT 19:50 - 20:10 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

SECRET CINEMA

onsite
Erin L. Young, Utah Public Health Laboratory, USA
Erin L. Young

Talk title

Long-read sequencing enables in-depth characterization of plasmids encoding KPC-2 in Citrobacter freundii outbreak

Biography

Erin Young, PhD works as a bioinformatician at the Utah Public Health Laboratory (UPHL). Her current research focuses on using sequencing of bacterial isolates to identify genes correlated with antimicrobial resistance and assisting in potential outbreak investigations using both short- and long-read sequencing. 

Abstract 

Antimicrobial resistance among bacteria such as Citrobacter freundii is a public health concern. Sequencing bacterial isolates to identify genes associated with antimicrobial resistance enhances the capacity to understand and minimize outbreaks. Twelve isolates of C. freundii obtained from patients in Utah exhibited reduced susceptibility to antimicrobials. Nanopore sequencing revealed 11 isolates that harbored a plasmid encoding KPC-2 and one with KPC-3, which are class A carbapenem-hydrolyzing enzymes associated with β-lactam resistance. Phylogenetic analysis was used to compare the core genome of chromosomal sequences (2,822 genes), resulting in two distinct clusters of isolates containing eight and three isolates, respectively. The similarity of the core genomes was suggestive of two concurrent outbreaks. During the process of characterizing the plasmids encoding KPC-2 of the two clusters, a surprising amount of variation was observed in the plasmids of the eight-isolate cluster, with plasmid sizes ranging from 57kb to 208kb (median = 70kb) with large rearrangements observed in three of the eight plasmids.

Recent publications 

Alam, J.M. et al. Emergence of severe metastatic hypervirulent Klebsiella pneumoniae infections in Texas. medRxiv 2021.06.08.21257347 (2021). https://doi.org/10.1101/2021.06.08.21257347

Smith, A.R. et al.  Infection control response to an outbreak of OXA-23 carbapenemase-producing carbapenem-resistant Acinetobacter baumannii in a skilled nursing facility in Utah. Am J Infect Control. 49(6), 792–799 (2021). https://doi.org/10.1016/j.ajic.2020.11.012 

Tobias Viehboeck, University of Vienna, Austria
Tobias Viehboeck

Talk title

Use of Pore-C to explore the 3D organization of animal symbiont chromosomes

Biography

Tobias Viehboeck is a PhD student at the Department of Functional and Evolutionary Ecology at the University of Vienna, Austria, and is studying how the (epi-)genome is shaped by the environment.

Abstract 

As we increasingly appreciate the variability in eukaryotic chromosome biology, the chromosome conformation of only a few model bacteria has been studied so far. Here, we investigate the chromosome spatial arrangement of a longitudinally dividing symbiont thriving in the oral cavity of mammals including humans. Using high-throughput chromosome conformation capture techniques coupled to Oxford Nanopore sequencing, we identified 65 loops engaging 32 different chromosomal regions. Strikingly, loop analysis revealed four regions or domains with different loop densities. From a functional perspective, loops contain genes predicted to be involved in attachment (e.g., adhesins, O-antigen-modifying enzymes) and immune evasion (e.g., immunoglobulin-binding proteins, membrane sialyation, host epithelium permeabilization). Using Pore-C, we conclude that the chromosomes of animal symbionts bear a stable, host-polarized 3D organization that may facilitate animal surface colonization.

Recent publications 

Nyongesa, S. et al. Evolution of longitudinal division in multicellular bacteria of the Neisseriaceae family. Nat Commun. 13:4853 (2022). https://doi.org/10.1038/s41467-022-32260-w

Secret Cinema
14:45 - 15:05 EST 11:45 - 12:05 PST 19:45 - 20:05 GMT 20:45 - 21:05 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

LIGHTNING TALKS

online onsite
Sung won Lim, Binomica Labs, USA
Sung won Lim

Talk title

MinION outcome in amateur research: three genomes from 2018 to 2022

Biography

Sung won Lim is an amateur biologist in NYC, currently studying as part of a small research group called Binomica Labs. Working under the motto 'Small Thoughtful Science', his primary interests are microbial sequencing and assembly, screening the East River for phages, and pondering different practical methods for studying phylogeny and evolutionary biology.  

Abstract 

The Oxford Nanopore Technologies MinION platform presents a compelling new research tool for modern amateur researchers. However, practical examples of MinION usage in amateur settings are still few, and overwhelmingly represent people with existing academic, technical, or professional backgrounds. We present three MinION sequencing, assembly, and analysis projects carried out from 2018 to 2022 by adult amateur researchers without prior training, describing first plastid genome (2018) of the plant Oxalis stricta (CM045551.1), first closed genome (2019) of the bacterium Deinococcus radiophilus (GCF_020889625.1), and first genome (2022) of the archaea Halococcus dombrowskii (GCF_022870485.1). Analysis of each of genome revealed unexpected and unique mechanisms and suggests avenues for further, in-depth research. 

Recent publications 

Lim, S.W. et al. Analysis of the complete genome sequence for Halococcus dombrowskii ATCC BAA-364T. bioRxiv preprint (2022). doi: https://doi.org/10.1101/2022.08.16.504008 

Sarah Scott, Minnesota Public Health Laboratory, USA
Sarah Scott

Talk title

Exploration of Oxford Nanopore long-read sequencing to contribute to influenza surveillance at the state level

Biography

Sarah Scott is a current APHL-CDC Bioinformatics Fellow who is conducting her fellowship at the Minnesota Department of Health, Public Health Laboratory. She is a recent graduate from George Mason University, with a Master’s degree in Biology. Her fellowship projects in Minnesota includes characterization of the influenza virus using whole-genome sequencing, SARS-CoV-2 sequencing optimization, and foodborne outbreak investigation using a long-read platform. 

Abstract 

Influenza is a rapidly mutating virus that can cause severe respiratory disease and is responsible for excessive illness and death in the United States. Influenza virus circulation and genetic diversity were reduced in the fall and winter of 2020/2021, likely due to measures that were taken to mitigate the transmission of SARS-CoV-2. As social behavioral changes trended towards a pre-pandemic state, we observed changes in Minnesota’s seasonal flu trends at the Minnesota Department of Health Public Health Laboratory. Influenza detections were lower than years prior to the COVID-19 pandemic, resulting in a prolonged flu season. The public health response to the ongoing SARS-CoV-2 pandemic has shown the significance of respiratory pathogen genomic surveillance utilizing next-generation sequencing, including Oxford Nanopore sequencing. We piloted a method using the Oxford Nanopore sequencing platform and existing CDC-developed wet laboratory methods to characterize the influenza virus found in specimens collected for influenza surveillance.

Søren Heidelbach, Aalborg University, Denmark
Søren Heidelbach

Talk title

Developing new bioinformatics methods to identify modifications from nanopore sequencing

Biography

Søren Heidelbach is a PhD student at Aalborg University, Denmark. His work focuses on the integration of DNA modification into metagenomic binning workflows, facilitated by his interest in microbial communities and data science.

Abstract 

There are microbes everywhere and they play an important role in almost every aspect of life. To gain a deeper understanding of these organisms, it is necessary to identify epigenetic modifications, as understanding the epigenome enables both functional analysis and manipulation. Modification diversity and sequence context also differentiate microbes and provide an additional dimension of resolution to metagenomic analyses. Nanopore sequencing is a readily available sequencing platform that has the potential to detect DNA modifications. The majority of current tools rely on pretrained models to predict the presence of modified motifs, limiting the detection of DNA modifications to already known types. In order to uncover novel modifications and use them in metagenomic studies, it is necessary to develop new methods to identify the full spectrum of modifications and motifs.   Here, we explore de novo identification of modification motifs using a comparison-based approach. This approach allows identification of modified motifs without any prior knowledge. 

Auditorium
15:05 - 15:30 EST 12:05 - 12:30 PST 20:05 - 20:30 GMT 21:05 - 21:30 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

Clinical and functional significance of germline variation in cancer susceptibility and disease

online onsite
Katherine Dixon, The University of British Columbia, Canada
Katherine Dixon

Talk title

Clinical and functional significance of germline variation in cancer susceptibility and disease

Biography

Katie Dixon is a postdoctoral research fellow in medical genetics at The University of British Columbia in Vancouver, Canada. With a background in molecular genetics, her current research interests include the application of novel technologies to the diagnosis of rare disease, including congenital disorders and cancer predisposition syndromes. Through collaborations with the Provincial Medical Genetics Program and Hereditary Cancer Program, this work aims to address current challenges in constitutional variant interpretation and identify opportunities for emerging molecular techniques in the clinic. 

Abstract 

Germline variants in cancer susceptibility genes contribute to 10–12% of all cancers. To date, we have performed nanopore genome sequencing for more than 100 individuals with a known or suspected susceptibility to cancer. Nanopore sequencing was sensitive to simple, complex, and epigenetic variants in well-characterized cancer predisposition genes. Long reads defined haplotypes associated with founder variants and revealed unforeseen allelic heterogeneity at the loci of recurrent deletions. Duplications identified by panel-based sequencing were found to occur frequently in tandem; informed by tumour pathology, indicating a duplication of uncertain significance as a strong candidate cause of disease. In research samples obtained from a case series of familial tumours, integrating long-read germline genome sequencing and short-read tumour genome and RNA sequencing implicated specific cancer pathways in disease. Together, our research findings suggest that long-read sequencing may provide insights into the natural history, functional consequence, and clinical significance of disease-causing genetic variation. 

Auditorium
Human & translational research
15:30 - 15:55 EST 12:30 - 12:55 PST 20:30 - 20:55 GMT 21:30 - 21:55 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

Single molecule methylation profiles of cell-free DNA in cancer with nanopore sequencing

online onsite
Billy Lau, Stanford University School of Medicine, USA
Billy Lau

Talk title

Single molecule methylation profiles of cell-free DNA in cancer with nanopore sequencing

Biography

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

Abstract 

Epigenetic characterization of cell-free DNA (cfDNA) is an emerging approach for detecting and characterizing diseases such as cancer. We developed a strategy using nanopore-based, single-molecule sequencing to measure cfDNA methylomes. This approach generated up to hundreds of millions of reads per cfDNA sample using research samples obtained from cancer patients, which is an order of magnitude improvement over existing nanopore sequencing methods. We developed a single-molecule classifier to determine whether individual reads originated from a tumor or immune cells. Leveraging methylomes of matched tumors and immune cells, we characterized cfDNA methylomes in research samples from cancer patients and demonstrate the potential of using this for longitudinal monitoring during treatment. 

Recent publications 

Lau, B.T. et al. Single molecule methylation profiles of cell-free DNA in cancer with nanopore sequencing. bioRxiv 2022.06.22.497080 (2022). https://doi.org/10.1101/2022.06.22.497080

Auditorium
Human & translational research
15:55 - 16:20 EST 12:55 - 13:20 PST 20:55 - 21:20 GMT 21:55 - 22:20 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

Long-read genome sequencing in Scottish patients with rare disease

online onsite
Tim Aitman, Centre for Genomic and Experimental Medicine, University of Edinburgh, UK
Tim Aitman

Talk title

Long-read genome sequencing in Scottish patients with rare disease

Biography

Professor Tim Aitman is the Director of the Centre for Genomic and Experimental Medicine within the MRC Institute of Genetics and Cancer and Consultant Physician in NHS Lothian. He is co-PI of the Scottish Genomes Partnership and was the Specialist Advisor for the 2009 House of Lords Inquiry in Genomic Medicine. His research uses genome technology and information to elucidate the genetic basis of common and rare human disorders and innovative approaches to cancer diagnostics and management by liquid biopsy.

Abstract 

The Scottish Genomes Partnership (SGP) is a collaborative programme between Scottish Genetics Centres and Genomics England, for sequence analysis and diagnosis of patients in the Scottish NHS with suspected rare Mendelian disease. In SGP Phase 1, 999 whole-genome sequences were generated from patients and family members with suspected rare Mendelian disease undiagnosed by previous clinical and molecular investigation. A diagnostic rate of 20–40% was achieved across a range of diseases in SGP Phase 1. In SGP Phase 2, long-read whole-genome sequences (>10kb, Oxford Nanopore) were generated from 73 patients/family members who remained undiagnosed from Phase 1 to detect structural variants (SVs) not identified by short-read sequencing. We developed and benchmarked a trio structural variation calling and filtering pipeline and assessed the impact of size selection and DNA fragmentation on read length, mapping, and SV discovery. A custom SV prioritisation strategy was developed to filter SVs down to a manageable number of potentially pathogenic variants. From our long-read sequence data, we confirmed the presence of (i) a likely pathogenic, 1.4-Mbp de novo inversion in a neurodevelopmental gene, AUTS2, and (ii) a potentially pathogenic, 55-Kbp de novo deletion in a gene for skeletal dysplasia, FN1. We are now customising our pipeline to identify additional pathogenic de novo/autosomal recessive/X-linked SVs in the SGP cohort, including instances of compound heterozygosity, using both short- and long-read genomes available in these families. The overall aim is to demonstrate the capability of long-read sequence data to make molecular diagnoses in families undiagnosed after panel and short-read sequencing. 

 

Auditorium
16:20 - 17:15 EST 13:20 - 14:15 PST 21:20 - 22:15 GMT 22:20 - 23:15 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

ON DEMAND

ondemand

Please visit the virtual platform to view a host of content including posters, Masterclass tutorials, pre-recorded Mini Theatre presentations, as well as product information in the Product display area. All content will be available until Friday December 16th 2022

16:25 - 17:15 EST 13:25 - 14:15 PST 21:25 - 22:15 GMT 22:25 - 23:15 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

FLOW CELL LOADING

onsite

Perfect your flow cell loading technique and learn how to load a VolTRAX cartridge for automated sample prep in this hands-on, expert-led demonstration

Product Display Area
16:30 - 17:15 EST 13:30 - 14:15 PST 21:30 - 22:15 GMT 22:30 - 23:15 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

VIRTUAL BREAKOUT: CONSERVATION

online
Gabriela Pozo, Universidad San Francisco de Quito, Ecuador
Gabriela Pozo

Talk title

Whole-genome sequencing of the Ecuadorian brown-headed spider monkey (Ateles fusciceps fusciceps), a critically endangered species

Biography

Gabriela Pozo is an Assistant Professor and Researcher at Universidad San Francisco de Quito in Ecuador, where she has worked since August 2016. She studied biology at Pontificia Universidad Católica del Ecuador and received her Master’s in Business and Science, with a concentration in biotechnology and genomics at Rutgers University, USA. Her main interests are genomics, genetic diversity, and population structures, and she has worked with a variety of species including mammals, invasive and native plants, insects, and microorganisms.  

Abstract 

The Ecuadorian brown-headed spider monkey (Ateles fusciceps fusciceps) is a primate that inhabits tropical forests in Northwestern Ecuador. Deforestation has led to the habitat of this subspecies being greatly reduced, and the IUCN Red List classifies it as a critically endangered species. Stronger conservation efforts are needed to avoid its extinction, which should include genome studies. However, a genomic approach requires a reference genome, which is why the main objective of this research is to sequence and assemble the genome of Ateles fusciceps fusciceps. To do so, DNA was extracted from the blood of one male individual. Libraries were prepared using the Oxford Nanopore SQK-LSK112 kit and protocol and sequenced on a MinION Mk1C device using six flow cells. Reads were filtered, assembled, mapped, and polished. Preliminary results indicate that a good quality genome assembly can be obtained, which would be an important resource for future studies that will aid the conservation of this critically endangered species.   

Recent publications 

Guadalupe, J. et al. Presence of SARS-CoV-2 RNA on surfaces of public places and a transportation system located in a densely populated urban area in South America. Viruses 14(1):19 (2021). https://doi.org/10.3390/v14010019   

Alarcón-Bolaños, P. et al. Evaluation of heterologous microsatellite markers (SSRs) in Rubus niveus for genetic diversity studies in the Galapagos Islands. Avances En Ciencias E Ingenierías 13(2):20 (2021) https://doi.org/10.18272/aci.v13i2.2293.   

Urquía, D. et al. Origin and dispersion pathways of guava in the Galapagos Islands inferred through genetics and historical records. Ecol Evol 11(21):15111-15131 (2021). https://doi.org/10.1002/ece3.8193  

Urquía, D. et al. Understanding the genetic diversity of the guayabillo (Psidium galapageium), an endemic plant of the Galapagos Islands. Glob. Ecol Conserv. 24:e01350 (2020) https://doi.org/10.1016/j.gecco.2020.e01350 

Urquía, D. et al. Psidium guajava in the Galapagos Islands: Population genetics and history of an invasive species. PLoS One 14(3):e0203737 (2019). https://doi.org/10.1371/journal.pone.0203737  

 

Jhakelin Gloria Reyes Vasquez, Amazon Conservation Association (ACCA), Peru
Jhakelin Gloria Reyes Vasquez

Talk title

Population monitoring with in situ conservation genetics in the Peruvian Amazon

Biography

Jhakelin Reyes is a conservation geneticist. In 2021, she initiated as Senior Manager at the Wildlife Conservation Laboratory, part of the In Situ Labs Initiative in the Amazon rainforest. She works on amplicon-based biodiversity surveillance in a wide variety of tissue types, automated pipeline development for DNA extraction and PCR, disease surveillance, and soon, reference genome and mitogenome assembly. Her hope is to further the reaches of in situ laboratory science to advance the knowledge and understanding of Peruvian biodiversity.

Abstract 

The Peruvian rainforest is one of the world's most significant biodiversity hotspots, but its remoteness hinders access to modern technologies for biodiversity studies. The Wildlife Conservation Laboratory, operated by Conservación Amazonica and Field Projects International, is an in situ molecular laboratory in the Madre de Dios region of Peru. Here, Peruvian scientists receive training and apply it to DNA barcoding, mitogenomics, pathogen surveillance, and metabarcoding studies. To tackle the challenge of population monitoring for species of interest, we developed and validated a highly informative set of SNPs for two sympatric primate species using nanopore technology. We genotyped 60 animals across both species, verifying sex, individual, and species identities without samples ever leaving the forest in which they were collected. This sets the stage for low-cost population monitoring for a multitude of endangered and managed species in the region and forms a critical improvement to the conservation toolbox available to scientists.  

 

Karla Estefania Rojas López, Universidad San Francisco de Quito, Ecuador
Karla Estefania Rojas López

Talk title

Draft genome of mortiño (Vaccinium floribundum), a wild berry species of the Andean paramo

Biography

Karla Estefania Rojas López has worked as a lecturer and researcher at Universidad San Francisco de Quito (USFQ) in Ecuador since 2019. She obtained her bachelor’s degree as a Biotechnology Engineer at USFQ in 2013 (Magna Cum Laude) and worked at the Plant Biotechnology Laboratory as a research assistant until 2015. In 2016, she obtained a MSc in Genetics of Human Disease at the University College London with honours (Distinction) and worked as a research assistant at the UCL Institute of Ophthalmology until 2018. 

Abstract 

Mortiño (Vaccinium floribundum) is a wild berry species that inhabits the Andean paramo, a high-altitude tundra-like ecosystem. This ecosystem is vulnerable to the effects of climate change and human intervention, which affects mortiño by reducing the areas where it grows. To date, there is no genetic information that would help elucidate the phylogeny of the mortiño, which would improve our understanding of its population status and contribute to its conservation. The main objective of this research was to create genomic resources to further study mortiño. High-molecular-weight DNA was extracted and sequenced using nanopore technology. Long-read data was assembled with Canu (2700 contigs, N50=0.5 Mb), wtdbg2 (2906 contigs, N50=0.8 Mb), and Flye (691 contigs, N50=3 Mb). BUSCO metric identified 86% (Canu), 72% (SMART de novo), and 93.1% (Flye) of the conserved orthologs as complete. The genomic resources generated in this study could provide vital information to better conserve and use V. floribundum

Recent publications 

Rojas López, K.E. et al. Exploring the genetic diversity and population structure of Mobula birostris in two key aggregation zones in the eastern tropical Pacific. Mar Ecol. Prog.Ser. 699:75-89 (2022) https://doi.org/10.3354/meps14171    

Alarcón-Bolaños, P. et al. Evaluation of heterologous microsatellite markers (SSRs) in Rubus niveus for genetic diversity studies in the Galapagos Islands. Avances En Ciencias E Ingenierías 13(2):20 (2021) https://doi.org/10.18272/aci.v13i2.2293     

Baquero-Méndez, V. et al. Genetic characterization of a collection of Tsantsas from Ecuadorian museums. Forensic Sci Int. 325:110879 (2021). https://doi.org/10.1016/j.forsciint.2021.110879  

Hardcastle, A. J. et al. A multi-ethnic genome-wide association study implicates collagen matrix integrity and cell differentiation pathways in keratoconus. Commun Biol. 4(1):266 (2021). https://doi.org/10.1038/s42003-021-01784-0  

Nanopore Community Theatre
Plant & animal research
09:00 - 09:15 EST 06:00 - 06:15 PST 14:00 - 14:15 GMT 15:00 - 15:15 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

WELCOME BACK TO THE NANOPORE COMMUNITY MEETING 2022

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

Biography

Rosemary Sinclair Dokos, SVP 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 and 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. Prior to joining Oxford Nanopore, she led the Market Development and Life Science division of VWR UK where she was responsible for teams in technical sales, field marketing, and contracts. In this role she worked with customers across all scientific industry sectors and managed a portfolio of over 600,000 products. Rosemary holds a BSc in Marine Sciences from the University of Southampton and is currently undertaking an executive MBA at Warwick Business School.

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
09:15 - 09:40 EST 06:15 - 06:40 PST 14:15 - 14:40 GMT 15:15 - 15:40 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

Long-read sequencing resolves complex structural variants and identifies missing pathogenic variants in unsolved hemophilia cases

online onsite
Danny E. Miller, University of Washington, USA
Danny E. Miller

Talk title

Long-read sequencing resolves complex structural variants and identifies missing pathogenic variants in unsolved hemophilia cases

Biography

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 & Pathology. His research mission is twofold — to reduce the burden of undiagnosed genetic diseases on patients and their families, and to better understand the causes of human genetic disease. To do this, the Miller lab (www.millerlaboratory.com) uses new technologies, such as long-read DNA and RNA sequencing, to improve the efficiency and effectiveness of genetic testing and identify and characterize novel disease-causing genetic variation.  

Abstract 

Despite recent advances in genetic testing, many individuals with inherited bleeding disorders remain unsolved after a complete clinical evaluation. In some cases, no variant is found in a particular gene or genes of interest, while in other cases a large structural variant (SV) is found or suspected that cannot be resolved using existing methods. In MyLifeOurFuture, a large U.S. hemophilia genotyping initiative, approximately 2% of participants with hemophilia A had no F8 variant identified despite exhaustive investigation. Additionally, large SVs were common in severe hemophilia and associated with inhibitor risk but were incompletely characterized in nearly all cases. We hypothesized that long-read sequencing would identify missing disease-causing variants and fully characterize SVs associated with hemophilia in these individuals.
 

Auditorium
Human & translational research
09:55 - 10:50 EST 06:55 - 07:50 PST 14:55 - 15:50 GMT 15:55 - 16:50 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

PANEL PLENARY: DELIVERING THE FUTURE OF GENOMIC PATHOGEN SURVEILLANCE

online onsite
Kame A. Galan-Huerta, Autonomous University of Nuevo Leon, Mexico
Kame A. Galan-Huerta

Talk title

Identification of resistance mutations to direct-acting antiviral agents against HCV in infected subjects in Mexico

Biography

Dr. Galán-Huerta is an associate professor and founder member of Medical Virology Research and Innovation Center, at the Faculty of Medicine of the Autonomous University of Nuevo Leon. His primary research interests are epidemiology and emerging and re-emerging viral diseases.

Abstract 

Death due to liver damage caused by hepatitis C virus (HCV) represents one of the most frequent health threats in Mexico. Direct-acting antiviral agents are available; nevertheless, HCV has gained mutations that hinder their antiviral effect. The aim of this study was to identify resistance-associated substitutions in HCV from Mexico. We evaluated subjects with hepatitis C who sought medical care in Monterrey, Mexico from May 2016 to August 2019. We extracted RNA and amplified the whole genome of HCV using tiled PCR. Amplicons were sequenced with MinION. The phylogenetic analysis of the complete genome showed that sequences from Mexico were related to viruses isolated in United States of America, Indonesia, and Japan. We detected one virus with resistance to daclatasvir and probable resistance to ledipasvir and velpatasvir.

Sarah Hill, Royal Veterinary College, UK
Sarah Hill

Talk title

Genomic investigation into yellow fever virus spread at the animal–human interface

Biography

Sarah Hill is an independent research fellow at the Royal Veterinary College (RVC), currently supported by a Sir Henry Wellcome Postdoctoral Research Fellowship. Before joining the RVC in 2020, Sarah obtained a DPhil and held two postdoctoral positions at the University of Oxford’s Department of Zoology. Sarah’s research focuses on investigating viral epidemiology in animal and human populations through generating and analysing virus genomes.

Abstract 

Zoonotic viruses that originate in wildlife harm global human health and economic prosperity. Zoonotic disease emergence is highest in biodiverse, tropical forests undergoing intensive land-use change. Phylodynamic analyses of virus genomes can powerfully test epidemiological hypotheses but are rarely applied to viruses of animals inhabiting these habitats, because virus genomes are typically unavailable. In 2016–2021, the densely populated Atlantic Forest and Cerrado region in Brazil experienced an explosive human outbreak of sylvatic yellow fever, caused by repeated virus spillover from wild neotropical primates. Using a portable nanopore sequencing approach, we generated 498 yellow fever virus genomes, resulting in an exceptionally well-sampled dataset of zoonotic virus genomes sampled from wild mammals. We used yellow fever virus genome sequences and epidemiological data from neotropical primates, humans, and mosquito vectors to identify the environmental, demographic, and climatic factors that influence virus spread.

Recent publications 

Hill, S.C.et al. Climate and land-use shape the spread of zoonotic yellow fever virus. Medrxiv 2022.08.25.22278983 (2022).https://doi.org/10.1101/2022.08.25.22278983

Sean Wang, Minnesota Department of Health, USA
Sean Wang

Talk title

A unified molecular epidemiology approach for SARS-CoV-2 whole-genome sequencing — a state public health perspective

Biography

Dr. Sean Wang currently serves as the Sequencing and Bioinformatics Supervisor at Minnesota Public Health Laboratory, Minnesota Department of Health. He provides national leadership in expanding the public health Advanced Molecular Detection infrastructure. He is a co-founder of State Public Health Bioinformatics (StaPH-B) group, serves on various of committee of Association of Public Health Laboratory (APHL), and is the Principal Investigator of the CDC Pathogen Genomics Centers of Excellence (PGCoE) Minnesota Site.

Abstract 

The Minnesota Department of Health (MDH) has continuously sequenced SARS-CoV-2 since its introduction. Since 2020, the MDH Public Health Laboratory has sequenced more than 40,000 SARS-CoV-2 genomes, established the Minnesota surveillance of SARS-CoV-2 (MN-SOS) consortium to coordinate sequencing efforts and logistics in Minnesota, and collaborated closely with epidemiologists to investigate SARS-CoV-2 transmission dynamics in congregate settings. They have also tracked and identified emerging variants, including tracking the spread of the Alpha variant, the nation’s first Gamma variant, and the first domestically transmitted Omicron variant, as well as reporting SARS-CoV-2 lineage prevalence in clinical samples to inform public health policy. SARS-CoV-2 sequencing has proven to be a vital tool in the larger COVID-19 pandemic response, particularly in characterizing disease severity, vaccine breakthrough infections, and characterizing specific events that may have led to further spread of disease. From a state public health perspective, a robust sequencing infrastructure and unified molecular epidemiology approach are key components for current and future pandemic responses.

Auditorium
Microbiology
10:55 - 11:55 EST 07:55 - 08:55 PST 15:55 - 16:55 GMT 16:55 - 17:55 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

ON DEMAND

ondemand

Please visit the virtual platform to view a host of content from posters, Masterclass tutorials, pre- recorded Mini Theatre presentations, as well as product information in the Product display area. All content will be available until Friday December 16th 2022

11:00 - 11:50 EST 08:00 - 08:50 PST 16:00 - 16:50 GMT 17:00 - 17:50 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

FLOW CELL LOADING

onsite

Perfect your flow cell loading technique and learn how to load a VolTRAX cartridge for automated sample prep in this hands-on, expert- led demonstration

Product Display Area
11:00 - 11:20 EST 08:00 - 08:20 PST 16:00 - 16:20 GMT 17:00 - 17:20 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

SECRET CINEMA

onsite
Paweł Krawczyk, International Institute of Molecular and Cell Biology, Poland
Paweł Krawczyk

Talk title

In vivo re-adenylation of mRNA-1273 vaccine revealed with direct RNA sequencing 

Biography

Paweł is a post-doctoral researcher in the lab of Prof. Andrzej Dziembowski in the Laboratory of RNA Biology — ERA Chairs Group, International Institute of Molecular and Cell Biology in Warsaw, Poland. There, he is working on a project to identify transcripts regulated by cytoplasmic poly(A) polymerases. His current research interests also include mRNA therapeutics.

Abstract 

In this study we used Oxford Nanopore direct RNA sequencing (DRS) for a comprehensive analysis of the Moderna mRNA-1273 COVID-19 vaccine. Interestingly, analysis of raw ionic currents revealed that mRNA-1273 ends with mΨCmΨAG nucleotides after the poly(A) tail. We modified the nanopolish-polya segmentation algorithm for mΨCmΨAG identification, what allowed us to monitor mRNA-1273 poly(A) tail dynamics in cells. Additionally, as the vaccine mRNA has all uridines replaced with N1-methyl-pseudouridine (mΨ) which causes inefficient basecalling, we used a dynamic time warping approach to recover mRNA-1273-specific reads. We demonstrated that in the model cell-lines, the vaccine mRNA is swiftly degraded in a process mediated by CCR4-NOT de-adenylation. Unexpectedly, after intramuscular injection in mice, mRNA-1273 undergoes re-adenylation, causing increased vaccine efficacy. Re-adenylation occurs in macrophages, the main group of antigen-presenting cells taking up vaccine mRNA and is mediated by TENT5 poly(A) polymerases.

 

 

Mauricio Lisboa Perez, Genome Institute of Singapore — A*STAR, Singapore
Mauricio Lisboa Perez

Talk title

Direct high-throughput deconvolution of unnatural bases via nanopore sequencing and bootstrapped learning

Biography

Mauricio Lisboa Perez is a Postdoctoral Fellow at the Genome Institute of Singapore — A*STAR, working at the MTMS lab, where he researches machine learning methods for nanopore signal analysis and genomics data. He obtained his PhD in 2021 from the School of Electrical and Electronic Engineering in NTU, researching computer vision algorithms. He received his Computer Science MSc degree from University of Campinas in 2016 and his BSc degree from Federal University of São Carlos in 2012, both in Brazil.

Abstract 

The discovery of synthetic xeno-nucleic acids (XNAs) that can basepair as unnatural bases 
(UBs) to expand the genetic alphabet has spawned interest in many applications, from synthetic biology to DNA storage. However, the inability to read XNAs in a direct, high-throughput manner has been a significant limitation for xenobiology. We demonstrate that XNA-containing templates can be directly and robustly sequenced (>2.3 million reads/flowcell, similar to DNA controls) on a MinION sequencer from Oxford Nanopore Technologies to obtain signal data that is significantly different relative to natural bases (median fold-change >5). To enable training of machine learning models that directly call XNAs along with natural bases, we developed a framework to synthesize a complex pool of 1,024 XNA-containing templates with different sequence contexts and high XNA purity (>90% on average). Combining this with a bootstrapping approach to filter non-XNA-containing templates during machine learning, we show that a model can be trained to call natural as well as unnatural bases with high accuracy (>91%). These results highlight the versatility of nanopore sequencing as a platform for interrogating nucleic acids for xenobiology applications, and the potential to study genetic material beyond those that use canonical bases.

Secret Cinema
11:55 - 12:50 EST 08:55 - 09:50 PST 16:55 - 17:50 GMT 17:55 - 18:50 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

ENVIRONMENTAL MICROBIOLOGY

online onsite
Samuel Fisch, Tulane University School of Public Health and Tropical Medicine
Samuel Fisch

Talk title

Monitoring the circulation of SARS-CoV-2 variants through community wastewater sequencing

Biography

Samuel Fisch is a senior at Tulane University studying Public Health, Anthropology, and Religious Studies. As a member of Dr. Tiong Gim Aw's Environmental Health Microbiology and Water Quality Research Group, his research interests pertain to microbial prevalence within municipal wastewater, particularly disease-causing viruses and bacteria. Grounded in social sciences, his ability to critically evaluate potentially harmful pathogens' lived effects enable him to understand the disease burden fully. He plans to pursue a career specializing in infectious disease prevention and control.

Abstract 

Wastewater surveillance of SARS-CoV-2 has acted as a complementary approach to clinical surveillance to monitor levels of the virus in wastewater as an early warning indicator of increasing community infections. In this study, we evaluated the efficacy of a rapid sequencing approach for SARS-CoV-2 in wastewater to identify dominant variants circulating in communities. SARS-CoV-2 N1 and N2 genes were measured using digital PCR. Library preparation was performed using two primer pools to amplify the viral genomes and sequenced using nanopore MinION sequencer. Sequencing data were analyzed using IDseq and EPI2ME bioinformatics tools. We identified that the dominant variants in wastewater by year were 20C in 2020, 21J (Delta) in 2021, and 21K (Omicron) in 2022. These results demonstrate that wastewater sequencing can be used as a rapid real-time, cost-effective public health tool to detect emerging SARS-CoV-2 variants, thus allowing public health officials to respond to virulent strains in the community adequately.

Celine Petersen, Aalborg University, Denmark
Celine Petersen

Talk title

MinION sequencing of 94 fungal genomes to create a comprehensive Penicillium pangenome

Biography

Celine Petersen is a PhD student working in the Plant and Fungal Biotechnology research group at Aalborg University. Her research focuses on genome sequencing and genetic engineering of filamentous fungi primarily Penicillium spp. In this context, she also works on associating candidate genes with natural compounds.  

Abstract 

The Penicillium genus is known to produce several natural compounds utilized both in food and pharmaceutical industries. In general, the entire biosynthetic potential of these fungi is yet to be characterized. Advancements in DNA sequencing technologies have enabled the possibility to generate high-quality fungal genome assemblies, which can be used to create a pangenome to evaluate the genetic potential of the genus. Ninety-four different Penicillium isolates spanning the diversity of the Penicillium genus were selected to generate a pangenome. High-molecular-weight DNA was extracted and sequenced in-house using a MinION device to generate de novo assembled genome drafts of high quality. The proteomes of the genome drafts were clustered into orthogroups to create the Penicillium pangenome, which was divided into core and accessory genes. We further used the Penicillium pangenome in an association study linking candidate genes (orthogroups from the pangenome) to metabolomic metadata (known mycotoxins). 

Recent publications 

Petersen, C. et al. High molecular-weight DNA extraction methods lead to high quality filamentous ascomycete fungal genome assemblies using Oxford Nanopore sequencing. Microb Genom. 8(4):000816. (2022) https://doi.org/10.1099/mgen.0.000816 

Sørensen, T. et al. A highly contiguous genome assembly of Arthrinium puccinoides. Genome Biol Evol. 14(1):evac010. (2022) https://doi.org/10.1093/gbe/evac010

 

Mantas Sereika, Aalborg University, Denmark
Mantas Sereika

Talk title

Targeted deep metagenomics for the recovery of novel closed microbial genomes from highly complex communities

Biography

Since his Master’s thesis, Mantas has been working on genome-centric metagenomics using state-of-the-art long-read sequencing and high-throughput bioinformatics under the supervision of professor Mads Albertsen at Aalborg University, Denmark. After temporarily putting his research on pause to assist in the national surveillance of SARS-CoV-2 variants in Denmark, Mantas has returned to working on long-read metagenomics as part of his PhD studies.

Abstract 

Metagenomics enables researchers to gain insight into unculturable microorganisms through the recovery of metagenome-assembled genomes (MAGs). An example of an unculturable microorganism includes cable bacteria, which are centimetres-long filamentous bacteria capable of conducting long-distance electron transfer. However, due to reliance on short-read metagenomics, publicly available cable bacteria MAGs are fragmented, while many are incomplete, missing 16S rRNA and other key functional genes. Here, we have performed long-read nanopore sequencing (total 162.4 Gbp) of environmental and enrichment samples to recover two closed as well as two high-quality cable bacteria MAGs. The genome drafts were compared against existing cable bacteria MAGs to detect novel genes and genomic elements missing from short-read MAGs. Phylogenetic analysis revealed that two single-contig MAGs recovered in this study belonged to novel species and one of these novel species was found to encode genes for certain physicochemical traits that challenge the current taxonomic framework of cable bacteria.  

Recent publications 

Sereika, M. et al. Oxford Nanopore R10.4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or reference polishing. Nat Methods 19:823–826 (2022). https://doi.org/10.1038/s41592-022-01539-7  

Lamurias, A. et al. Metagenomic binning with assembly graph embeddings. Bioinformatics 
38(19):4481–4487 (2022). https://doi.org/10.1093/bioinformatics/btac557

Nanopore Community Theatre
Microbiology
11:55 - 12:50 EST 08:55 - 09:50 PST 16:55 - 17:50 GMT 17:55 - 18:50 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

SINGLE-CELL AND SPATIAL TRANSCRIPTOMICS

onsite
Sheridan Cavalier, The Johns Hopkins University School of Medicine, USA
Sheridan Cavalier

Talk title

Single-cell transcript isoform sequencing of the activated adult mouse hippocampus with 10x Genomics and Oxford Nanopore

Biography

Sheridan is a 5th year PhD student co-mentored by Winston Timp and Richard Huganir at The Johns Hopkins School of Medicine. She is developing a single-cell long read transcriptome of the mouse hippocampus using 10x Genomics and Oxford Nanopore to reveal the transcript-isoform landscape of neuronal activity in different brain cell types following learning.

Abstract 

Using the rolling circle amplification to concatemeric consensus (R2C2) Nanopore error-correction protocol developed by Volden et al., we generated single-cell long-read transcriptomics data in the adult mouse hippocampus with 10x Chromium-generated cDNA. We are able to generate enough reads on the Oxford Nanopore PromethION device to successfully perform meaningful differential gene expression analysis for cell clustering and identification. The complete exon coverage generated by our single cell long reads allows for transcript isoform identification. We are applying this single cell isoform sequencing approach to the discovery of learning-specific transcript isoforms in a mouse model of contextual learning. The transcriptional response that cells of the brain undergo during activity begets mRNA regulation and synaptic protein function. We demonstrate, with Oxford Nanopore long-read sequencing, our ability to capture the diverse transcript isoform landscape of the activity induced transcriptional response with cell-type specificity.

Anoushka Joglekar, Weill Cornell Medicine, USA
Anoushka Joglekar

Talk title

A spatiotemporal view of alternative splicing in the mouse brain

Biography

Anoushka Joglekar obtained her undergraduate degree at the Ohio State University, where she was immediately enthralled by computational biology. Wanting to explore this further, she pursued a PhD with Dr. Hagen Tilgner at Weill Cornell Medicine where she has been working on elucidating the molecular architecture of the brain. Her work focusses on the alternative splicing landscape at a single cell level and feels extremely fortunate in being able to tinker with and explore cool new technologies.  

Abstract 

Complex systems such as the brain leverage alternative splicing to expand the proteome. To enable splicing studies in distinct cell types, we developed methods for the identification of full-length isoforms from single cells. Using our computational framework, we identified approximately 400 genes displaying isoform differences between the mouse prefrontal cortex and hippocampus at postnatal day 7. In most cases, a single cell type is responsible for regional splicing differences. However, regional identity can sometimes override cell-type identity, suggesting that the microenvironment may influence splicing patterns of multiple cell types in a brain region. Our efforts to spatially resolve isoform sequencing revealed some developmentally regulated genes display regional splicing gradients throughout the mouse brain. Particularly, we identified genes wherein exon inclusion undergoes switching for developmentally regulated genes along an anterior-posterior gradient. Our ongoing work applies these methods to more developmental timepoints and brain regions where we have identified temporally and regionally mediated patterns of splicing.

Recent publications 

Joglekar, A. et al. A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain. Nat Commun. 19;12(1):463 (2021) https://doi.org/10.1038/s41467-020-20343-5

Kathleen Zeglinski, Walter and Eliza Hall Institute of Medical Research, Australia
Kathleen Zeglinski

Talk title

NAb-seq: an accurate, rapid, and cost-effective method for antibody long-read sequencing in hybridoma cell lines and single B cells

Biography

Kathleen is a second year PhD student at the Walter and Eliza Hall Institute of Medical Research in Melbourne, Australia. She has a strong interest in long-read sequencing and bioinformatics, including their application to antibody discovery.

Abstract 

Despite their common use in research, monoclonal antibodies are currently not systematically sequenced. Sanger sequencing has been ‘the gold standard’ for antibody gene sequencing but relies on the availability of species-specific degenerate primer sets and is lengthy and expensive. We developed Nanopore Antibody Sequencing (NAb-seq), a three-day, species-independent, and cost-effective workflow to characterize paired, full-length immunoglobulin light- and heavy-chain genes from hybridoma cell lines using Oxford Nanopore long-read sequencing. When compared with Sanger sequencing of two hybridoma cell lines, NAb-seq was highly accurate, reliable, amenable to high-throughput and identified the presence of multiple productive heavy and light chains within a single cell. We further show that the method is applicable to single cells, allowing efficient antibody discovery in rare populations, such as memory B cells. In summary, NAb-seq promises to accelerate the identification and validation of hybridoma and single B-cell-derived antibodies used in research, diagnostics, and therapeutics.

Recent publications 

Subas Satish, H.P. et al. NAb-seq: an accurate, rapid, and cost-effective method for antibody long-read sequencing in hybridoma cell lines and single B cells. mAbs 14(1):2106621 (2022). https://doi.org/10.1080/19420862.2022.2106621

Innovation Stage
Human & translational research
11:55 - 12:50 EST 08:55 - 09:50 PST 16:55 - 17:50 GMT 17:55 - 18:50 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

HUMAN CLINICAL RESEARCH

online onsite
Griet De Clercq, Ghent University, Belgium
Griet De Clercq

Talk title

Long-read sequencing resolves cryptic structural variation in individuals with syndromic intellectual disability

Biography

Griet De Clercq graduated as a bioinformatician from Ghent University and started her PhD in 2019 at the Center of Medical Genetics at the University Hospital Ghent. In her work, she applies nanopore long-read sequencing to patients with unresolved syndromic intellectual disability. Her research focusses on the identification of cryptic, or de novo, structural variation that is potentially causal for the patient’s phenotype.

Abstract 

A genetic diagnosis in intellectual disability (ID) is crucial for further disease management yet is currently lacking in 40% of patients. This can be partly explained by missed structural variants 
(SVs), which are large genomic rearrangements that are hard to discover through conventional methods. We applied nanopore long-read sequencing onto 13 proband-parent trios with unexplained ID, and three single proband cases to identify, or further specify, cryptic (de novo) SVs. We found approximately 21,700 SVs per individual and zero to one de novo variants per proband in a trio setting. Five de novo events and single case variants were further unravelled, revealing more complex rearrangements in three out of five cases. Oxford Nanopore long-read sequencing can uncover significantly more variants compared with short-read sequencing, as well as pinpoint exact breakpoints and reveal complex rearrangements and de novo variants. This study highlights the potential of nanopore long-read sequencing as a standard molecular method for SV identification.

Ailsa MacCalman, University of Exeter, UK
Ailsa MacCalman

Talk title

Ultra-deep targeted transcript sequencing identifies isoform diversity across human pancreatic development

Biography

Ailsa was awarded a PhD studentship at the University of Exeter in 2019, under the supervision of Prof. Jon Mill, Dr. Elisa De Franco, and Dr. Aaron Jeffries, with collaboration from Prof. Noel Morgan and Prof. Andrew Hattersley. Ailsa’s PhD is focused on genomic and transcriptomic regulation in the development of the human pancreas and her project will evaluate the epigenetic and transcriptional changes which occur in the pancreas as it develops in utero, compared with patterns of gene regulation in the fully developed adult pancreas. This will facilitate a systematic exploration of hypotheses related to the developmental origins of diseases affecting the pancreas. Ailsa graduated with a Master’s degree in Biomedical Science in 2018, where she researched autoimmune responses in type 1 diabetes patients and HLA-DR4/DQ8 transgenic mice.

Abstract 

The human pancreas is an incredibly complex organ with multiple functions. There is limited knowledge surrounding the genomic and epigenomic regulation in the development of the pancreas. While some studies have investigated the gene expression levels of the developing pancreas using short-read sequencing, there is a lack of transcript-level assessment to catalog isoform diversity over time. We used Oxford Nanopore long-read transcriptome sequencing to investigate alternative splicing events in 31 human fetal pancreas samples, spanning 6 to 21 weeks post-conception. Using a targeted approach, we performed ultra-deep sequencing of 330 genes associated with diabetes, neurodevelopmental disorders, and schizophrenia. We identified significant isoform diversity across diabetes-associated genes throughout the development of the pancreas, detecting novel transcripts that were not present in existing gene annotations, including the identification of fusion transcripts utilizing exons from adjacent genes. Our long-read transcriptome data indicates the importance of alternative splicing in the developing pancreas, highlighting dynamic changes of transcript isoforms over time. This data also provides a unique resource for understanding the landscape of the transcriptome across pancreatic development.

Fritz Sedlazeck, The Baylor College of Medicine Human Genome Sequencing Center, USA
Fritz Sedlazeck

Talk title

Rapid structural variant calling across AllOfUs using Oxford Nanopore sequencing

Biography

Dr. Fritz Sedlazeck is an Associate Professor at Baylor College of Medicine and an Adjunct Associate Professor at Rice University. His research focuses on developing computational methods to detect and analyze genomic variations with a focus on structural variations (SVs). Dr. Sedlazeck’s group focuses on the mechanisms of the formation of SVs across multiple species to improve our understanding of how these complex alleles evolve and impact phenotypes

Abstract 

AllOfUs is an important endeavor in the USA to characterize thousands of people to improve clinical sequencing and interpretation. As part of this project, we started to sequence individuals using long-read sequencing from Oxford Nanopore Technologies.  
We improved Sniffles, our structural variation (SV) caller, to be able to analyze the high number of genomes from this project or others. These improvements include not only greater speed and accuracy but also population/cohort analysis as well as mosaic and somatic SV calling improvements.  
I will give an update on our AllOfUs program and describe the important updates on Snifflesv2 and their implications for other ongoing projects.    

Mini Theatre
Human & translational research
12:50 - 13:55 EST 09:50 - 10:55 PST 17:50 - 18:55 GMT 18:50 - 19:55 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

ON DEMAND

ondemand

Please visit the virtual platform to view a host of content from posters, Masterclass tutorials, pre- recorded Mini Theatre presentations, as well as product information in the Product display area. All content will be available until Friday December 16th 2022

12:55 - 13:50 EST 09:55 - 10:50 PST 17:55 - 18:50 GMT 18:55 - 19:50 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

FLOW CELL LOADING

onsite

Perfect your flow cell loading technique and learn how to load a VolTRAX cartridge for automated sample prep in this hands-on, expert- led demonstration

Product Display Area
13:00 - 13:20 EST 10:00 - 10:20 PST 18:00 - 18:20 GMT 19:00 - 19:20 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

SECRET CINEMA

onsite
Isabel Rodriguez, National Cancer Institute, USA
Isabel Rodriguez

Talk title

Analysis of viral and human oncogene expression in human papillomavirus-driven cancer

Biography

Isabel Rodriguez completed her undergraduate degree at Florida International University and earned a BSc in Biochemistry. Recently, she joined the Laboratory of Translational Genomics at the National Cancer Institute working in Michael Dean’s lab where the main research focus is on HPV and cervical cancer, with a minor focus on breast, liver, and pediatric cancers.

Abstract 

Human papillomaviruses (HPVs) cause nearly all cervical cancers and expresses two potent oncogenes, E6 and E7. HPV often integrates into the human genome, causing complex local amplification of viral and human DNA. We applied long-read DNA and RNA sequencing to 20 cervical and head-and-neck cancer cell lines to identify HPV integration sites and HPV transcription patterns, as well as host gene mutations. HPV expression and expression of the E6 and E7 genes vary widely between cell lines. We identified host genes disrupted or activated by integration and alterations in DNA methylation due to integrations. HT-3 cells have integrated HPV30, an HPV type not previously associated with cancer. HT-3 cells also have somatic mutations in the TP53 and RB1 tumor suppressor genes and immune evasion genes. Together, these methods show promising potential in accelerating the diagnosis and subclassification of HPV-driven cancers and guiding therapeutic approaches.

Vahid Akbari, BC Cancer — Genome Sciences Centre, Canada
Vahid Akbari

Talk title

Simultaneous haplotyping and parent-of-origin assignment of homologous chromosomes without parental sequence data

Biography

Vahid Akbari is a PhD student in medical genetics at the University of British Columbia and the Canada's Michael Smith Genome Sciences Centre. His research is focused on epigenomics, especially characterization of DNA methylation in normal and cancerous cells.

Abstract 

While phasing algorithms are able to distinguish homologous chromosomes, parent-of-origin 
(PofO) assignment of phased homologs requires access to parental sequence data. Here, we demonstrate chromosome-scale phasing and PofO detection without the need for parental sequencing information. We demonstrate that single-cell DNA template strand sequencing 
(Strand-seq) in combination with long-read Oxford Nanopore sequencing allows the construction of chromosome-scale haplotypes. Subsequently, we inferred DNA methylation at CpG dinucleotides from nanopore raw signals and used the known origin (paternal or maternal) of methylation at human imprinted intervals to assign PofO to haplotyped homologs. We were able to assign PofO for autosomal chromosomes with an average mismatch error rate of 0.31% for SNVs and 1.89% for indels. Because our method can determine whether an inherited allele originated from the mother or the father, we predict that it will improve genealogy and diagnosis and management of many genetic diseases where the phenotype is affected by the parental origin of the allele.

Secret Cinema
13:55 - 14:15 EST 10:55 - 11:15 PST 18:55 - 19:15 GMT 19:55 - 20:15 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

LIGHTNING TALKS

online onsite
Yuan (Daniel) Xu, University of California, Santa Cruz, USA
Yuan (Daniel) Xu

Talk title

Determination of the centromere protein A landscape at single-molecule resolution

Biography

Dan Xu is a PhD student in the Miga lab at the University of California, Santa Cruz.  Fascinated by the mystery and the unknown of the human genome, he is motivated to be a part of the effort that utilizes cutting edge sequencing technologies to decipher and understand the genetic function of the most repeat-rich and unexplored part of our genome.

Abstract 

Centromere protein A (CENP-A) is a histone H3 variant that specifies the location of each chromosome’s centromere, which is essential for proper kinetochore attachment and chromosome segregation. Mislocalization and misregulation of CENP-A can drive chromosomal breakage and rearrangement, leading to cancer and chromosomal aneuploidies. Measuring and comparing the density and spacing of CENP-A-containing nucleosomes within and between endogenous human centromeres will provide new insight into the structure of the inner kinetochore, as well as how this structure helps to ensure proper centromeric function and strength.  

Recently, directed methylation with long-read sequencing (DiMeLo-seq) was developed, which deposits exogenous adenine methylation marks near a desired protein then uses nanopore long-read sequencing to quantify this exogenous adenine methylation directly along with endogenous cytosine methylation. Here, we present the distribution of CENP-A on ultra-long single molecules using DiMeLo-seq in the HG002 cell line. Furthermore, we discuss a probabilistic algorithm for predicting the positions of single CENP-A nucleosomes on single chromatin fibers. 

Karine Choquet, Harvard Medical School, USA
Karine Choquet

Talk title

Direct RNA sequencing reveals multi-intron splicing order and poly(A) tail lengths across subcellular compartments

Biography

Karine Choquet is originally from Ottawa, Canada and completed her undergraduate degree in Biochemistry and Molecular Medicine at the University of Montreal, followed by a PhD in Human Genetics at McGill University. Her PhD thesis focused on the genetic and molecular basis of rare inherited neurological diseases. She has been a post-doctoral fellow in Stirling Churchman’s lab at Harvard Medical School since 2018, where her work focuses on the use of direct RNA nanopore sequencing to better understand pre-mRNA processing.

Abstract 

Newly synthesized messenger RNAs (mRNAs) undergo several processing steps prior to their export to the cytoplasm. To explore the landscape of full-length mRNA isoforms across different subcellular compartments, we performed direct RNA nanopore sequencing of poly(A)-selected RNA from whole-cell, chromatin, cytoplasm, and polysome fractions in human cells. This revealed that multi-intron pre-mRNA splicing order is not stochastic, but largely predetermined, with most genes using only a small number of splicing orders out of the many possible ones available to reach a fully spliced transcript. Furthermore, we observed that pre-mRNA splicing and polyadenylation progress in parallel on chromatin, where poly(A) tail lengths were also associated with the time that each transcript spends on chromatin. In the cytoplasm, long-lived transcripts tended to have shorter poly(A) tails than those that were rapidly degraded. Together, we describe the first transcriptome-wide characterization of splicing and polyadenylation across long mRNA isoforms in distinct subcellular compartments.  

Recent publications 

Choquet, K. et al. Pre-mRNA splicing order is predetermined and maintains splicing fidelity across multi-intronic transcripts. bioRxiv 2022.08.12.503515 (2022). 
https://doi.org/10.1101/2022.08.12.503515  

Smalec, B.M. et al. Genome-wide quantification of RNA flow across subcellular compartments reveals determinants of the mammalian transcript life cycle. bioRxiv 2022.08.21.504696 (2022).  https://doi.org/10.1101/2022.08.21.504696 

Courtney Hall, University of North Texas Health Science Center, USA
Courtney Hall

Talk title

STRspy-ing hidden variation in forensic DNA profiles using the MinION device

Biography

Courtney Hall is a PhD candidate at the University of North Texas Health Science Center in Fort Worth where she recently defended her dissertation on forensic STR profiling using the MinION device. In addition to forensic applications of ONT sequencing, her research focuses on the detection of disease-relevant alterations in the DNA and microRNA contained within extracellular vesicles.  

Abstract 

Short tandem repeats (STRs) are the gold standard for human identification in forensic investigations. Despite the power and reliability of current typing techniques, sequence-level information within and around STRs are masked in conventional length-based profiles. To harness the advantages of the portable MinION device in forensic genetics, we developed STRspy, a novel method capable of generating accurate length- and sequence-based allele designations for autosomal STRs from ONT reads. Here, we expand on STRspy to enable simultaneous profiling of autosomal and Y-STRs as well as flanking SNPs in casework-relevant samples. STRspy predicted the correct alleles across all 22 autosomal and 23 Y-STRs and identified SNPs in the flanking regions with a high level of accuracy. These results demonstrate that STRspy can produce accurate profiles for the largest combined autosomal and Y-STR amplification panel, further increasing the forensic potential of the MinION device in future applications.

Recent publications 

Hall, C.L. et al. Accurate profiling of forensic autosomal STRs using the Oxford Nanopore Technologies MinION device. Forensic Sci Int Genet. 56:102629 (2022). 
https://doi.org/10.1016/j.fsigen.2021.10262.

Auditorium
14:15 - 14:40 EST 11:15 - 11:40 PST 19:15 - 19:40 GMT 20:15 - 20:40 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

Oxford Nanopore technology expands the research scope and increases resolution in microbiome research

online onsite
Jun Wang, Institute of Microbiology, Chinese Academy of Sciences, China
Jun Wang

Talk title

Oxford Nanopore technology expands the research scope and increases resolution in microbiome research

Biography

Prof. Jun Wang is Max-Planck Partner group leader at the Institute of Microbiology, Chinese Academy of Sciences, and his laboratory is mainly interested in bioinformatic tools and computational methods for studying the healthy and disease-related microbiome. Since its establishment in 2017, the working group has published more than 30 papers in journals including Nature Biotechnology, Nature Communications, Advanced Science, Microbiome, Protein Cell, and Arthritis and Rheumatology, among others.

Abstract 

Human microbiomes are complex and play essential roles in health and disease, and their study has been mainly driven by advances in sequencing technology. In our group, we have demonstrated that the capacity of Oxford Nanopore sequencing technology in producing long reads, sequencing RNA directly, and detecting methylation greatly expands the scope and resolution of microbiome research. Long reads from Oxford Nanopore help to increase the quality of metagenomic assembly and resolve a large number of structural variations that define strain-level functional differences in gut bacteria. RNA sequencing increases the efficiency of microbial profiling in difficult samples, such as blood or lung, and assists the identification of pathogens. Oxford Nanopore also improves the power to understand other components of the microbiome, including the virome and mycobiome. Currently, we are further expanding our research using Oxford Nanopore technology to study the epigenomics of the microbiome, and even proteomics.

Recent publications 

Chen, L. et al. Nanopore sequencing expands individualized and metabolic-relevant structural variations in gut metagenome. Nat Commun. 13(1):3175 (2022) https://doi.org/10.1038/s41467-022-30857-9

Liu, X. et al. Gut microbial methionine impacts circadian clock gene expression and reactive oxygen species level in host gastrointestinal tract. Protein Cell (2022) pwac021, 
https://doi.org/10.1093/procel/pwac021 

Auditorium
Microbiology
14:45 - 15:30 EST 11:45 - 12:30 PST 19:45 - 20:30 GMT 20:45 - 21:30 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

VIRTUAL BREAKOUT: ADVANCES IN PLANT AND ANIMAL GENOMICS

online
Patrick G.S. Grady, University of Connecticut, USA
Patrick G.S. Grady

Talk title

Highly accurate telomere-to-telomere level tammar wallaby genomes and methylomes assembled from Oxford Nanopore ultra-long reads

Biography

Patrick Grady is a 5th year PhD candidate in Rachel O’Neill’s lab at the University of Connecticut (UConn) working on telomere-to-telomere level genomics of wallabies, kangaroos, and other marsupials, with a focus on repetitive elements in karyotypic evolution. He has also collaborated with the T2T-CHM13 project working on novel repeats and their expansion in primate genomes, the Tasmanian Tiger project with Colossal Biosciences, and directly predicting non-B DNA in Oxford Nanopore reads with UConn’s Computer Science Department.  

Abstract 

We present two telomere-to-telomere (T2T) assemblies and epigenetic profiles of the tammar wallaby (Macropus eugenii). This wallaby has long served as the model organism for marsupials, ranging from early genetics to reproductive biology to drug discovery. An XX and XY individual were both assembled with Oxford Nanopore PromethION long reads, ultra-long reads, Hi-C, and short reads for polishing. These fully annotated genomes are extremely high quality and complete, with high Merqury QV scores of >40 and gapless chromosomes. Chromosome contigs contain complete centromeres, telomeres, and rDNA arrays. The genomes are deeply annotated, including phased diploid versions, extensive methylation data derived from Oxford Nanopore reads, and tissue-specific transcriptomics. Methylation data derived from Oxford Nanopore reads allow the exploration of epigenetics of many previously unknown genome structures. Overall, these new genome assemblies and accompanying data represents a significantly improved resource for a deeply studied model organism that will continue to provide insights into mammalian evolution. 

Recent publications 

Hoyt, S.J. et al. From telomere to telomere: the transcriptional and epigenetic state of human repeat elements. Science (New York, N.Y.) 376(6588):eabk3112 (2022). https://doi.org/10.1126/science.abk3112  

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

McEvoy, S. L. et al. Profiling genome-wide methylation in two maples: fine-scale approaches to detection with nanopore technology. Biorxiv 2022.08.02.502577 (2022). https://doi.org/10.1101/2022.08.02.502577

 

Anastasia McKinlay, Indiana University & Howard Hughes Medical Institute, USA
Anastasia McKinlay

Talk title

Sequencing and assembly of Arabidopsis thaliana nucleolus organizer regions reveals the distribution of active and inactive rRNA gene subtypes

Biography

Anastasia McKinlay is a Research Associate in Prof. Craig Pikaard’s Lab in the Department of Biology at Indiana University. She is attracted by the opportunities provided by ultra-long sequencing technologies to ‘close’ the remaining gaps in the Arabidopsis thaliana genome. Specifically, Anastasia focuses on the sequencing and assembly of highly repetitive ribosomal RNA gene-containing loci, known as nucleolus organizer regions (NORs).    

Abstract 

Nucleolus organizer regions (NORs) are megabase-long regions within genomes at which ribosomal RNA genes are repeated in long tandem arrays. Due to their repetitive nature, these regions are not fully assembled in any sequenced genomes. In Arabidopsis thaliana, NORs are located at the distal ends of Chr2 (NOR2) and Chr4 (NOR4) and consist of hundreds of rRNA genes. Using Oxford Nanopore sequencing technology with specialized assembly strategies based on unique sequence patterns, we obtained end-to-end NOR2 sequence assembly and nearly complete NOR4 assembly. To determine rRNA gene activity within NORs, we combined Oxford Nanopore sequencing with fluorescence-activated nucleoli sorting to deduce which regions of the NORs are enriched within isolated nucleoli, which had been shown to correlate with rRNA gene transcriptional activity.  

 

George Chung, New York University, USA
George Chung

Talk title

Genomic mechanisms of asexual reproduction

Biography

George Chung is interested in the evolution of genomes, with an emphasis on the molecular adaptations in meiosis, chromosome biology, and germ cell development that enabled a parthenogenetic mode of reproduction from a gonochoristic (male and female) ancestor. His research aims to establish a complementary model system in Diploscapter organisms alongside the established Caenorhabditis and Pristionchus models to determine the evolutionary forces that shaped the different biological processes in these organisms.

Abstract 

Diploscapter pachys is a parthenogenetic nematode from a long-lived (around 18 million years) asexual lineage with an abridged meiosis, a highly heterozygous genome with an unusual karyotype of 2n = 2. To continue to explore the evolutionary trajectory of D. pachys from sexual reproduction to parthenogenesis, we are undertaking a comparative analysis of genome evolution across the clade of parthenogenetic species against a closely related sexual outgroup. Our goal is to determine whether the changes in genome architecture enabled an evolutionary shift to parthenogenesis. For all the species under investigation, we are generating phased diploid chromosome-level assemblies using nanopore long-read DNA sequencing with scaffolding using Pore-C chromatin conformation data. We will present the evidence for linear Diploscapter chromosomes with divergent telomeres and a history of fusion and rearrangements of ancestral chromosomes.

Nanopore Community Theatre
15:30 - 16:15 EST 12:30 - 13:15 PST 20:30 - 21:15 GMT 21:30 - 22:15 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

ON DEMAND

ondemand

Please visit the virtual platform to view a host of content from posters, Masterclass tutorials, pre- recorded Mini Theatre presentations, as well as product information in the Product display area. All content will be available until Friday December 16th 2022

15:35 - 16:10 EST 12:35 - 13:10 PST 20:35 - 21:10 GMT 21:35 - 22:10 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

FLOW CELL LOADING

onsite

Perfect your flow cell loading technique and learn how to load a VolTRAX cartridge for automated sample prep in this hands-on, expert- led demonstration

Product Display Area
15:40 - 16:00 EST 12:40 - 13:00 PST 20:40 - 21:00 GMT 21:40 - 22:00 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

SECRET CINEMA

onsite

Nanopore Community Meeting 2022 Studio
Highlights of the exclusive speaker interviews from the Auditorium

Erin L. Young, Utah Public Health Laboratory, USA
Erin L. Young

Talk title

Long-read sequencing enables in-depth characterization of plasmids encoding KPC-2 in Citrobacter freundii outbreak

Biography

Erin Young, PhD works as a bioinformatician at the Utah Public Health Laboratory (UPHL). Her current research focuses on using sequencing of bacterial isolates to identify genes correlated with antimicrobial resistance and assisting in potential outbreak investigations using both short- and long-read sequencing. 

Abstract 

Antimicrobial resistance among bacteria such as Citrobacter freundii is a public health concern. Sequencing bacterial isolates to identify genes associated with antimicrobial resistance enhances the capacity to understand and minimize outbreaks. Twelve isolates of C. freundii obtained from patients in Utah exhibited reduced susceptibility to antimicrobials. Nanopore sequencing revealed 11 isolates that harbored a plasmid encoding KPC-2 and one with KPC-3, which are class A carbapenem-hydrolyzing enzymes associated with β-lactam resistance. Phylogenetic analysis was used to compare the core genome of chromosomal sequences (2,822 genes), resulting in two distinct clusters of isolates containing eight and three isolates, respectively. The similarity of the core genomes was suggestive of two concurrent outbreaks. During the process of characterizing the plasmids encoding KPC-2 of the two clusters, a surprising amount of variation was observed in the plasmids of the eight-isolate cluster, with plasmid sizes ranging from 57kb to 208kb (median = 70kb) with large rearrangements observed in three of the eight plasmids.

Recent publications 

Alam, J.M. et al. Emergence of severe metastatic hypervirulent Klebsiella pneumoniae infections in Texas. medRxiv 2021.06.08.21257347 (2021). https://doi.org/10.1101/2021.06.08.21257347

Smith, A.R. et al.  Infection control response to an outbreak of OXA-23 carbapenemase-producing carbapenem-resistant Acinetobacter baumannii in a skilled nursing facility in Utah. Am J Infect Control. 49(6), 792–799 (2021). https://doi.org/10.1016/j.ajic.2020.11.012 

Tobias Viehboeck, University of Vienna, Austria
Tobias Viehboeck

Talk title

Use of Pore-C to explore the 3D organization of animal symbiont chromosomes

Biography

Tobias Viehboeck is a PhD student at the Department of Functional and Evolutionary Ecology at the University of Vienna, Austria, and is studying how the (epi-)genome is shaped by the environment.

Abstract 

As we increasingly appreciate the variability in eukaryotic chromosome biology, the chromosome conformation of only a few model bacteria has been studied so far. Here, we investigate the chromosome spatial arrangement of a longitudinally dividing symbiont thriving in the oral cavity of mammals including humans. Using high-throughput chromosome conformation capture techniques coupled to Oxford Nanopore sequencing, we identified 65 loops engaging 32 different chromosomal regions. Strikingly, loop analysis revealed four regions or domains with different loop densities. From a functional perspective, loops contain genes predicted to be involved in attachment (e.g., adhesins, O-antigen-modifying enzymes) and immune evasion (e.g., immunoglobulin-binding proteins, membrane sialyation, host epithelium permeabilization). Using Pore-C, we conclude that the chromosomes of animal symbionts bear a stable, host-polarized 3D organization that may facilitate animal surface colonization.

Recent publications 

Nyongesa, S. et al. Evolution of longitudinal division in multicellular bacteria of the Neisseriaceae family. Nat Commun. 13:4853 (2022). https://doi.org/10.1038/s41467-022-32260-w

Secret Cinema
16:15 - 16:40 EST 13:15 - 13:40 PST 21:15 - 21:40 GMT 22:15 - 22:40 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

Using nanopore sequencing to investigate genome evolution in fungal symbioses: ploidy, repetitive elements, and reproduction

online onsite
Jessica Allen, Eastern Washington University, USA
Jessica Allen

Talk title

Using nanopore sequencing to investigate genome evolution in fungal symbioses: ploidy, repetitive elements, and reproduction

Biography

Jessica Allen is an assistant professor in the Department of Biology at Eastern Washington University. Her research focuses primarily on untangling the factors that shape the distributions of symbiotic organisms using an interdisciplinary approach that incorporates biodiversity informatics, population genomics, and comparative genomics. Jessica earned her PhD from the City University of New York Graduate Center and The New York Botanical Garden and conducted post-doctoral research at The Swiss Federal Institute for Forest, Snow and Landscape Research, WSL.

Abstract 

Symbiotic fungi perform many globally essential ecosystem services. They are fascinating research systems that expand our understanding of biological processes, including symbiont co-evolution, microbial community dynamics, and metabolite economies. Lichenized fungi, which form mutualistic relationships with algae and/or cyanobacteria, are highly specialized and are abundant and diverse in all terrestrial ecosystems. Nineteen lichen metagenomes assembled with long-read data generated on Oxford Nanopore Technologies platforms yielded some of the most complete and contiguous genomes for lichenized fungi. These data revealed that lichenized fungi can be polyploid, repetitive elements in genomes have proliferated in specific lineages, and putatively asexual lineages retain functional mating genes. Near telomere-to-telomere assemblies have also allowed for chromosome number inferences in species for which flow cytometry is challenging or impossible. Routine production of highly complete and contiguous genomes from long-read sequencing of environmental fungal samples promises to rapidly advance knowledge of fungal genome architecture and evolution.

Recent publications 

Allen, J.L. et al. Draft genome of the lichenized fungus Bacidia gigantensis. Microbiol Resour Announc. 4;10(44):e0068621. (2021) https://doi.org/10.1128/MRA.00686-21

McKenzie, S.K. et al. Complete, high-quality genomes from long-read metagenomic sequencing of two wolf lichen thalli reveals enigmatic genome architecture. Genomics 112(5): 3150–3156. (2020) https://doi.org/10.1016/j.ygeno.2020.06.006

Allen, J.L. et al. A call to reconceptualize lichen symbioses. Trends Ecol Evol. 37(7):582–589 (2022) https://doi.org/10.1016/j.tree.2022.03.004

Allen, J.L. and Lendemer, J.C. Urban Lichens: A Field Guide for Northeastern North America. Yale University Press. (2021)

Auditorium
Microbiology
16:40 - 17:05 EST 13:40 - 14:05 PST 21:40 - 22:05 GMT 22:40 - 23:05 CET
Add to Calendar Add to Calendar Add to Calendar Add to Calendar

A long-read nanopore sequencing platform for Indigenous genomics

online onsite
Andre Reis, Garvan Institute of Medical Research, Australia
Andre Reis

Talk title

A long-read nanopore sequencing platform for Indigenous genomics

Biography

Dr. Andre Reis is an early career researcher at the Garvan Institute of Medical Research with expertise in genomics, biotech development and bioinformatics. Andre previously completed a PhD in 2021 at the Garvan Institute under Dr. Tim Mercer and currently works at the Genomic Technologies research group led by Dr. Ira Deveson within the Garvan's Centre for Population Genomics. His current focus is on the use of long-read sequencing technologies in a diverse set of research areas, ranging from indigenous genomics to reptile sex determination.  

Abstract 

Indigenous Australians harbour rich and unique genetic diversity that is currently missing from global genomics resources, which limits their suitability for the interpretation of genetic disease in Indigenous families. Failure to address this representation gap will lead to increasing inequity in the benefit of genomic medicine, exacerbating health disparities between Australia's Indigenous and non-Indigenous communities. In addition, most population-scale catalogues of genetic variation have relied on short-read sequencing technologies, which largely limits their scope to small variants (SNVs and indels) within simple, non-repetitive genome regions. To address these issues, we are using population-scale Oxford Nanopore long-read sequencing to build a detailed catalogue of repetitive, structural, and complex genetic variation across Australian Indigenous communities, in partnership with the National Centre for Indigenous Genomics. To date, we have performed whole-genome nanopore sequencing on 68 individuals from four Indigenous communities in Northern Australia and a non-Indigenous comparison cohort. We are using this data to explore the unique genetic variation among Indigenous Australians at unprecedented resolution and create genomics resources that will be critical to achieving equitable outcomes in genomic medicine in Australia.

Auditorium
Human & translational research