Nanopore Community Meeting 2020 Online
1st – 3rd December
Registration
The Nanopore Community Meeting is a 3-day conference during which scientists across a breadth of research areas will share their latest work using nanopore technology.
This year, the meeting will take place online and is free to attend.
Be sure to follow the action on Twitter @nanoporeconf.
Agenda
The Nanopore Community Meeting featured plenary talks, breakout sessions, lighting presentations, posters, networking and more.
Abstract submission is now closed and you can view the full agenda and read more about our fantastic line-up of speakers below.
Sample extraction
Abstract
Participants of this masterclass will learn about:
- Considerations when beginning your experimental planning
- Choosing the sequencing kit and device best suited to your experimental needs
- Leveraging the Nanopore community resources for guidance on various aspects of your experimental design
Bio
Vânia Costa is an Applications Scientist at Oxford Nanopore Technologies. Her role is to test and optimize DNA extractions on a variety of sample types for downstream analysis with nanopore devices. Before joining Oxford Nanopore she was involved on a Ph.D. focused on population genomics and evolution.

Vânia Costa, Applications Scientist
Experimental design
Abstract
Participants of this masterclass will learn about:
- The importance of extracting high-quality DNA/RNA for your nanopore sequencing experiment
- How to choose the most suitable extraction method for your experiment
- Guidance through QC, sample storage, and where to find more information
Bio
Akelia is a Technical Applications Specialist at Oxford Nanopore Technologies. Her role is to provide technical support to scientists using nanopore sequencing for their intended projects. Prior to joining Oxford Nanopore, she was a post-doctoral fellow at Synaptic Research, where she used bioengineering techniques to optimize the algae and bacterial protein expression platforms of therapeutic nanobodies. Prior to that, she obtained her Ph.D. from the University of Maryland Baltimore County (UMBC) where she worked on the multicellular green algae, Volvox carteri first, to identify and characterize novel class II transposons for gene tagging and second, to develop a more robust gene knockdown system in V. carteri.

Akelia Wauchope-Odumbo, Technical Services Specialist
Flow Cell Loading demo
Abstract
Participants of this masterclass will:
- Learn how to load a sequencing library on to a Flongle Flow Cell
- Have the chance to practice flow cell loading during the masterclass, using their own demo kit
Bio
Andrada Tomoni is a QC & Validation Scientist at Oxford Nanopore Technologies. Her role ensures all products reaching customers, from kits to flowcells and software versions, have been rigorously tested and optimised for a satisfactory customer experience. Before ONT, she has worked at the NIHR National Biosample Centre, now the MK Lighthouse Laboratory, optimising nucleic acid extractions for the 100 000 Genome Project, and has published work on pseudokinases and their potential as drug targets.

Andrada Tomoni, Baseline Sequencing & Validation Scientist
Bioinformatics: first principles
Abstract
Participants of this masterclass will learn about:
- Different file types and formats
- The command-line and its importance
- Foundational analysis principles, focusing on data QC and alignment
- Using EPI2ME Labs, including a real-time demo
Bio
Bryant Catano is a Technical Services Specialist at Oxford Nanopore Technologies. His role is to support customers end-to-end, from initial experimental design all the way through data analysis. His graduate work at William Paterson University investigated the bacterial communities associating with various strains of Karenia brevis, a marine dinoflagelatte responsible for toxic algal blooms along the Gulf of Mexico. Prior to switching fields to molecular biology, he worked as an organic chemist specializing in transition metal-catalyzed reaction methodology.

Bryant Catano, Technical Services Specialist – Bioinformatics
Bioinformatics: secondary analysis
Abstract
Participants of this masterclass will learn about:
- Data analysis software offerings and solutions for Oxford Nanopore data
- Representative analysis workflows, highlighting a structural variant detection workflow
- Demonstration of EPI2ME Labs as a best practice analysis and data exploration platform
- Applications enabled by EPI2ME Labs, plus more info on open datasets, pipelines and software
Bio
Anthony joined Oxford Nanopore Technologies in May 2019 as a Technical Services Specialist. He obtained his Ph.D. from Maynooth University, Ireland, focusing on bioinformatics and systems biology approaches to investigate the functional basis of muscle growth in domesticated animal species. Following his Ph.D., he held joint positions as a senior bioinformatician at the Wellcome Trust Sanger Institute and the European Bioinformatics Institute, both based in Cambridge, UK. While in Cambridge, Anthony worked on creating de novo genome assemblies, and characterising whole genome variation primarily in humans and mouse models of human disease.

Anthony Doran, Technical Services Specialist – Bioinformatics
Oxford Nanopore Technologies
Bio
Sissel Juul joined Oxford Nanopore in the summer of 2014 to lead the company’s Genomic Applications group, setting up a lab in New York City. Recently, the Genomic Applications group has expanded, with the opening of a second lab, in the San Francisco Bay Area. These 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. This leads to scientific papers, posters, and presentations at conferences. Prior to joining Oxford Nanopore, Sissel did her postdoctoral research at Duke University, NC, and has a Ph.D. in molecular biology and nanotechnology from Aarhus University, Denmark.

Sissel Juul
Targeted long-read sequencing clarifies complex genetic results and identifies missing variants
Abstract
Despite advances in clinical genetic testing, many patients with suspected genetic diseases remain undiagnosed. Sometimes, testing reveals complex structural changes that are difficult to evaluate using standard clinical methods. Other times, a single variant is identified in suspected recessive disorders, or no variants at all in suspected dominant or X-linked disorders. Thus, there is a need for better tools to more fully understand cases with suspected but undiagnosed genetic diagnoses. We tested whether targeted long-read sequencing using Read Until on the Oxford Nanopore platform could be used to evaluate cases such as these. Using Read Until, we identified known pathogenic structural variants, resolved complex structural changes, and identified missing disease-causing variants in patient DNA.
Bio
Danny Miller is a combined pediatrics and medical genetics resident at Seattle Children’s Hospital and University of Washington in Seattle, Washington, USA. He is interested in unsolved genetic disorders and in developing clinical applications of long read sequencing.

Danny E. Miller
Targeted long-read sequencing clarifies complex genetic results and identifies missing variants
Abstract
Despite advances in clinical genetic testing, many patients with suspected genetic diseases remain undiagnosed. Sometimes, testing reveals complex structural changes that are difficult to evaluate using standard clinical methods. Other times, a single variant is identified in suspected recessive disorders, or no variants at all in suspected dominant or X-linked disorders. Thus, there is a need for better tools to more fully understand cases with suspected but undiagnosed genetic diagnoses. We tested whether targeted long-read sequencing using Read Until on the Oxford Nanopore platform could be used to evaluate cases such as these. Using Read Until, we identified known pathogenic structural variants, resolved complex structural changes, and identified missing disease-causing variants in patient DNA.
Bio
Danny Miller is a combined pediatrics and medical genetics resident at Seattle Children’s Hospital and University of Washington in Seattle, Washington, USA. He is interested in unsolved genetic disorders and in developing clinical applications of long read sequencing.

Danny E. Miller
Welcome to the Nanopore Community Meeting 2020 online
Bio
Gordon Sanghera was co-founder of Oxford Nanopore, together with Hagan Bayley and IP Group, and was appointed CEO in June 2005. He brings over 20 years' experience in the design, development and global launch of disruptive platform sensor technologies. Dr. Sanghera’s Ph.D. in bioelectronics sensing was followed by a career at MediSense, an Oxford spin-out that delivered a new generation glucose technology to the market. Following the acquisition of MediSense by Abbott Laboratories, Dr. Sanghera held both UK and US VP and Director-level positions, including VP Worldwide Marketing, Research Director and Manufacturing Process Development Director. Before its acquisition by Abbott, Gordon led the R&D of Medisense Inc. where he was instrumental in the launch of several generations of blood glucose bio-electronic systems for the consumer and hospital medical markets. He has also developed and validated production processes to meet with the regulatory requirements for USA and Europe. Gordon has a Ph.D. in bio-electronic technology and a degree in Chemistry. Read the article about Dr. Sanghera in the Financial Times.

Gordon Sanghera
Welcome to the Nanopore Community Meeting 2020 online
Bio
Gordon Sanghera was co-founder of Oxford Nanopore, together with Hagan Bayley and IP Group, and was appointed CEO in June 2005. He brings over 20 years' experience in the design, development and global launch of disruptive platform sensor technologies. Dr. Sanghera’s Ph.D. in bioelectronics sensing was followed by a career at MediSense, an Oxford spin-out that delivered a new generation glucose technology to the market. Following the acquisition of MediSense by Abbott Laboratories, Dr. Sanghera held both UK and US VP and Director-level positions, including VP Worldwide Marketing, Research Director and Manufacturing Process Development Director. Before its acquisition by Abbott, Gordon led the R&D of Medisense Inc. where he was instrumental in the launch of several generations of blood glucose bio-electronic systems for the consumer and hospital medical markets. He has also developed and validated production processes to meet with the regulatory requirements for USA and Europe. Gordon has a Ph.D. in bio-electronic technology and a degree in Chemistry. Read the article about Dr. Sanghera in the Financial Times.

Gordon Sanghera
Oxford Nanopore Technologies
Bio
Sissel Juul joined Oxford Nanopore in the summer of 2014 to lead the company’s Genomic Applications group, setting up a lab in New York City. Recently, the Genomic Applications group has expanded, with the opening of a second lab, in the San Francisco Bay Area. These 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. This leads to scientific papers, posters, and presentations at conferences. Prior to joining Oxford Nanopore, Sissel did her postdoctoral research at Duke University, NC, and has a Ph.D. in molecular biology and nanotechnology from Aarhus University, Denmark.

Sissel Juul
Analysis of human papillomavirus integration sites in cervical cancer using long-read sequencing technology
Abstract
Human papillomavirus (HPV) infection is the cause of 95% of cervical cancers. We performed whole-genome long-read sequencing of the SiHa and CaSki cervical cancer cell lines covering the sequence of integrated HPV16 genomes and flanking DNA, and identified HPV concatemers too large to resolve with short-read technology. We identified 42 HPV integration sites at 39 loci not previously observed. Long-read RNA sequencing of HPV provided details on the complex HPV/human junction transcripts, and we used CRISPR cutting to target sequencing to specific loci. We plan to apply this technology to the study of cervical tumors collected in Guatemala.
Bio
Dr. Michael Dean is a senior investigator in the Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics at the National Cancer Institute, NCI in Rockville, Maryland, USA. Dr. Dean is interested in inherited genetic variation, somatic mutations in tumors, and their effects on cancer risk, progression, and response to therapy. The lab has a major focus on human papillomavirus, cervical cancer, and cancer health disparities in the U.S. and Latin America.
Ms. Nicole Rossi is a Post-Bac fellow in the Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics at the National Cancer Institute, NCI in Rockville, Maryland, USA. She earned her Honors Bachelor of Science Degree in biological sciences from the University of Delaware. As an undergraduate, she worked in Dr. Melinda K Duncan’s lab, studying the role of Lactase-Like (LCTL) gene in lens cell homeostasis and cataract formation.

Michael Dean

Nicole Rossi
Transforming complex immune disease through personalised medicine using nanopore technologies
Abstract
Immune diseases are among the most complex and destructive in medicine, affecting 10% of the world population with profound clinical impact, societal consequences, and multi-billion-dollar economic burdens. Modern biological research is rapidly advancing our understanding of the complex immune inter-relationships between inflammatory disease, transplantation, viral infection, and oncology, and is developing novel diagnostic tools and therapies, from single-cell biology and epitope mapping to RNA silencing, multi-specific antibodies, cellular therapeutics or gene editing to address these. The Genome Canada program links over 70 Principal Investigators in 22 universities across Canada, the US, EU, and UK and employs a systems immunology framework integrating molecular and clinical components to explore cutting-edge discovery sciences, translate these innovations into novel diagnostic sciences, and coordinate delivery sciences through highly connected computationally-supported clinical teams. We present here the model integrating structural biology, molecular monitoring, systems pharmacology, and societal evaluation employed to prevent transplant rejection. Compatibility of Human Leukocyte Antigen (HLA) genes between transplant donors and recipients improves graft survival, but is difficult to achieve due to the heterogeneity of this gene complex. Consideration of structural epitopes on the HLA molecules reduces this complexity and informs recipient selection to improve compatibility. We have sequenced the full complement of 11 classical HLA genes in nearly 5,000 ethnically diverse renal patients and donors using NGS and confirm the clinical role of nanopore sequencing for both donor and recipient high-resolution sequence level typing even within the stringent 6-hr time requirements for donor evaluation. Using this data we have created the first population map of antibody-binding eplets expressed on these molecules using in silico models, and are extending this to include TCR recognized epitopes. We show that eplets are more uniformly and more fully shared between donor and recipient groups than are the respective HLA isoforms. By simulation modeling, we demonstrate that targeted eplet matching affords a high probability of ensuring compatibility, particularly at the clinically important HLA class II loci, and is achievable with a patient waiting list of common size. We are employing this data to define immunodominant eplets and to enhance allocation within a national program and extending this framework to sequence and explore the full MHC haplotype. We are also examining the immunopeptidome and T-cell recognition elements in autoimmunity, viral infection, and malignancy, and paralleling these investigations with deep cytometry, TCR gene utilization, cell-free DNA/RNA analysis and related technologies to monitor immune activity, target injury, and guide systems pharmacology strategies.
Bio
Karen Sherwood is Lead Genome Scientist and Director of Scientific Programs for the Genome Canada Transplant Consortium. She received her Ph.D. degree in Edinburgh, with post-doctoral research in gene sequencing and neuropathology in the UK and Canada. This international program links over 70 principal investigators in 22 leading universities across Canada, the US, EU, and UK to address the molecular mechanisms and clinical therapeutics of graft rejection in transplantation. Its four pillars include structural biology and epitope compatibility, molecular mechanisms and immunological monitoring, systems pharmacology and personalized therapy, and societal impact and economic benefit. This program forms the basis for an integrated international Network of Excellence in Immune Sciences to translate innovative laboratory sciences to clinical application for complex immune diseases.
Paul Keown is Professor of Medicine and Director of Immune Sciences at the University of British Columbia and Lead of the Genome Canada Transplant Consortium. He received his MD and DSc degrees in the UK with post-doctoral research in immunology and clinical medicine in Europe and Canada.

Paul Keown

Karen Sherwood
Flye and metaFlye: algorithms for long-read de novo assembly using repeat graphs
Abstract
In this talk, I will cover the algorithmic aspects of de novo genome and metagenome assembly from long reads. I will highlight our Flye assembler that uses repeat graphs to generate accurate and contigouos assemblies of various genomes. I will also present our new metagenomic assembler metaFlye, which addresses important long-read metagenomic assembly challenges, such as uneven bacterial composition and intra-species heterogeneity. Using metaFlye, we were able to recover complete or nearly-complete bacterial genome from complex environmental samples, such as human gut or cow rumen. We also showed that long-read assembly of human microbiomes enables the discovery of full-length biosynthetic gene clusters that encode biomedically important natural products.
Bio
Mikhail Kolmogorov is a postdoctoral fellow at UC San Diego, in a joint appointment with Dr. Pavel Pevzner and Dr. Rob Knight. The focus of Mikhail's research is computational biology - algorithms, mathematical models, and tools, aiming to answer fundamental questions about living systems through the analysis of large-scale biological data. He is specifically interested in computational genomics, and is the lead developer of long-read genome assemblers Flye and metaFlye.

Mikhail Kolmogorov
LRA: a long read aligner for sequences and assembly contigs
Abstract
It is computationally challenging to detect variation by aligning long reads from SMS instruments, or megabase-scale contigs from SMS assemblies. Sequence variation is more accurately modeled when alignments are scored with a convex-cost gap function than a linear-cost. Because existing aligners that have a convex gap penalty are either inefficient or use heuristics, we developed lra, a method that uses sparse dynamic programming with a convex-cost gap penalty to align long-read sequences from PacBio and Oxford Nanopore, as well as de novo assembly contigs. When using Truvari analysis to benchmark SV calls detected from long reads alignments, lra has higher F1 scores than minimap2 and ngm-lr on all data types.
Bio
Jingwen Ren is a currently fourth year Ph.D. student from Prof. Mark Chaisson’s lab in University of Southern California. Jingwen is interested in applying advanced computational algorithms to practical biological questions, with the current focus on sequence alignment. She has developed Ira, a long read aligner for aligning long-read sequences from PacBio and Oxford Nanopore, as well as de novo assembly contigs to the reference.

Jingwen Ren
Welcome back to the Nanopore Community Meeting 2020 online
Bio
Zoe McDougall, VP of Corporate and Communications, joined Oxford Nanopore in 2008. As part of the leadership team, she works across corporate and commercial teams at the Company. Zoe started her career in sales & marketing at SmithKline Beecham. She subsequently managed a range of strategic scientific and healthcare communications at the agency Porter Novelli, where clients included GSK, BMS, Pfizer and a range of other healthcare clients. During this time Zoe also worked on crisis communications around the nvCJD issue. Before joining Oxford Nanopore, Zoe was part of the IPO team and subsequently led investor relations for a UK specialty pharma company Sinclair Pharma. In 2005 she worked with a medical humanitarian organisation in Sri Lanka.

Zoe McDougall
Welcome back to the Nanopore Community Meeting 2020 online
Bio
Zoe McDougall, VP of Corporate and Communications, joined Oxford Nanopore in 2008. As part of the leadership team, she works across corporate and commercial teams at the Company. Zoe started her career in sales & marketing at SmithKline Beecham. She subsequently managed a range of strategic scientific and healthcare communications at the agency Porter Novelli, where clients included GSK, BMS, Pfizer and a range of other healthcare clients. During this time Zoe also worked on crisis communications around the nvCJD issue. Before joining Oxford Nanopore, Zoe was part of the IPO team and subsequently led investor relations for a UK specialty pharma company Sinclair Pharma. In 2005 she worked with a medical humanitarian organisation in Sri Lanka.

Zoe McDougall
Nanopore sequencing in single-cell and spatial transcriptomics
Abstract
Examination of gene expression with single cell or spatial resolution led to important advances in our understanding of physiology and disease. The most widely used single cell sequencing workflows use co-encapsulation of cells with barcoded beads into emulsion droplets. A recently developed spatial transcriptomics approach synthesizes cDNA on slides that contain grids of spatial barcodes. When Illumina sequencing is used in either of those approaches, only 3’ terminal sequence information is obtained and most information on splicing and SNVs is lost. We demonstrated previously that nanpore sequencing combined with Illumina data guided barcode and UMI assignment, allowing profiling of transcript isoforms and identification of SNVs with single cell or spatial resolution. Recent improvements in nanopore read accuracy and a novel barcode and UMI assignment strategy now allow skipping of Illumina sequencing to perform accurate nanopore single cell and spatial transcript isoform sequencing without any guidance by Illumina data.
Bio
Dr. Rainer Waldmann received his Ph.D. at the faculty of Chemistry at the University of Würzburg, Germany. He is a INSERM researcher and currently associated with Pascal Barbry’s group at the University of Nice, France. His current research interests focus on the development of single cell sequencing approaches.

Rainer Waldmann
Nanopore sequencing in single-cell and spatial transcriptomics
Abstract
Examination of gene expression with single cell or spatial resolution led to important advances in our understanding of physiology and disease. The most widely used single cell sequencing workflows use co-encapsulation of cells with barcoded beads into emulsion droplets. A recently developed spatial transcriptomics approach synthesizes cDNA on slides that contain grids of spatial barcodes. When Illumina sequencing is used in either of those approaches, only 3’ terminal sequence information is obtained and most information on splicing and SNVs is lost. We demonstrated previously that nanpore sequencing combined with Illumina data guided barcode and UMI assignment, allowing profiling of transcript isoforms and identification of SNVs with single cell or spatial resolution. Recent improvements in nanopore read accuracy and a novel barcode and UMI assignment strategy now allow skipping of Illumina sequencing to perform accurate nanopore single cell and spatial transcript isoform sequencing without any guidance by Illumina data.
Bio
Dr. Rainer Waldmann received his Ph.D. at the faculty of Chemistry at the University of Würzburg, Germany. He is a INSERM researcher and currently associated with Pascal Barbry’s group at the University of Nice, France. His current research interests focus on the development of single cell sequencing approaches.

Rainer Waldmann
Allele-specific methylation in human brains
Abstract
Frontotemporal dementia is a subtype of dementia predominantly characterized by language and behavioral impairment. We use PromethION genome sequencing on DNA extracted from the frontal cortex from patients and controls to identify structural and epigenetic variants underlying the disease. Nanopore sequencing enables the detection of modified nucleotides, such as methylcytosine, and phasing of reads in parental haplotypes, and based on this we can detect allele-specific epigenetic marks. These marks will include loci for which allele-specific modifications is a biological feature, such as parental imprinting. More interestingly, this approach can also provide epigenetic evidence of disease-associated variants.
Bio
Wouter De Coster is a postdoctoral researcher and bioinformatician in the VIB-UAntwerp Rosa Rademakers lab. His focus is on the genetic background of frontotemporal dementia, a less frequent and rather heterogeneous subtype of dementia, primarily characterized by language and behavioral impairment. He uses nanopore long-read sequencing to identify structural variants and nucleotide modifications with a role in the disease. Wouter has developed multiple software packages for quality assessment and visualization of long reads and methylation data.

Wouter De Coster
Allele-specific methylation in human brains
Abstract
Frontotemporal dementia is a subtype of dementia predominantly characterized by language and behavioral impairment. We use PromethION genome sequencing on DNA extracted from the frontal cortex from patients and controls to identify structural and epigenetic variants underlying the disease. Nanopore sequencing enables the detection of modified nucleotides, such as methylcytosine, and phasing of reads in parental haplotypes, and based on this we can detect allele-specific epigenetic marks. These marks will include loci for which allele-specific modifications is a biological feature, such as parental imprinting. More interestingly, this approach can also provide epigenetic evidence of disease-associated variants.
Bio
Wouter De Coster is a postdoctoral researcher and bioinformatician in the VIB-UAntwerp Rosa Rademakers lab. His focus is on the genetic background of frontotemporal dementia, a less frequent and rather heterogeneous subtype of dementia, primarily characterized by language and behavioral impairment. He uses nanopore long-read sequencing to identify structural variants and nucleotide modifications with a role in the disease. Wouter has developed multiple software packages for quality assessment and visualization of long reads and methylation data.

Wouter De Coster
Johns Hopkins University, USA
Abstract
Improvements in sequencing technology and computational assembly methods have led to remarkable milestones in human genome assembly. Recently, the Telomere-to-Telomere (T2T) consortium generated the first telomere-to-telomere assembly of a complete human genome, due in part to the use of ultralong nanopore sequencing reads to stretch across these difficult regions. For the first time, we have a complete human reference spanning multi-megabase satellite arrays and rDNA arrays in the peri/centromeric regions and acrocentric short arms, as well as regions enriched in segmental duplications. While these large repetitive regions of the genome remain largely unexplored, there is evidence that epigenetic control of repeats contributes strongly to genome stability and disease. Previous attempts to study epigenetics in centromeric, pericentromeric, telomeric, and macrosatellite regions have been precluded by the difficulty in mapping conventional NGS data to large repetitive arrays. Ultra-long (>100kb) reads allow us to accurately map nanopore reads to these regions and investigate the epigenome of previously unassembled and unannotated sequences. We investigated the methylome of the centromeric higher order repeat (HOR) arrays, and observed a distinctive pattern of hyper and hypomethylation. Furthermore, we can use allele-specific methylation alone to phase microsatellite repeats, which we have demonstrated on the DXZ4 region of the X chromosome. There we found two clusters of reads which we attribute to either the active or inactive X allele. Our demonstrated ability to probe the epigenome of these repetitive areas will allow us to gain a greater understanding of their regulation and significance.
Bio
Ariel Gershman is a Ph.D. student in the Biochemistry, Cellular and Molecular Biology program in the Timp lab at Johns Hopkins University, where she focuses on using long-read sequencing for genome and transcriptome assembly. She has worked on generating reference genomes for the Ruby throated hummingbird (Archilochus colubris) and Tobacco Hornworm moth (Manduca sexta). Ariel is also interested in exploring the epigenome using nanopore sequencing in hard to assemble areas, contributing to methylation analysis in the Telomere-to-Telomere consortium.

Ariel Gershman
Johns Hopkins University, USA
Abstract
Improvements in sequencing technology and computational assembly methods have led to remarkable milestones in human genome assembly. Recently, the Telomere-to-Telomere (T2T) consortium generated the first telomere-to-telomere assembly of a complete human genome, due in part to the use of ultralong nanopore sequencing reads to stretch across these difficult regions. For the first time, we have a complete human reference spanning multi-megabase satellite arrays and rDNA arrays in the peri/centromeric regions and acrocentric short arms, as well as regions enriched in segmental duplications. While these large repetitive regions of the genome remain largely unexplored, there is evidence that epigenetic control of repeats contributes strongly to genome stability and disease. Previous attempts to study epigenetics in centromeric, pericentromeric, telomeric, and macrosatellite regions have been precluded by the difficulty in mapping conventional NGS data to large repetitive arrays. Ultra-long (>100kb) reads allow us to accurately map nanopore reads to these regions and investigate the epigenome of previously unassembled and unannotated sequences. We investigated the methylome of the centromeric higher order repeat (HOR) arrays, and observed a distinctive pattern of hyper and hypomethylation. Furthermore, we can use allele-specific methylation alone to phase microsatellite repeats, which we have demonstrated on the DXZ4 region of the X chromosome. There we found two clusters of reads which we attribute to either the active or inactive X allele. Our demonstrated ability to probe the epigenome of these repetitive areas will allow us to gain a greater understanding of their regulation and significance.
Bio
Ariel Gershman is a Ph.D. student in the Biochemistry, Cellular and Molecular Biology program in the Timp lab at Johns Hopkins University, where she focuses on using long-read sequencing for genome and transcriptome assembly. She has worked on generating reference genomes for the Ruby throated hummingbird (Archilochus colubris) and Tobacco Hornworm moth (Manduca sexta). Ariel is also interested in exploring the epigenome using nanopore sequencing in hard to assemble areas, contributing to methylation analysis in the Telomere-to-Telomere consortium.

Ariel Gershman
Welcome back to the Nanopore Community Meeting 2020 online
Bio
Zoe McDougall, VP of Corporate and Communications, joined Oxford Nanopore in 2008. As part of the leadership team, she works across corporate and commercial teams at the Company. Zoe started her career in sales & marketing at SmithKline Beecham. She subsequently managed a range of strategic scientific and healthcare communications at the agency Porter Novelli, where clients included GSK, BMS, Pfizer and a range of other healthcare clients. During this time Zoe also worked on crisis communications around the nvCJD issue. Before joining Oxford Nanopore, Zoe was part of the IPO team and subsequently led investor relations for a UK specialty pharma company Sinclair Pharma. In 2005 she worked with a medical humanitarian organisation in Sri Lanka.

Zoe McDougall