Nanopore Community Meeting 2021 online
30th November – 2nd December
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.
The Nanopore Community Meeting features plenary talks, breakout sessions, lighting presentations, posters, networking and more.
Abstract submission has now closed, all entries are currently under review. If you have any questions regarding abstract submission, please contact email@example.com
Nanopore 101: how to get started and plan your first experiment
Find out how nanopore sequencing works, its key benefits, and how to set up your nanopore sequencing experiment for success.
In this Masterclass you will learn:
- How nanopore sequencing works
- Key benefits and features of nanopore sequencing technology
- How to plan a nanopore sequencing experiment — including the importance of control runs, and where to find further online resources to support you
James Brayer has been supporting customer success in his role as a member of the Oxford Nanopore commercial team for nine years. He currently leads the Global Segment Marketing Team, and through his role he has the opportunity to speak with members of the Nanopore Community about the many different applications of nanopore sequencing technology. The Segment Marketing Team is also focused on building awareness of our technology with prospective nanopore users, ensuring success across a broad range of applications.
Akelia received her Ph.D. from the University of Maryland, Baltimore County (UMBC) where she worked on the multicellular green algae, Volvox carteri, to identify and characterize class II transposons for gene tagging, and to develop a more robust gene knockdown system. As a post-doctoral fellow at Synaptic Research, she used bioengineering techniques to optimize the algae and bacterial protein expression platforms of therapeutic nanobodies. Before joining the technical services team at Oxford Nanopore in 2016, she was a project manager at GENEWIZ where she played a key role in managing and streamlining client projects.
Sample prep: how to extract high-quality DNA and RNA
Discover tips and tricks on getting and properly storing the best quality DNA and RNA from your samples.
In this masterclass you will learn:
- The steps involved in DNA and RNA extraction — including how to perform quality checks
- Best practices for storing and handling nucleic acids — including the impact of freeze/thaw cycles and storage conditions
- How to optimise an extraction protocol according to your sample type, via a worked example
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. Her Ph.D., gained at the University of Porto, Portugal, focused on population genomics and evolution.
Library prep: how to generate ultra-long reads
Learn how to generate ultra-long reads, from extraction right through to sequencing.
In this masterclass you will learn:
- About the benefits of ultra-long reads for your genomics research
- How to perform an ultra-long nanopore sequencing experiment — from DNA extraction through to flow cell loading
- What to expect from data produced in an ultra-long nanopore sequencing experiment
Simon Mayes is a Principal Applications Scientist at Oxford Nanopore Technologies. He has an interest in pushing the boundaries of the sequencing platform, in particular with ultra-long sequencing reads. He has worked with a number of different sequencing technologies throughout his career before joining Oxford Nanopore nine years ago.
Library prep: how to choose the right nanopore sequencing kit
Find out which library preparation method best suits your experimental goals.
In this masterclass you will learn:
- About the different library preparation options available for nanopore sequencing of DNA, RNA, and cDNA
- The difference between rapid and ligation chemistry
- The applications and benefits of different sequencing techniques — including targeted approaches, and PCR-based and PCR-free options
Marta joined Oxford Nanopore’s Technical Services team in October 2018 and provides technical support and training for customers. Previously, she obtained her Ph.D. in Genomics from Trinity College Dublin, Ireland, focusing on sequencing and analysing whole genomes of ancient cattle and aurochs to understand the effects of domestication and human migration in these populations. Previous work has also included looking at pseudo-autosomal regions of the Y chromosome recombination hotspots in populations, and looking at putative Viking ancestry through Y chromosome genotyping.
Sequencing: how to load a Flongle Flow Cell
Learn how to load a Flongle Flow Cell in this interactive, hands-on demo, including additional information on loading MinION and PromethION Flow Cells.
In this masterclass you will learn:
- How to load a sequencing library onto a Flongle Flow Cell, via a practical demonstration
- The basics of loading MinION and PromethION Flow Cells
Mark Wyatt is the Production Sequencing and Kit Release team lead at Oxford Nanopore Technologies. Mark has been with the company for four years and in that time has accrued a large amount of experience working with all kits, platforms, and devices. The team’s largest accomplishment of the last year was the release of over 1.5 million LamPORE tests worth of kits, used in the effort to test for COVID-19 cases and help protect the NHS and the public.
Analysis: how to basecall and detect methylation
Find out how to basecall your data, how to choose the right basecalling model for you, and how to call methylation in your data.
In this masterclass you will learn:
- The basics of nanopore sequencing data analysis, including the different approaches available and file types involved
- About the basecalling options available, and how to choose a basecalling model to suit your experimental goals
- How to call methylation from PCR-free nanopore sequencing datasets, including the tool options available
Prior to working as a Technical Applications Scientist with Oxford Nanopore Technologies, Jessica spent time in academia researching cell differentiation by examining the mechanisms by which heterocysts 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 the Oxford Nanopore PromethION device to sequence large, complex plant genomes for de novo assembly.
Analysis: how to generate assemblies and call variants
Discover the approaches available for assembling your data and calling variants, including SNVs and structural variants.
In this masterclass you will learn:
- Different approaches for assembling nanopore sequence data
- About analysis workflows for calling variants — including structural variants and single nucleotide variants
- The different file formats involved in nanopore sequencing data analysis
Anthony joined Oxford Nanopore Technologies in 2019 and currently works as a bioinformatics specialist as part of the global services team. Previously, 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 a visiting researcher at 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 G. Doran
Welcome to the Nanopore Community Meeting 2021 online
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 bioelectronic 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 bioelectronic technology and a degree in Chemistry.
SARS-CoV-2 sequencing: on the midnight train to throughput
The SARS-CoV-2 pandemic has been well sequenced globally, including by our team at the University of Wisconsin-Madison AIDS Vaccine Research Laboratory. Over 30,000 SARS-CoV-2 genomes have been sequenced for cases throughout the state of Wisconsin; our research group has contributed almost 20% of those sequences. We focus on a combination of general variant surveillance sequencing and specific interesting cases. We have recently transitioned from the ARTIC to the Midnight protocol to increase throughput and reduce cost per genome. The Midnight protocol so far has greatly reduced hands-on time and increased our depth of pooling per flow cell without sacrificing genome coverage.
Julie Karl is a Researcher at the University of Wisconsin-Madison. Her primary focus is on the genetics of the immune system in non-human primates, particularly the major histocompatibility complex. She is also quite adept at next-generation sequencing, performing hundreds of ultra-long read Oxford Nanopore Technologies sequencing runs. Currently Ms. Karl provides support for the SARS-CoV-2 sequencing efforts of the team at the AIDS Vaccine Research Laboratory.
Robert Maddox is a Research Specialist at the University of Wisconsin-Madison. His primary focus was on the genetics of the major histocompatibility complex in non-human primates. For the past year, he has shifted his focus to assisting the team at the AIDS Vaccine Research Laboratory with their SARS-CoV-2 sequencing efforts.
For want of a nail: investigating somatic and germline variations in cancer
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.
Phill's Ph.D. involved using molecular methods to attempt to understand the diversity and distribution of environmental microbes at the landscape scale. Using these skills in subsequent postdoc positions at Warwick and Imperial, Phill's research focussed on both environmental reservoirs of disease, and microbial perturbations in human respiratory systems under disease conditions. Phill joined Oxford Nanopore Technologies in 2016 and is now the Associate Director for Clinical Applications. Phill undertakes a wide variety of projects, which focus on demonstrating and applying novel uses of nanopore sequencing within a research setting.
Classification of pediatric acute leukemia using full-length transcriptomics
Health centers in low- and middle-income countries lack tools required for accurate classification of acute pediatric leukemias. We show the feasibility of nanopore full-length cDNA sequencing and demonstrate a novel composite machine learning classification approach to predict acute leukemia lineage and major molecular subtypes. Based exclusively on gene expression profiles, 96.2% of lineages with prediction probabilities >0.8 are classified with 100% accuracy, along with 94.1-96.2% of major subtypes. This work demonstrates the potential of low-coverage, full-length transcriptomics to improve the accessibility and accuracy of cancer diagnosis in low-resource settings.
Jeremy Wang is an Assistant Professor in the Genetics Department at UNC Chapel Hill where his lab applies high-performance computational methods to efficiently analyze high-throughput sequence data, with a particular focus on long-read technologies. Applications of these tools include de novo genome assembly, phylogenomics, characterization of microbial populations, and gene expression and isoform analysis from full-length transcriptomes.
Resolution of complex human papillomavirus and human sequences
Human papillomaviruses (HPV) cause cervical cancers and often integrate, causing complex amplifications. We previously showed arrays of integrated genomes on multiple chromosomes (HPV Superspreading). Ultra-long DNA and adaptive sampling (UltraAdapt) yielded HPV+ reads up to 347 kb. We applied this method to SNU-1000, a cell line with episomal HPV16, and obtained long HPV+ reads. We sequenced 65 tumors and identified tumors with only monomer episomes. Some tumors with episomes contain deletions and rearrangements in the E1 or E2 genes. Therefore, HPV can cause cervical cancer without integration. Ultra-long read sequencing is essential in resolving the complex genomic events in tumors.
Ms. Nicole Marie Rossi is a Post-Bacc 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 the Lactase-Like (LCTL) gene in lens cell homeostasis and cataract formation.
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 (germline) 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 (HPV) and cervical cancer, and cancer health disparities in the U.S. and in Latin America.
ORG.one: a new program to promote sequencing biodiversity
In recent decades, we have seen an alarming rate of decay in biodiversity, both in population numbers and in number of species. Every single action we can take to help to revert this process, including ecological restoration, education, and restoring and storing biodiversity, should be a priority. As part of this global action, the ORG.one project was born to help create a molecular legacy of the most endangered species in the world.
Dr. Marques-Bonet is an ICREA Research Professor at the Universitat Pompeu Fabra and head of the Comparative Genomics group at the Institute of Evolutionary Biology in Barcelona, Spain, where his group is focused on studying the genomics diversity on non-human primates and the evolution of epigenetics. Dr. Marques-Bonet is also a Howard Hughes Medical Institution (HHMI) Early International Career Scientist and was awarded an ERC Starting Grant in 2010 and an ERC Consolidator Grant in 2019.
Genomic skimming on the MinION uncovers cryptic hybridization in the buffy-tufted marmoset, one of the world’s most threatened primates
Callithrix aurita, one of the world’s most endangered primates, is threatened by anthropogenic hybridization. We developed a minimal, PCR-free protocol to rapidly generate genomic data on the MinION, with which we successfully determined the complete mitogenome of a marmoset with a C. aurita phenotype. Phylogenetics unexpectedly revealed the specimen to be a cryptic hybrid, with a C. aurita phenotype and C. penicillata mitogenome lineage. Mitogenomics holds great potential to address deficiencies in genomic data for endangered, non-model species. We discuss the utility and implications of our genomic skimming/nanopore approach for mammalian conservation and evolutionary studies.
As an evolutionary biologist, Joanna Malukiewicz is interested in how primate hybridization shapes biodiversity and influences disease susceptibility. After earning a Ph.D. in Biology in 2013 from Arizona State University, Joanna spent nearly eight years in Brazil as an independent post-doctoral scholar, researching marmoset evolutionary genomics. Since recent Flavivirus outbreaks in Brazil, she has expanded her work into immunogenetics and metagenomics (bacterial and viral) of marmosets and howlers. Joanna is currently a Marie Curie fellow at the German Primate Center.
The Wollemia nobilis genome: using long-read nanopore sequencing technology to study the genomic architecture of a 'living fossil'
'Living fossils' are organisms that are able to withstand significant changes in climate and survive over extremely long periods of time, without speciation. Wollemia nobilis, a prime example of a living fossil, has existed since the early Cretaceous period but is now critically endangered. The New York Plant Genomics Consortium has sequenced the Wollemia nobilis genome using Oxford Nanopore long-read sequencing, and has generated a reference-quality genome assembly in which to study the mechanisms of survival for this stalwart conifer.
Working in the McCombie lab at CSHL, Melissa has been part of the efforts to sequence reference genomes of several model organisms of animals and plants, including human and Arabidopsis. She transitioned from the bench to bioinformatics, and has worked with data from a variety of sequencing platforms in an endeavour to investigate genomic variants that contribute to complex traits.
Welcome back to the Nanopore Community Meeting 2021 online
The annotation of novel genes in a complete human genome
In 2021, the Telomere-to-Telomere (T2T) consortium released the first gapless assembly of a human genome. Advancements in long-read sequencing and assembly methods enabled the completion of the final 8% of the genome that has been missing from the human reference genome since its initial release two decades ago. Efforts to annotate the T2T assembly revealed 1,956 novel genes (including 99 protein-coding genes) contained within the 200 million base pairs of novel sequence. Presented here, are the computational methods used to identify these novel genes, in addition to examples of novel genes with medically-relevant paralogs.
Alaina Shumate is Ph.D. candidate in the Biomedical Engineering department at Johns Hopkins University where she is advised by Dr. Steven Salzberg. Her research is focused on the development and application of computational methods for genome annotation. Prior to starting her Ph.D., she completed her B.S. in Bioengineering at Stanford University in 2016.
Affordable GPU compute makes nanopore sequencing even more disruptive and empowering
In this talk, I will discuss our experiences with nanopore sequencing, particularly focusing on the potential of GPUs (graphics processing units) and their implementation into the workflow, highlighting the many facets of genomics that it unlocks in the process. I will do this through a series of case studies, touching on a couple of personal anecdotes. This journey has led me to form international, collaborative, cross-programme studies, with the singular goal of deploying disruptive, portable, and affordable sequencing technology into the hands of the wider community to empower their health, well-being, and curiosity.
At the bottom of the world in Aotearoa, New Zealand, Miles Benton is a computational geneticist interested in all facets of biology and technology. Miles works at the Institute of Environmental Science and Research as a Senior Bioinformatician in the Human Genomics Team. He has a passion for making science broadly accessible and understandable.
DNA and RNA modifications: how nanopore is giving us new biological insights — from COVID to gene expression
One of the unique properties of nanopore sequencing is its ability to sense nucleotide modifications, on both DNA and RNA. For well known DNA modifications, such as cytosine methylation, nanopore sequencing provides accurate called sites of modifications in the context of often long read lengths. For the less well known RNA modifications, of which there are over 100 types of modifications already described, we are at the foothills of exploring and calling the nanopore signal, but even these initial explorations are pointing to an exciting world of characterising RNA modifications. I will provide an overview of the current state of the art in modification sensing in nanopore sequencing, and provide two examples from my own research group; in the exploration of DNA modifications as mediators of genetic differences underlying differential risk to hospitalisation on infection by SARS-CoV-2, focusing on DNA modifications, and then discussion on RNA modifications involved in gene expression.
Ewan Birney is Deputy Director General of EMBL. He is also Director of EMBL-EBI with Dr Rolf Apweiler, and runs a small research group. Ewan completed his PhD at the Wellcome Sanger Institute with Richard Durbin. In 2000, he became Head of Nucleotide data at EMBL-EBI and in 2012 he took on the role of Associate Director at the institute. He became Director of EMBL-EBI in 2015. In 2020, Ewan became the Deputy Director General of EMBL. In this role, he assists the EMBL Director General in relation to engagement with EMBL Member States and external representation. Ewan led the analysis of the Human Genome gene set, mouse and chicken genomes, and the ENCODE project, focusing on non-coding elements of the human genome. Ewan’s main areas of research include functional genomics, DNA algorithms, statistical methods to analyse genomic information (in particular information associated with individual differences in humans and medaka fish), and use of images for chromatin structure. Ewan is a non-executive Director of Genomics England, and a consultant and advisor to a number of companies, including Oxford Nanopore Technologies, Dovetail Genomics, and GSK. Ewan was elected an EMBO member in 2012, a Fellow of the Royal Society in 2014, and a Fellow of the Academy of Medical Sciences in 2015. In 2019, Ewan became a Board Member of the Biotechnology and Biological Sciences Research Council (BBSRC). He has received a number of awards including the 2003 Francis Crick Award from the Royal Society, the 2005 Overton Prize from the International Society for Computational Biology, and the 2005 Benjamin Franklin Award for contributions in Open Source Bioinformatics.
Towards comprehensive genetic diagnosis of repeat expansion disorders with targeted nanopore sequencing
Short-tandem repeat (STR) expansions are an important class of pathogenic genetic variants. Over 40 neurological and neuromuscular diseases are caused by STR expansions, with 37 different genes implicated to date. Here, we describe the use of programmable targeted long-read sequencing with Oxford Nanopore’s Read Until function for parallel genotyping of all known neuropathogenic STRs in a single, simple assay. Our approach enables accurate, haplotype-resolved assembly and DNA methylation profiling of expanded and non-expanded STR sites. In doing so, the assay correctly classifies all individuals in a cohort of patients (n = 27) with various neurogenetic diseases, including Huntington’s disease, fragile X syndrome, cerebellar ataxia (CANVAS), and others. Even in our relatively small cohort, we observe a wide diversity of STR alleles of known and unknown pathogenicity, suggesting that long-read sequencing will redefine the genetic landscape of STR expansion disorders.
Dr. Ira Deveson is an early career researcher at the Garvan Institute of Medical Research with expertise in genomics, biotech development, and bioinformatics. Ira leads the Genomic Technologies research group within Garvan's Kinghorn Centre for Clinical Genomics. His current focus is on the development and implementation of long-read sequencing technologies in a diverse set of research areas — ranging from clinical genome analysis to reptile sex determination. Ira previously completed a PhD (2014–2017) and post-doc (2018–2019) at the Garvan Institute under Dr. Tim Mercer. He is supported by an MRFF Investigator Grant and philanthropic funding from the Kinghorn Foundation.