LC22 Agenda

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Day 1 - Wednesday, 18th May Day 2 - Thursday, 19th May Day 3 - Friday, 20th May
11:00 - 11:30 BST 12:00 - 12:30 CET 6:00 - 6:30 EST
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INTRODUCTION: Getting started with nanopore sequencing & planning your experiment

online
Concetta Dipace, Technical Services Manager, Oxford Nanopore Technologies
Concetta Dipace

Abstract

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 and what to expect when setting up your first nanopore  sequencing run

11:35 - 12:15 BST 12:35 - 13:15 CET 6:35 - 7:15 EST
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PREPARATION: Extracting high-quality DNA and RNA

online
Vânia Costa, Applications Scientist, Oxford Nanopore Technologies
Vânia Costa

Abstract 


Get expert advice on extracting and properly storing high-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

Biography

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. 

12:20 - 12:50 BST 13:20 - 13:50 CET 7:20 - 7:50 EST
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PREPARATION: Selecting the right library prep method for your experiment

online
Tomek Dobrzycki, Oxford Nanopore Technologies

Abstract 


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

Biography
 

12:50 - 13:25 BST 13:50 - 14:25 CET 7:50 - 8:25 EST
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LIVE LOUNGE ACTIVITIES

online ondemand

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

Live lounge
12:50 - 13:25 BST 13:50 - 14:25 CET 7:50 - 8:25 EST
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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 Live Lounge. All content will be available until Friday 27th May

13:25 - 13:55 BST 14:25 - 14:55 CET 8:25 - 8:55 EST
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SEQUENCING: Choosing the right nanopore sequencing device for you

online
Bryant Catano, Oxford Nanopore Technologies
Bryant Catano

Abstract

Learn about the range of nanopore sequencing devices available and find out which best suits your experimental goals. In this masterclass you will learn:

 
•    About MinION, PromethION, and Flongle Flow Cells, and which would fit your sequencing needs

•    About the range of nanopore sequencing devices available, from portable to benchtop, and their benefits

•    How to select a nanopore sequencing device that best suits your application
     Biography

14:00 - 15:00 BST 15:00 - 16:00 CET 9:00 - 10:00 EST
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SEQUENCING: Loading a Flongle Flow Cell

online
Mark Wyatt, TT Platform QC Sequencing & Validation Scientist, Oxford Nanopore Technologies

Abstract

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

Biography

15:00 - 15:30 BST 16:00 - 16:30 CET 10:00 - 10:30 EST
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LIVE LOUNGE ACTIVITIES

online

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

Live lounge
15:00 - 15:30 BST 16:00 - 16:30 CET 10:00 - 10:30 EST
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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 Live Lounge. All content will be available until Friday 27th May

15:30 - 16:30 BST 16:30 - 17:30 CET 10:30 - 11:30 EST
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ANALYSIS: Basecalling your data and detecting methylation

online
Jessica Anderson, Technical Applications Scientist, Oxford Nanopore Technologies
Jessica Anderson

Abstract

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

Biography

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.    

16:35 - 17:35 BST 17:35 - 18:35 CET 11:35 - 12:35 EST
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ANALYSIS: Generating assemblies and calling variants

online
Anthony G. Doran, Technical Applications Scientist, Oxford Nanopore Technologies

Abstract

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

•    The different file formats involved in nanopore sequencing data analysis

•    About analysis workflows for calling variants — including structural variants and single nucleotide variants

•    Different approaches for assembling nanopore sequence data

•    The different file formats involved in nanopore sequencing data analysis

•    About analysis workflows for calling variants — including structural variants and single nucleotide variants

11:00 - 11:15 BST 12:00 - 12:15 CET 6:00 - 6:15 EST
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Welcome to London Calling 2022

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


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

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

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

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

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
11:15 - 11:40 BST 12:15 - 12:40 CET 6:15 - 6:40 EST
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The potential of ultrarapid nanopore genome sequencing for critical care medicine

online onsite
Euan Ashley, Stanford University, USA
Euan Ashley

Abstract

Rapid genetic diagnosis can guide clinical management, improve prognosis, and reduce costs in critically ill patients. Although most critical care decisions must be made in hours, traditional genetic testing takes weeks and rapid testing takes days. We have found that nanopore genome sequencing shows the potential to accurately and rapidly provide genetic diagnoses in such patients. Our workflow combines streamlined preparation of nanopore sequencing, distributed cloud-based bioinformatics, and a custom variant-prioritization approach that demonstrates the potential to achieve a diagnostic rate of 42% and make diagnoses in as little as 7 hours 18 minutes, less than half the time of the previously reported fastest whole-genome diagnosis.

Biography

Born in Scotland, Dr. Ashley graduated with a 1st class Honors in Physiology and Medicine from the University of Glasgow. He completed medical residency and a Ph.D. at the University of Oxford before moving to Stanford University where he trained in cardiology and advanced heart failure, joining the faculty in 2006. His group is focused on the science of precision medicine. In 2010, he led the team that carried out the first clinical interpretation of a human genome. The article became one of the most cited in clinical medicine that year and was later featured in the Genome Exhibition at the Smithsonian in DC. Over the following three years, the team extended the approach to the first whole-genome molecular autopsy, to a family of four, and to a case series of patients in primary care. They now routinely apply genome sequencing to the diagnosis of patients at Stanford hospital where Dr. Ashley directs the Clinical Genome Program and the Center for Inherited Cardiovascular Disease. Dr. Ashley has a passion for rare genetic disease and was the first co-chair of the steering committee of the Undiagnosed Diseases Network. He was a recipient of the National Innovation Award from the American Heart Association and the NIH Director’s New Innovator Award. He is part of the winning team of the $75m One Brave Idea competition and co-founder of three companies: Personalis Inc ($PSNL), Deepcell Inc, and SVExa Inc. He was recognized by the Obama White House for his contributions to Personalized Medicine and in 2018 was awarded the American Heart Association Medal of Honor for Genomic and Precision Medicine. He was appointed Stanford Associate Dean in 2019. In 2021, his first book, The Genome Odyssey — Medical Mysteries and the Incredible Quest to Solve Them, was released. Father to three young Americans, in his ‘spare’ time, he tries to understand American football, plays jazz saxophone, and conducts research on the health benefits of single malt Scotch whisky.

Recent publications

Gorzynski, J. E. et al. Ultrarapid nanopore genome sequencing in a critical care setting. N Engl J Med. 386(7):700-702 (2022). Goenka, S. D. et al. Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing. Nat Biotechnol. doi: 10.1038/s41587-022-01221-5 (2022). 

Auditorium Whole-genome sequencing
11:40 - 12:05 BST 12:40 - 13:05 CET 6:40 - 7:05 EST
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Identification of novel genomic structures and regulation patterns at HPV integration events in cervical cancer

online onsite
Vanessa Porter, University of British Columbia, Canada
Vanessa Porter

Abstract

Human papillomavirus (HPV) is a necessary driver of cervical cancer. We sequenced whole genomes of 66 cervical cancers from Uganda (HTMCP) and the USA (TCGA) on the PromethION to identify the genomic consequences of HPV integration. We were able to classify integration events into six categories based on their structure and impact on the human genome. DNA methylation was studied on the human and viral regions around the integration; the integrated HPV genome was hypermethylated when compared to episomal HPV, but the degree of methylation varied by HPV type. Haplotype-resolved genomes and methylomes have enabled a detailed view of the structure and function of HPV integration events.

Biography

Vanessa Porter is a Ph.D. candidate in Dr. Marco Marra’s lab at the Canada’s Michael Smith Genome Sciences Centre in Vancouver. This is Vanessa’s fifth year in the Doctor of Medical Genetics program at the University of British Columbia. Her project investigates how HPV in different contexts affects the structure and regulation of cervical cancer genomes using multiomics analyses.

Recent publications

Gagliardi, A. et al. Analysis of Ugandan cervical carcinomas identifies human papillomavirus clade–specific epigenome and transcriptome landscapes. Nature genetics. 52(8): 800-810 (2020). 

Auditorium Cancer research
12:05 - 12:20 BST 13:05 - 13:20 CET 7:05 - 7:20 EST
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SPOTLIGHT SESSION

online onsite
Richard Goodman, Liverpool School of Tropical Medicine, UK
Richard Goodman

Title

The bacterial black market: utilising sequencing to study the inter-cellular and intra-cellular transfer of AMR genes in bacteria

Abstract

Antibiotic resistance genes spread through bacterial populations by transferring between cells (inter-cellular transfer) and within cells (intra-cellular transfer). We have recently shown how the clinically important mcr-1 gene transfers between E. coli cells on a conjugative plasmid. In this study, we delved further into the movement of the mcr-1 gene by using an entrapment vector to capture mobile genetic elements associated with the gene. Utilising the long-read sequencing power of the MinION allowed for rapid detection of novel transposon movements and has been able to reveal more information about how genes move within the cells of clinically important bacteria.

Biography

Richard is undertaking a Ph.D. at the Liverpool School of Tropical Medicine with the title: “Assessing the impact of horizontal gene transfer on the evolution of antimicrobial resistance in Enterobacteriaceae”. The Ph.D. involves conjugation studies, molecular biology techniques, sequencing, bioinformatics, and computer programming in R and Linux to provide a robust system to explain antibiotic resistance evolution and inform clinical treatment regimens of antibiotics. This involves collaboration with ongoing projects in Malawi, which employ a One Health perspective to tackle AMR.

Recent publications

Manyahi, J. et al.  First identification of blaNDM-5 producing Escherichia coli from neonates and HIV infected adult in Tanzania. Journal of Medical Microbiology. 71(2) (2022).

Tansirichaiya, S. et al Intracellular transposition and capture of mobile genetic elements following intercellular conjugation of multidrug resistance conjugative plasmids from clinical Enterobacteriaceae isolates. Microbiology Spectrum. 10(1) (2022).

Michael, S. M. et al. Mobile colistin resistance gene mcr-1 is detected on an IncI1 plasmid in E. coli from meat. Journal of Global Antimicrobial Resistance. 23:145–148 (2020). 

Emily Patterson, University of Leicester, UK
Emily Patterson

Title

Whole mitogenome variation in domestic cats discovered via nanopore sequencing

Abstract

Domestic cats are popular household pets, whose shed and transferred hairs can provide important forensic evidence in crime scenes. Traditionally, a 402 bp mitochondrial DNA segment is Sanger-sequenced and compared to a population database; however, >60% of cats have one of four common haplotypes, limiting utility. To identify additional variation, we used nanopore technology to sequence the whole 17 kb mitogenomes of 93 cat blood samples in two overlapping ~9 kb amplicons, allowing us both to avoid a prominent nuclear mitochondrial insertion sequence and to distinguish 74 different haplotypes. We also used nanopore sequencing of 60 overlapping short amplicons to generate whole mitogenome sequences from cat hairs.  

Biography 

Emily is a Ph.D. student in the Department of Genetics and Genome Biology at the University of Leicester. 

Leena Putzeys, KU Leuven, Belgium
Leena Putzeys

Title

Unlocking the transcriptomic architecture of bacterial viruses with ONT-cappable-seq

Abstract

Bacterial viruses or (bacterio)phages recognize their microbial host, infect it, and convert the cell into a virus-producing machine within a matter of minutes. Classic RNA sequencing has become the method of choice to profile the transcriptional landscape of this infection process. However, short-read RNA sequencing approaches generally fail to capture key transcriptional features in dense viral genomes, such as operon structures and transcription start and stop sites. Taking advantage of the nanopore sequencing platform, we developed ONT-cappable-seq for end-to-end sequencing of primary prokaryotic transcripts to explore the dense and complex transcriptomes of phages and their bacterial hosts in unprecedented detail.

Biography

Leena Putzeys graduated from the University of Leuven, Belgium with an MSc in Bioscience Engineering in 2019. She is currently a Ph.D. student in the Lab of Gene Technology at the University of Leuven. Her research focuses on the genomic and transcriptomic analysis of the regulatory elements of bacterial viruses for novel synthetic biology applications in Pseudomonas

Auditorium
12:20 - 12:30 BST 13:20 - 13:30 CET 7:20 - 7:30 EST
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STUDIO INTERVIEWS

online

Exclusive live speaker interviews from the previous session straight from the London Calling stage

Auditorium
12:25 - 13:10 BST 13:25 - 14:10 CET 7:25 - 8:10 EST
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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

Live lounge
12:35 - 12:50 BST 13:35 - 13:50 CET 7:35 - 7:50 EST
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MINI THEATRE: Extensive structural variation and large chromosomal inversions driving adaptive divergence in yellow monkeyflowers

online onsite
Chad Niederhuth, Michigan State University, USA
Chad Niederhuth

Abstract

Structural variation is a major source of diversity and adaptive divergence. In particular, large chromosomal inversions reduce recombination and maintain the linkage of adaptive variants, forming so-called “super-genes”. The complexity and large size of these inversions has limited our understanding of their structure, and evolution. Coastal populations of Mimulus guttatus have evolved a late-flowering perennial life history, while inland populations have an early-flowering annual life history. Using Oxford Nanopore long reads we have assembled genomes for both populations and identified extensive structural variation between these populations, including a nearly 5.5 megabase pair chromosomal inversion associated with the major adaptive QTL.

Biography

Chad Niederhuth did a Ph.D. in Biological Sciences at the University of Missouri under Dr. John Walker. This was followed by a postdoc at the University of Georgia with Dr. Bob Schmitz. Chad subsequently joined Michigan State University as an Assistant Professor in 2018, where the lab studies the evolution and function of plant epigenomes.

Blondie room
13:20 - 14:10 BST 14:20 - 15:10 CET 8:20 - 9:10 EST
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DATA ANALYSIS TOOLS

onsite
Logan Mulroney, EMBL-EBI & IIT-CGS, Italy
Logan Mulroney

Title

Detecting RNA modifications from nanopore ionic current signals

Abstract

To date, over 150 naturally occurring RNA modifications have been identified. Oxford Nanopore’s direct RNA technology senses RNA molecules directly, permitting RNA modification detection during sequencing. Presently, Guppy cannot always accurately interpret the signals of modified nucleotides, leading to errors. We developed Nanocompore that compares ionic current signals from two different samples to detect modified nucleotides agnostic of basecalling training. We tested Nanocompore using several datasets and find that our results correlate with other RNA modification detection methods, confirm previous observations on the distribution of N6-methyladenosine sites, and provide insights into the distribution of RNA modifications in coding and non-coding transcripts.

Biography

Logan Mulroney is an ETPOD fellow jointly at EMBL-EBI and the Center for Genomic Science at the Italian Institute of Technology where he is working with Ewan Birney and Francesco Nicassio. His research interests include developing computational methods to detect nucleotide modifications in direct RNA nanopore sequencing data. Logan completed his Ph.D. at the University of California, Santa Cruz in the nanopore group with Mark Akeson. At UCSC, he developed nanopore sequencing methods for protein substrates and full-length RNA strands. 

Alex Sneddon, Australian National University, Australia
Alex Sneddon

Title

RISER: real-time in silico enrichment of RNA species from nanopore signals

Abstract 

Standard library preparation protocols for nanopore direct RNA sequencing (DRS) produce libraries containing a medley of RNA species with 3’ poly-A tails. Specialised biochemical enrichment protocols are currently required if only a specific RNA species is of interest. Here, we present the first method for real-time in silico enrichment of RNA species (RISER) during DRS. RISER accurately classifies protein-coding from non-coding species directly from four seconds of raw DRS signal. RISER has been integrated with the Read Until API to enact real-time sequencing decisions that allow enrichment of mRNAs or non-coding RNAs, as well as real-time tagging of reads with RNA species.

Biography

Alex is a Ph.D. candidate at The Australian National University and the EMBL Australia Partner Laboratory Network, working on computational methods to interrogate RNA biology from nanopore sequencing signals. She is also developing statistical models of RNA ‘language’ and exploring ways to integrate domain knowledge into deep learning methods. Alex has previously worked as a software engineer at Saluda Medical and received bachelor’s degrees in advanced computer science and biomedical engineering with first-class honours from The University of Sydney. 

The Clash Room
13:20 - 14:10 BST 14:20 - 15:10 CET 8:20 - 9:10 EST
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CANCER RESEARCH

online onsite

Breakouts: A series of 3 x 10 minute talks followed by a 15-minute panel discussion

Kieran O'Neill, Canada's Michael Smith Genome Sciences Centre / BC Cancer Canada
Kieran O'Neill

Title

Nanopore sequencing shows potential for personalised oncogenomics

Abstract

Since 2012, our centre has run a successful personalised oncogenomics (POG) trial for patients with advanced cancers using short-read whole-genome and transcriptome analysis of tumours to inform clinical decisions. But nanopore sequencing can improve structural variant resolution, while providing phasing and methylation information. To assess these capabilities, we have sequenced and analysed seven tumours from the POG trial. We will showcase these results, and highlight opportunities for bioinformatics tool development. We have recently sequenced 182 additional cases, with a focus on those with suspected epigenomic dysregulation and complex structural variants. We will show preliminary results from these studies.

Biography

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

Recent publications

Chin, H. L. et al. An approach to rapid characterization of DMD copy number variants for prenatal risk assessment. Am J Med Genet A. 185(8):2541–2545(2021).

Akbari, V. et al. Megabase-scale methylation phasing using nanopore long reads and NanoMethPhase. Genome Biol. 22(1):68 (2021).

Thibodeau, M. L. et al. Improved structural variant interpretation for hereditary cancer susceptibility using long-read sequencing. Genet Med. 22(11):1892–1897 (2020). 

Abderaouf Hamza, Institut Curie, France
Abderaouf Hamza

Title

Targeted nanopore sequencing ushers in the era of routine long-read sequencing in translational research laboratories

Abstract

Nanopore sequencing offers attractive prospects for clinical laboratories with translational research activities: methylation analysis, variant phasing, gene fusion detection, and single nucleotide and structural variant detection. Using a collection of tumor and germline samples, we show how targeted sequencing with adaptive sampling enables the in-depth characterization of relevant genomic regions on a single MinION Flow Cell per sample. This illustrates how nanopore sequencing can be made accessible for small-scale projects, and scalable to the systematic characterization of samples in a translational research setting.

Biography

Abderaouf Hamza, PharmD, is a molecular pathology fellow and a doctoral researcher at the Curie Institute, a cancer research and treatment center in Paris. His research interests are tumor genetics, diagnostic innovation, and bioinformatics. 

Federica Di Maggio, CEINGE-Advanced Biotechnologies, Italy
Federica Di Maggio

Title

Sequencing of tumoroids derived from study subjects with colorectal cancer, including WGS-strategy

Abstract 

In recent years, the study of precision medicine has become increasingly important for the treatment of cancer patients; in our case, with specific reference to colorectal cancers (CRC). CRC is the fourth most frequent malignancy and the third leading cause of cancer death worldwide. In this context, the study of three-dimensional cell models, such as tumoroids, has great potential in translational clinical research. Indeed, the stabilization of patient-derived organoids (PDOs) is one of the tools of choice for cancer studies for their capacity to hold some characteristics of the tumors from which they derive. In our project, we established 15 PDOs derived from patients with CRC who had agreed to be study subjects. We have observed them during the various phases of their growth with microscopy analyses. Furthermore, we also verified the origin of our tumoroid cells by immunofluorescence analyses by testing Cytokeratin-20. To better understand the mutation pattern of each stabilized PDO, we carried out molecular analyses: first, using a customized multigene panel (n=58), and then using whole-genome sequencing (WGS) with Oxford Nanopore technology. These analyses were performed on four different genomes derived from the same patient (blood, PDOs, tumor-derived tissue, and locally paired healthy tissue). Using this strategy, we found in our patients, 14 mutations in genes related to CRC predisposition (blood samples), and pathogenic mutations at somatic level in the PDOs. Thus, with this strategy, the research suggests whole-genome sequencing (WGS) with Oxford Nanopore technology has the potential to elucidate mutations from which 
‘personalized precision medicine’ could be defined by clinicians. Experiments are ongoing to extend this comparative analysis of sequences to the whole mutation spectrum in the framework of precision medicine studies, including library screening of colorectal anticancer drugs for specific mutations.  

Biography

Federica is a post-doc at the University of Naples Federico II. She graduated in 2018 in Medical Biotechnology at the University of Naples. Soon after, at the same university she undertook a Ph.D. in molecular medicine and medical biotechnology, finishing in January 2022. Federica is currently training at Imperial College London after being awarded a scholarship by the University of Naples. 

Blondie room
13:20 - 14:10 BST 14:20 - 15:10 CET 8:20 - 9:10 EST
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INFECTIOUS DISEASE

online onsite

Breakouts: A series of 3 x 10 minute talks followed by a 15-minute panel discussion

Madjid Morsli, Mediterranean Infection Foundation & Aix-Marseille University, France
Madjid Morsli

Title

Point-of-care, real-time, metagenomics-based pathogen genome detection of life-threatening community-acquired meningitis

Abstract

Community-acquired meningitis (CAM) is a life-threatening condition whose prognosis partially depends on the causative pathogen genotype. Current point-of-care (POC) diagnosis of CAM is based on multiplex RT-PCR assays targeting the 14 pathogens mostly identified in the cerebrospinal fluid (CSF). This required additional in vitro investigations for pathogen genotyping and antibiotic susceptibility testing. Herein, we proposed the real-time metagenomics (RTM) sequencing for one-shot identification, genotyping, and in silico antibiotic resistance directly from CSF samples. Furthermore, RTM allowed us to detect pathogen genomes in a leftover CSF sample from a patient with meningitis of unknown etiology. This could potentially be implemented as routine POC diagnostic of CAM in the future.

Biography

Madjid Morsli, Ph.D., is a researcher at Mediterranean Infection Foundation and Aix-Marseille University France. The main research project focuses on the improvement of community-acquired meningitis diagnosis using both metagenomics next-generation sequencing and real-time metagenomics, and its implementation at the point-of-care laboratory.

Recent publications

Morsli, M. et al. Direct diagnosis of Pasteurella multocida meningitis using next-generation sequencing. The Lancet Microbe. 3(1):6 (2022). Morsli, M. et al. Real-time whole-genome sequencing direct diagnosis of Streptococcus pneumoniae meningitis: a case report. J Infect. 10:14–6 (2021). Morsli, M. et al. Haemophilus influenzae meningitis direct diagnosis by metagenomic next-generation sequencing: A case report. Pathogens. 10(4):461 (2021). 

Kalyani Amarendra Karandikar, ICMR-National Institute for Research in Reproductive and Child Health, India
Kalyani Amarendra Karandikar

Title

Association of gut microbiome composition with severity of SARS-CoV-2 infection

Abstract

Gastrointestinal tract involvement has been reported in cases of SARS-CoV-2 infection. This is likely to involve modulation of the gut microbiome, which in turn may influence immune response to infection. In view of this, we profiled the gut microbiome composition of study subjects with differing severity of COVID-19 using the Oxford Nanopore, MinION platform. The results indicated the occurrence of gut dysbiosis in COVID-19 subjects with symptomatic infection, along with the existence of a putative protective microbiome signature in individuals with asymptomatic infection. These were further found to be associated with systemic immune responses as well as clinical features of infection.

Biography

Kalyani Amarendra Karandikar is a Ph.D. research scholar at ICMR-National Institute for Research in Reproductive and Child Health, and was awarded the Lady Tata Memorial Trust fellowship for her Ph.D. research. Her area of interest is the microbiome and immunology, and she studied Life Sciences and Medical Biotechnology at graduate and postgraduate level, respectively. Kalyani Amarendra Karandikar was a Gold medallist in the Dr. Homi Bhabha young scientist exam, and has conducted workshops and lectures regarding microbiome analysis. She has been part of  the team carrying out diagnostic and research work in COVID-19.

Recent publications

Meshram, H. et al. Hepatic interferon γ and tumor necrosis factor a expression in infants with neonatal cholestasis and cytomegalovirus infection. Clin Exp Hepatol. 6(4):367–373 (2020). Jawade, K. et al. A novel ORF1a-based SARS-CoV-2 RT-PCR assay to resolve inconclusive samples. Int J Infect Dis. 106:395–400 (2021). 

Christian Brandt, Jena University Hospital, Germany
Christian Brandt

Title

Potential clinical applications of adaptive sampling

Abstract

Depletion and enrichment by Oxford Nanopore’s adaptive sampling provides potential new application options for sequencing in the hospital. For instance, alterations of the vaginal microbiome are associated with adverse pregnancy outcomes but these samples deal with high amounts of host DNA and thus low microbial load. We demonstrated how selective 'human host depletion' resulted in increased sequencing depth, while the microbial composition remains consistent. We further leveraged the enrichment capabilities as a flexible antimicrobial resistance genotyping panel for routine microbiology covering 1,147 antimicrobial resistance genes. Our study examined the limitations and the relationship between database, sequence similarities, and prepared DNA.

Biography

Dr. Christian Brandt is a post-doc at the Institute for Infectious Diseases and Infection Control in Jena, Germany. He leads the CaSe-group, a research group centred around sequencing and bioinformatics, and is the CEO and founder of nanozoo. He studied pharma-biotechnology and after finishing his Ph.D. in Germany he went to Sweden to learn cloud computing and workflow development while investigating metagenomic samples as part of a research fellowship. In his spare time he literally goes up the wall 
(climbing).

Recent publications

Brandt, C. et al. poreCov — an easy to use, fast, and robust workflow for SARS-CoV-2 genome reconstruction via nanopore sequencing. Front Genet. 12:711437 (2021).

Marquwt, M. et al. Evaluation of microbiome enrichment and host DNA depletion in human vaginal samples using Oxford Nanopore’s adaptive sequencing. Sci Rep. 12(1):4000 (2022). 

Bowie room
14:15 - 15:00 BST 15:15 - 16:00 CET 9:15 - 10:00 EST
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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

Live lounge
14:25 - 14:40 BST 15:25 - 15:40 CET 9:25 - 9:40 EST
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MINI THEATRE: DoGsTAils: developing nanopore-based diagnostic approaches for the effective antimicrobial stewardship of canine infections

online onsite
Natalie Ring, The Roslin Institute, UK
Natalie Ring

Abstract

We are developing DNA extraction and sequencing methods to facilitate the rapid identification of pathogens in urine, skin, and blood samples from dogs. Our current protocol can detect species from as little as 0.50 ng gDNA, and in the near future we hope to start offering it in addition to the current culture-based tests already available at the University of Edinburgh Hospital for Small Animals. We intend our data analysis pipeline to also include the prediction of antimicrobial resistance from the same data, and are now testing a suite of existing tools to determine the best methods for this.

Biography

Natalie is a Postdoctoral Research Fellow at the Roslin Institute, UK. Her main interest is the development of long-read sequencing and assembly protocols for bacterial genomes; after a Ph.D. researching the repetitive genome of Bordetella pertussis, she is now applying long-read sequencing to a number of projects, including the potential use of the MinION in the diagnosis of bacterial infections in dogs. She also wrote a chapter on the genetics of regeneration for a book about Doctor Who!

Recent publications

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

Abrahams, J. S. et al. Towards comprehensive understanding of bacterial genetic diversity: large-scale amplifications in Bordetella pertussis and Mycobacterium tuberculosis. Microbial genomics. 8(2):000761 
(2022).

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

Blondie room
14:25 - 14:45 BST 15:25 - 15:45 CET 9:25 - 9:45 EST
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SECRET CINEMA

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Victoria Shabardina, Institute of Evolutionary Biology, Spain
Victoria Shabardina

Title

Enigmatic genome of Abeoforma whisleri helps our understanding of the origin of animals

Abstract

Abeoforma whisleri is unicellular but is also one of closest relatives of animals. By studying Abeoforma and other unicellular relatives we hope to reconstruct how the transition to multicellularity happened. Abeoforma recently was shown to exhibit spatial cell differentiation — a phenomena usually thought to be specific to complex multicellularity. Now, Abeoforma can change our understanding of the evolution of cell differentiation. However, its genome was not easy to assemble: neither with short reads, nor with nanopore. I will explain how to handle problematic genomes with nanopore sequencing and how the genome of Abeoforma helps us to understand the biology of this enigmatic organism. 

Biography

Victoria Shabardina graduated from Moscow University and completed her Ph.D. studies at the University of Muenster in the field of biochemistry. She became interested in evolution and bioinformatics while working in the Institute of Bioinformatics, Muenster, Germany. She is now a post-doc at the Institute of Evolutionary Biology in Barcelona, where she studies the origin of animal multicellularity. Her main interest is the evolution of protein families and their role in evolutionary novelties. 

Abigail Stack, Bayer Crop Science, USA
Abigail Stack

Title

The POREtal to advancing plant diagnostics: Flongle for tomato bacterial race typing and beyond

Abstract

Bacterial leaf spot is an economically important seed-borne disease of tomatoes globally. There are four known species (races) of Xanthomonas, which can cause the disease. Physical race typing is a bottleneck in industry as it involves a lengthy process of complicated phenotyping inoculated plants. Similarly, the genomes of the four races are highly conserved, so previous attempts at molecular diagnostics have been unsuccessful. Using nanopore sequencing on Flongle Flow Cells, we were able to obtain genetic resolution for distinction. This reduces turnaround time for diagnosis by 75% and allows us to make important pest management decisions for our fields.

Biography

Abigail (Abbie) Stack works in Vegetable R&D at Bayer Crop Science in California, USA. Abbie’s two areas of expertise are the testing and implementation of innovations for molecular plant disease diagnostics and plant virology. She was recently inducted as Bayer’s youngest R&D Science Fellow and is the acting president of the local chapter of the Association for Women in Science. Abbie holds a B.S. from Purdue University and an M.S. from the University of California, Davis. 

Secret cinema
15:15 - 15:30 BST 16:15 - 16:30 CET 10:15 - 10:30 EST
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LIGHTNING TALKS

online onsite
Mashiat Mimosa, University of Toronto, Canada
Mashiat Mimosa

Title

Optimization and validation of a nanopore-based sequencing method for potential molecular testing of CNS tumours

Abstract

Research shows MinION by Oxford Nanopore Technologies has the potential to overcome challenges posed by current NGS technologies used in isocitrate dehydrogenase (IDH) mutational testing for glioma diagnosis. However, MinION has not been validated for clinical practice using FFPE tissue. Thus, we developed and analytically tested a PCR amplicon-based assay in a CLIA setting to detect IDH SNVs on FFPE DNA using MinION. The assay revealed concordance, sensitivity, and specificity of 100%. Limit of blank was 1.5% and limit of detection was 3.3% at 500x depth. Total assay cost was $50–$134/sample with total turnaround time of less than two days.   

Biography

Mashiat is a research graduate student at the University of Toronto in the Department of Laboratory Medicine and Pathobiology. She has completed her HBSc. in Neuroscience and Molecular Biology, Immunology, and Disease from the University of Toronto. Currently, she is completing her MSc. In Dr. Rola Saleeb’s lab at the Li Ka Shing Knowledge Institute, St. Michael’s Hospital in Toronto, Canada. Her primary research interests are cancer diagnostics, neuro-oncology, and genomics.   

Bioinformatics, Cancer research, Human genomics, Targeted sequencing, MinION Mk1B, Flongle, R9 Flow Cells 

Gianluca Damaggio, University of Milan, Italy
Gianluca Damaggio

Title

Detection of endogenous CAG instability through nanopore sequencing of the Huntingtin exon 1

Abstract

We developed a hESC platform carrying different CAG repeat lengths to study CAG size variation at the endogenous HTT locus of self-renewing stem cells and in hESC-derived neurons. Leveraging Oxford Nanopore technology to sequence the unfragmented HTT locus, we measured CAG size in the cell population over time using Straglr and analyzed the distribution of CAG counts as an adjusted instability index. We showed significant CAG length increase only above 50Q in proliferating ESCs recapitulating somatic instability seen in patients with the highest change found in the 107Q lines that also show instability during neuronal differentiation, but at a slower pace.

Biography

Gianluca received a bachelor’s degree in Molecular Biology and a master’s degree in Biology at the University of Napoli Federico II. He is a second year Ph.D. student, visiting the Institute of Genetics and Biophysics of the Italian National Research Council in Naples. He is also a Junior Research Fellow at the University of Milan in the Laboratory of Elena Cattaneo where, using nanopore sequencing, he studies the instability of the CAG tract in the Huntington’s gene.

Recent publications

Buonaiuto, S. et al. Prioritization of putatively detrimental variants in euploid miscarriages. Sci Rep
12(1):1–12 (2022).

Capalbo, A. et al. O-115 parental whole-exome sequencing allows the discovery of genetic causes of extreme IVF phenotypes such as oocyte/embryo developmental arrest and recurrent low fertilization, Human Reproduction. 36(Supplement 1) (2021).

Balasco, N. et al. A global analysis of conservative and non-conservative mutations in SARS-CoV-2 detected in the first year of the COVID-19 world-wide diffusion. Scientific reports.11(1):1–14 (2021). Kahraman, S et al. Genomics analysis of maternal exomes reveals new candidate genes and pathways for the diagnosis and prediction of recurrent preimplantation embryo arrest in IVF cycles. Fertility and Sterility.

Auditorium
15:30 - 15:55 BST 16:30 - 16:55 CET 10:30 - 10:55 EST
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A single platform for multi-omics

online onsite
Dan Turner, Oxford Nanopore Technologies
Dan Turner

Dan leads the Applications Team at Oxford Nanopore Technologies. He is a highly experienced genomics scientist with expertise in all aspects of ‘next-generation’ sequencing. He provides scientific and strategic leadership for multi-disciplinary teams in Oxford, New York and San Francisco. The Applications group aims to bring together sample prep technologies, genomics applications, and bioinformatics, to expand the utility of Oxford Nanopore Technologies’ devices and help bring the benefits of these technologies to the wider world. 

Auditorium
15:55 - 16:45 BST 16:55 - 17:45 CET 10:55 - 11:45 EST
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ONLINE BREAKOUT: ENVIRONMENTAL CONSERVATION

online
Douglas Mendel, University of São Paulo, Brazil
Douglas Mendel

Title

Comparative metagenomics of natural and artificial ponds of the Atlantic Rainforest in Brazil using nanopore sequencing 

Abstract

A comparative metagenomic analysis was performed from nanopore sequencing data from natural and artificial ponds located in a fragment of the Atlantic Forest biome, in Brazil, to gather information on the biodiversity of microorganisms and genes involved with secondary metabolites, including toxins and antibiotic resistance genes. Together with our recent, firstly reported, metagenomic analysis of surface water from the Guarapiranga reservoir, which supplies drinking water for millions of people in the São Paulo metropolitan area, these data may help to bring new cues about the pollution impact on microbial diversity in aquatic ecosystems. An interactive metagenomic visualization is available at 
stevanilab.com/metagenomics.  

Biography

Dr. Douglas Mendel is a molecular biologist and post-doc at the Environmental & Green Chemistry Lab (Institute of Chemistry, University of São Paulo, Brazil) under the supervision of Dr. Cassius Stevani. In addition to the lab’s interest in biochemistry and biotechnology of fungal bioluminescence, they have also applied nanopore sequencing for environmental metagenomics projects from natural and artificial ponds, mostly in the Atlantic Forest biome. To find more information about their research group, visit: stevanilab.com.

Recent publications

Soares, D. M. M. et al. Exploring the microbiota of the Guarapiranga water reservoir with long-read sequencing technology. Front. Mar. Sci. 8:1–4:791101(2021). 

Ana Ramón-Laca, NOAA Fisheries (NWFSC) & University of Washington, USA
Ana Ramón-Laca

Title

Affordable de novo generation of fish mitogenomes using amplification-free targeted enrichment and deep sequencing of long fragments

Abstract

We developed protocols to sequence whole mitogenomes from fish species with the aim of generating comprehensive databases and simplify the discovery of mitogenomes of non-model or understudied fish taxa to a broad range of laboratories worldwide. Long-fragment sequencing with amplification-free targeted enrichment produced whole mitogenomes with deep coverage. This helped complete the mitogenome of species with homopolymeric regions, tandem repeats, and gene rearrangements, and described new mitogenomes. The experiments were mostly undertaken in a home office during the pandemic, showing that the lab requirements were kept to a minimum, which opens the possibility of generating ad hoc databases during field surveys or oceanographic campaigns.

Biography

Ana uses applied molecular ecology techniques to answer ecological questions and inform management decisions. Her main area of expertise lies within the non-invasive and low-copy DNA space. She has worked with almost every limited DNA sample possible — from saliva to eDNA, and from feathers to wasp gut content — to identify prey, predators, describe communities, or monitor fish stocks, and endangered and invasive species. She has worked in different labs in New Zealand, the United States, and currently in Spain.

Recent publications

Shelton, A. O. et al. Environmental DNA provides quantitative estimates of Pacific hake abundance and distribution in the open ocean. Proc Biol Sci. 289(1971) (2022).

Ramón-Laca, A., Wells, A., and Park, L. A workflow for the relative quantification of multiple fish species from oceanic water samples using environmental DNA (eDNA) to support large-scale fishery surveys. PloS one. 16(9) (2021). 

Robert Hatfield, Centre for Environment, Fisheries and Aquaculture Science, UK
Robert Hatfield

Title

Using nanopore sequencing to screen for aquatic microbial hazards in the lab was too easy, so we are doing it outside

Abstract

We have developed nanopore sequencing capabilities to monitor aquatic environments and detect biological threats, including waterborne pathogens and harmful algae. These assays offer fast and cost-effective methods for accurate characterization of hazards to humans, animals, and environmental health. It is envisaged that these assays could be used in the field, allowing faster identification of threats and consequently a timelier response. To facilitate this, we are developing mobile capabilities in sample concentration, sample preparation, a mobile sequencing platform, customized assays, and streamlined bioinformatic pipelines. This presentation summarizes the developments made, highlighting enhanced capabilities and practical hurdles overcome thus far.  

Biography

After training in biological sciences, Robert started his career as an analytical chemist, undertaking routine monitoring for plankton-borne toxins in shellfish. He has continued to work with harmful algae but now predominantly uses molecular tools, including nanopore sequencing. Amongst other projects, Robert is currently working on developing in-field molecular assays. This has included the development of sample collection, preparation, and sequencing processes, as well building a custom sequencing device built around a MinION Mk1B.

Recent publications

Hatfield, R. G. et al. The application of nanopore sequencing technology to the study of dinoflagellates: a proof of concept study for rapid sequence-based discrimination of potentially harmful algae. Front Microbiol. 11:844 (2020). 

Blondie room
15:55 - 16:20 BST 16:55 - 17:20 CET 10:55 - 11:20 EST
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Long-read transcriptome sequencing reveals isoform diversity across human neurodevelopment and aging

online onsite
Rosemary Bamford, University of Exeter, UK
Rosemary Bamford

Abstract

Alternative splicing dramatically increases transcriptomic and proteomic diversity from the coding genome. Long-read sequencing approaches can be used to generate full-length transcript sequences and characterise isoform diversity. We used Oxford Nanopore transcriptome sequencing to profile transcript diversity across human brain development and aging. We identify changes in alternative splicing, with differential transcript usage between human foetal and adult cortex. We show that genes associated with neurodevelopmental and neurodegenerative disorders are characterised by considerable RNA isoform diversity. Our data confirm the importance of alternative splicing in the human cortex and represent an important mechanism underpinning gene regulation in the brain.

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. 

Auditorium Transcriptomics
16:20 - 16:45 BST 17:20 - 17:45 CET 11:20 - 11:45 EST
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Exploring the genomic and epigenomic landscape of acute myeloid leukemia with nanopore sequencing

online onsite
Alberto Magi, University of Florence, Italy
Alberto Magi

Abstract

We report the first study that uses high-coverage whole-genome nanopore-sequencing to simultaneously analyse genomic and epigenomic alterations in cancer, and applied it to the analyses of clonal 
genomic/epigenomic evolution and mechanisms of drug-resistance in samples of acute myeloid leukemias (AMLs) at diagnosis and relapse, after chemotherapy. The results confirm that intratumoral epigenetic-heterogeneity is a common trait of relapsing/chemoresistant AMLs, which is distinguished from the genetic heterogeneity. The research further demonstrates that the relapse phenotype is most-frequently supported by the selection of a few abnormally-methylated transcription factors that induce massive transcriptional reprogramming and contribute to both clonal evolution and drug-resistance.

Biography

Alberto Magi is an Associate Professor of Bioengineering at the Department of Information Engineering, University of Florence. He is Principal Investigator of the Investigator Grant of the AIRC Foundation for Cancer Research entitled ‘Third Generation Cancer Genomics’. His research interests focus on computational genomics, in particular on the development of tools able to analyse the data generated by nanopore sequencing platforms in order to study cancer genetic variation.

Recent publications

Martignano, F. et al. Nanopore sequencing from liquid biopsy: analysis of copy number variations from cell-free DNA of lung cancer patients. Mol Cancer. 20(1):32 (2021).

Bolognini, D., and Magi, A. Evaluation of germline structural variant calling methods for nanopore sequencing data. Front Genet. 12:761791 (2021).

Magini, P. et al. Third generation cytogenetic analysis (TGCA): diagnostic application of long-read sequencing. bioRxiv. doi.org/10.1101/2021.08.13.456226 (2021).

Bolognini, D., Magi, A., Benes, V., Korbel, J. O., and Rausch, T. TRiCoLOR: tandem repeat profiling using whole-genome long-read sequencing data. Gigascience. 9(10) (2020).

Bolognini, D. et al. VISOR: a versatile haplotype-aware structural variant simulator for short- and long-read sequencing. Bioinformatics. 36(4):1267–1269 (2020).

anne, A. et al. Nano-GLADIATOR: real-time detection of copy number alterations from nanopore sequencing data. Bioinformatics. 35(21):4213–4221 (2019).

Semeraro, R., and Magi, A. PyPore: a python toolbox for nanopore sequencing data handling. Bioinformatics. 35(21):4445–4447 (2019).

Bartalucci, N. et al Long reads, short time: feasibility of prenatal sample karyotyping by nanopore genome sequencing. Clin Chem. 65(12):1605–1608 (2019). 

Auditorium Whole-genome sequencing
16:40 - 16:55 BST 17:40 - 17:55 CET 11:40 - 11:55 EST
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Human genome assembly and analysis using R10.4.1, Kit 14, and duplex data

online onsite
Miten Jain, UC Santa Cruz, USA
Miten Jain

Abstract

Recent improvements in read length, accuracy, and software have enabled ultra-rapid, nanopore-based whole-genome sequencing analysis. The addition of Kit 14 chemistry and the R10.4.1 nanopore could yield state-of-the-art, phased, de novo assemblies exceeding Q40+ accuracy. Furthermore, duplex data, combined with DNA methylation information, will contribute towards genome finishing applications. This scalable and affordable framework could result in a paradigm shift for population-level genomics and human health applications. We present our latest results on genome assembly, variant calling, and evaluation of the R10.4.1 pore and Kit 14.

Biography

Miten is an Assistant Research Scientist at the University of California, Santa Cruz. He did his Ph.D. in Biomolecular Engineering and Bioinformatics at UC Santa Cruz in the nanopore group. His prior work and research interests include developing biological methods and software for: i) analyzing genomics data; ii) long-read sequencing of DNA and RNA; iii) resolving complex repeats and base modifications; and iv) sequencing and analysis of different classes of RNA (mRNA, rRNA, tRNA, non-coding RNA). His long-term interests include combining sequence and structure information from DNA (genomics), RNA (coding and non-coding), and proteins, to better understand genome organization and function. 

Auditorium Whole-genome sequencing
17:00 - 17:10 BST 18:00 - 18:10 CET 12:00 - 12:10 EST
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STUDIO INTERVIEWS

online

Exclusive live speaker interviews from the previous session straight from the London Calling stage

Auditorium
17:05 - 17:35 BST 18:05 - 18:35 CET 12:05 - 12:35 EST
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FLOW CELL LOADING

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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

Live lounge
17:05 - 17:35 BST 18:05 - 18:35 CET 12:05 - 12:35 EST
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POSTER NETWORKING

online onsite

Join poster presenters in person and online, ask questions, network with your peers, and vote for your favourite poster

Posters
17:10 - 17:30 BST 18:10 - 18:30 CET 12:10 - 12:30 EST
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SECRET CINEMA

onsite ondemand
Jeroen de Ridder, Cyclomics & University Medical Center Utrecht, Netherlands
Jeroen de Ridder

Title

CyclomicsSeq: targeted and genome-wide detection of circulating tumor DNA using nanopore consensus sequencing

Abstract

Levels of circulating tumor DNA (ctDNA) in liquid biopsies may serve as a sensitive biomarker for real-time, minimally-invasive tumor diagnostics and monitoring. To detect lowly abundant ctDNA molecules based on somatic variants, extremely sensitive sequencing methods are required. CyclomicsSeq enables consensus sequencing of concatenated copies of a single DNA molecule, increasing the base accuracy by ~60x and enabling accurate detection of, for example, TP53 mutations at frequencies down to 0.02%. A genome-wide version of CyclomicsSeq integrates multiple signals derived from ctDNA, including SNVs, CNVs, and fragmentation patterns, enabling monitoring of cancer with unprecedented dynamic range, and paving the way for presymptomatic cancer screening.

Biography

Jeroen de Ridder is co-founder and CTO of Cyclomics BV, a start-up aimed at revolutionizing cell-free DNA-based liquid biopsy sequencing. In addition, Jeroen is a principal investigator and Associate Professor at the Center for Molecular Medicine of the University Medical Center Utrecht. His lab is developing novel genomics-based cancer diagnostic methods.

Recent publications

Marcozzi, A. et al. Accurate detection of circulating tumor DNA using nanopore consensus sequencing. NPJ Genom Med. 6(1):106 (2021). 

Anna Dolnik, Charité University Medicine Berlin, Germany
Anna Dolnik

Title

Combined CRISPR/Cas9 targeted enrichment and whole-genome sequencing allows real-time stratification of acute myeloid leukemia (AML) 

Abstract

Prompt testing of European LeukemiaNet molecular markers is pivotal for the risk stratification and treatment of AML patients. We have established a two-step 72-hour assay. First, based on targeted enrichment using a CRISPR/Cas9 system, relevant target regions such as FLT3, t(8;21), inv(16), and MLL translocations can be well covered (~44-fold coverage). Secondary whole-genome sequencing results in ~2-fold genome coverage with a copy number variation resolution of 0.1 Mbp. While additional testing of this AML panel within round-robin tests are warranted, introduction of this real-time sequencing approach could ultimately lead to improved leukemia diagnostics and patient-management.

Biography

Anna Dolnik is a post-doc at the Charité University Medicine Berlin, Germany. In 2016, Anna first obtained experience in Oxford Nanopore technology through resequencing of novel fusion genes found in acute myeloid leukemia (AML) with complex karyotype. Since the end of 2018, the lab routinely use a GridION for better characterization of hematologic malignancies. The focus of Anna’s research is clonal evolution in AML, identification of cancer driving genes, and characterization of complex changes in cancer genomes by whole-genome sequencing. 

Secret cinema
17:20 - 17:35 BST 18:20 - 18:35 CET 12:20 - 12:35 EST
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SHOWCASE STAGE

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John E. Gorzynski & Sneha D. Goenka, Stanford University, USA
John E. Gorzynski & Sneha D. Goenka

Title

Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing 

Abstract

Whole genome sequencing can identify variants that cause genetic disease, but the time required for sequencing and analysis has been a barrier to its use in critical care settings. Using nanopore sequencing, we developed a pipeline that was shown to identify clinically actionable genetic variants in as little as 7 hours 18 minutes. To achieve this, we accelerated sample preparation, leveraged the full capacity of PromethION 48 sequencing, developed a bioinformatics pipeline with near real-time basecalling and alignment plus accurate variant calling, and customized variant prioritization. Here, we will discuss these optimizations in detail, which supported the healthcare team to diagnose critically ill patients that led to lifesaving treatments.

Biography

John studied at the University of London’s, Royal Veterinary College where he earned a degree in veterinary medicine and continued his education at Stanford University where he obtained a Ph.D. in genetics. John is now a postdoc in the Euan Ashley lab at Stanford University and is interested in utilizing long-read (nanopore) genome sequencing to improve the health of human and non-human patients. Sneha is a Ph.D. candidate in the Department of Electrical Engineering at Stanford University, where she is advised by Prof. Mark Horowitz. Her current research interests lie at the intersection of computer architecture and computational genomics. She is a recipient of the NVIDIA graduate fellowship and Cadence Women in Technology scholarship. She has a B.Tech and M.Tech (Microelectronics) in Electrical Engineering from the Indian Institute of Technology, Bombay.

Recent publications

Gorzynski, J. E. et al. Ultrarapid nanopore genome sequencing in a critical care setting. N Engl J Med. 386(7):700-702 (2022).

Goenka, S. D. et al. Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing. Nat Biotechnol. doi: 10.1038/s41587-022-01221-5 (2022).

Gorzynski, J. E. et al. Ultra-rapid nanopore whole genome genetic diagnosis of dilated cardiomyopathy in an adolescent With cardiogenic shock. Circ Genom Precis Med. doi: 10.1161/CIRCGEN.121.003591 
(2022). 

Live lounge
17:45 - 19:15 BST 18:45 - 20:15 CET 12:45 - 14:15 EST
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Update from Oxford Nanopore Technologies

online onsite
Clive Brown, Chief Technology Officer, Oxford Nanopore Technologies
Clive Brown

Clive Brown is CTO of Oxford Nanopore, where he leads the innovation of breakthrough technologies and product development, that are designed to enable the analysis of anything, by anyone, anywhere. Clive has held a variety of roles in Genomics and Genetic R&D, he also played a key role in developing the Solexa NGS platform that is now the basis for Illumina’s sequencing technology.

James Clarke, VP, Platform Technology, Oxford Nanopore Technologies
James Clarke

Dr. James Clarke is responsible for the Research Division at Oxford Nanopore Technologies Ltd., working with Clive Brown to push the boundaries of nanopore technology. Over the last ten years, his work has included: pioneering strand sequencing chemistry at Oxford Nanopore, scaling up the membrane chemistry for the MinION platform, and managing the companies' nanopore consortium of world class academics.

Lakmal Jayasinghe, VP, R&D Biologics, Oxford Nanopore Technologies
Lakmal Jayasinghe

Dr. Lakmal Jayasinghe leads the biological nanopore research team at Oxford Nanopore Technologies.  Lakmal joined Oxford Nanopore in 2006 after finishing his Ph.D. in chemical biology in the University of Oxford. During his Ph.D. in the Hagan Bayley group, Lakmal has studied different nanopores and has gained a wealth of knowledge in engineering nanopores using genetic and chemical approaches. His responsibilities at Oxford Nanopore Technologies include improving the readout signal of the Oxford Nanopore platform by upgrading its current nanopore reader and discovering and engineering new nanopores to suit various Oxford Nanopore applications and platforms. Lakmal also works with many academic nanopore collaborators across the world to make sure Oxford Nanopore uses the best possible nanopore reader in its platforms.

Stuart Reid, VP, Development, Oxford Nanopore Technologies
Stuart Reid

Stuart Reid is VP of Development at Oxford Nanopore. Stuart is responsible for the specification, performance, and delivery of the company’s nanopore-based sensing products and applications into the marketplace. He joined Oxford Nanopore in 2006, with a particular interest in biophysical systems and signals analysis, following a DPhil in Physics (Bionanotechnology) from Oxford University as part of the Life Sciences Interface Doctoral Training Centre. He has been instrumental at all stages of the product development cycle, from the fundamental science and invention, through specification, implementation, and optimisation to delivery into the hands of our user community.

Rosemary Sinclair Dokos, SVP, Product & Programme Management, Oxford Nanopore Technologies
Rosemary Sinclair Dokos

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, 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
19:15 - 19:25 BST 20:15 - 20:25 CET 14:15 - 14:25 EST
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STUDIO INTERVIEWS

online

Exclusive live speaker interviews from the previous session straight from the London Calling stage

Auditorium
9:00 - 10:05 BST 10:00 - 11:05 CET 4:00 - 5:05 EST
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INFORMATICS UPDATE

onsite
George Pimm, Senior Director, Instrument Software, Oxford Nanopore Technologies
George Pimm

Title

The MinKNOW API and output file formats

Abstract

A low-level tour of the MinKNOW software and its API, and upcoming changes we are making.

  • How to use a nanopore sequencer from python
  • An introduction to Oxford Nanopore’s new output file format

Biography

George started his career writing software for authoring computer game animation. He then spent a short period professionally building robots to maintain nuclear fusion reactors before joining Oxford Nanopore. George has worked with the Instrument Software group for the last seven years building MinKNOW.

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

Title

Dorado — a modern, C++, Torch-based basecaller

Abstract

At Oxford Nanopore we are developing a new basecaller called Dorado. Our design objectives are to produce a tool which is flexible, high-performance, multi-platform, and user-friendly. This talk will describe the technologies we use, our design goals, roadmap, and show an early preview of Dorado.

Biography

Mike Vella is a Director of Machine Learning Operations at Oxford Nanopore. He received his Ph.D. 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.

Adrien Leger, Senior Research Scientist, Sequencing Chemistry, Oxford Nanopore Technologies

Title

Modified bases and synthetic training update

Abstract

Oxford Nanopore’s modified base detection tools have been evolving fast with the release of Remora and the proof of concept that models could be trained from synthetic oligomers. This talk will review our recent progress in the accurate detection of DNA modifications:

  • Upgraded 5mC CpG model for Kit 14
  • New synthetic randomer models
  • Progress on synthetic datasets

Biography

Adrien Leger is a computational biologist working in Oxford Nanopore’s research division on modified base detection. Before joining Oxford Nanopore Technologies, he worked at EMBL-EBI on DNA and RNA modifications related algorithms.

Richard Carter, Senior Director, Information Systems, Oxford Nanopore Technologies
Richard Carter

Title

Scaling up nanopore sequencing

Abstract

We will discuss some of the key factors that should be taken into consideration before starting to scale up nanopore sequencing in a production environment.

Biography

Richard Carter is the Senior Director of Information Systems at Oxford Nanopore Technologies. He has worked in next generation sequencing for over 15 years. He leads several software, engineering, and reporting teams that manage the collation, storage, and transformation of information across Oxford Nanopore. His teams manage data analysis pipelines, databases, and associated infrastructure. He is responsible for the manufacturing tracking systems for production across the company, which are currently being enhanced to support a more regulated environment. His teams also support bespoke analysis for the Research and Development groups.

The Clash Room
10:30 - 10:40 BST 11:30 - 11:40 CET 5:30 - 5:40 EST
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Welcome back to London Calling 2022

online onsite
Zoe McDougall, VP, Marketing and Corporate Affairs, Oxford Nanopore Technologies
Zoe McDougall

Zoe joined Oxford Nanopore in 2008 in a strategic marketing, communications, and investor facing role — the first person to be hired with a specific commercial remit.  She now leads our Commercial & Corporate Marketing and Corporate Affairs functions.  

Since the foundation of the company she has driven accessible and authentic communities and communication channels so anyone engaging with, or interested in, Oxford Nanopore understands the company, our technology and our philosophy, whatever the length or nature of their relationship with us. This supports sales and utilisation of the technology, as well as fundraising and investor relations. The Company has raised £613 million to date.    

During early commercialisation, Zoe and her team drove the creation of structures and activities that support the building up of Oxford Nanopore’s customer community; this enables many teams at Oxford Nanopore to collaborate with our thriving user base, to improve the technology, and expand the applications that it can perform.

Zoe started her career in sales and marketing at SmithKline Beecham. She subsequently worked at the strategic marketing and communications consultancy Porter Novelli where she ran healthcare-related campaigns across a range of clinical areas for clients including GSK, BMS, and Pfizer, across multiple areas including immunology, cancer, diabetes, cardiovascular and respiratory medicine.

Before joining Oxford Nanopore Zoe worked on the IPO and investor relations for a UK specialty pharma company. In 2004 she spent six months working with a medical humanitarian organisation in Sri Lanka. 

Auditorium
10:40 - 11:05 BST 11:40 - 12:05 CET 5:40 - 6:05 EST
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Understanding cancer epigenetics, immunogenetics, and energetics

online onsite
Michael Dean, National Cancer Institute, USA
Michael Dean

Abstract

We studied human papillomaviruses (HPV) and cervical cancer cell lines and tumors. We used ultra-HMW DNA and full-length direct RNA sequencing to identify HPV integration sites at known super-enhancer hotspots, extrachromosomal DNA, and altered DNA methylation. Pore-C reveals extensive interaction between HPV and the human genome. HLA class I sequencing found extensive deletion of MHC haplotypes and that the HPV E5 protein, an HLA inhibitor, has abundant strong binding peptides. From mitochondrial genomics, we are exploring cancer energetics and mitochondrial variants. In summary, long-read sequencing provides exciting new data to understand the complex phenotypes of cancer cells.

Biography

Dr. Michael Dean is a senior investigator in the Laboratory of Translational Genomics. He obtained his Ph.D. from Boston University. He is interested in inherited and somatic genetic mutations in tumors and has participated in cloning genes (PTCH, VHL) involved in inherited cancers. His focus is the study of human papillomaviruses (HPV) and cervical cancer. He also continues his investigations into the genetic components of cancer health disparities in the U.S. and Latin America.

Recent publications

Lou, H. et al. The D2 and D3 sublineages of human papilloma virus 16-positive cervical cancer in Guatemala differ in integration rate and age of diagnosis. Cancer Res. 80(18):3803–3809 (2020).

Rossi, N. M. et al. Extrachromosomal amplification of human papillomavirus episomes as a mechanism of cervical carcinogenesis. BioRxiv. 465367 (2021).

Auditorium Cancer research
11:20 - 12:10 BST 12:20 - 13:10 CET 6:20 - 7:10 EST
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PANEL PLENARY: ANIMAL CONSERVATION IN THE ERA OF ACCESSIBLE GENOMICS

online onsite
Ettore Fedele, University of Leicester, UK
Ettore Fedele

Title

Genomic tools for gorilla population dynamics and conservation

Abstract

Great apes are a global conservation concern. Reduced population numbers and continuous pressures pose serious threats to their survival. This project aimed to establish robust autosomal marker multiplexes for gorilla species identification and investigation of demographic processes. Owing to the difficulties that can be encountered while studying elusive wild gorillas, we developed an autosomal SNPs panel suited for degraded DNA, to be used in conjunction with Oxford Nanopore’s MinION for in-field sequencing of non-invasive samples. This technology allows us to assess population dynamics and structure in wild gorillas and can provide support to the fight against poaching and illegal wildlife trafficking.

Biography

Ettore Fedele joined the University of Leicester, Department of Genetics and Genome Biology, in 2018 as a NERC CENTA Ph.D. student. He studied Economics and Management at Ca’ Foscari University of Venice, and has an MSc in Conservation and Management of Protected Areas from Edinburgh Napier University. He has worked in Elba (Italy), South Africa, Uganda, and at Kew Gardens. His project focuses on genetic approaches to diversity and conservation in gorillas, involving a collaboration with Twycross Zoo. 

Zane Libke, Sumak Kawsay In Situ Genomics Lab & National Institute of Biodiversity, Ecuador
Zane Libke

Title

Flongle sequencing reveals cryptic amphibian diversity and builds local research capacity in the Ecuadorian Amazon

Abstract

Global biodiversity hotspots are under threat, and traditional sequencing methods are too inaccessible to adequately study mega-diverse ecological communities. To address this, we established a DNA barcoding laboratory at an educational research station in the Ecuadorian Amazon. With multiplexed amplicon sequencing on Flongle Flow Cells, we’ve uncovered cryptic diversity in amphibian communities, discovering several species new to science and informing conservation plans. Through practical, experiential-based courses and research experiences, we have capacitated 70+ Ecuadorian students and professionals in field-adapted molecular biology and nanopore sequencing techniques. As biodiversity hotspots continue to become threatened worldwide, we provide an example of an on-site, low-overhead nanopore sequencing laboratory that accelerates biodiversity research while capacitating local researchers to fight the biodiversity crisis.

Biography

Zane Libke is a researcher and educator with a passion for making science accessible to everyone. After receiving his Bachelor’s degree from Davidson College in 2021, Zane moved to Ecuador to start a field genetics lab at Sumak Kawsay In Situ. His research there focuses on better understanding cryptic diversity in the world’s largest vertebrate genus, the direct-developing frogs of the genus Pristimantis , as well as simplifying low-cost genetic sequencing labs. Zane also collaborates with the Mauricio Ortega Lab at the University of IKIAM to conduct field genetic courses and develop interactive teaching methods and materials. As an associate investigator at the National Institute of Biodiversity in Ecuador, Zane collaborates with researchers to study fungi, plant, mammal, herp, and soil microbial diversity with nanopore sequencing. 

Mrinalini Erkenswick Watsa, San Diego Zoo Wildlife Alliance, USA
Mrinalini Erkenswick Watsa

Title

Genomics in the jungle: a field laboratory success story 

Abstract

Conservation genomics has long been bottlenecked by a lack of access to biosamples from rare species within remote ecosystems; but this is changing, and fast. We tackled this bottleneck by flipping the paradigm on its head — why take samples to a lab when you can take labs to the samples? The miniaturisation and portability of sequencing devices is enabling conservation genomics to scale, in situ. Supported by the In Situ Lab Initiative, regional scientists are driving all aspects of the analysis pipeline, from sample to sequence.  

Biography

Dr. Watsa is a Scientist with the Population Sustainability Team at San Diego Zoo Wildlife Alliance. Her work brings cutting-edge genomics to remote parts of the Amazon rainforest as a potent research tool to better understand mammal and avian population structure, disease ecology, and the role that wildlife health may play in the human–wildlife interface. Her work is centered in the Peruvian Amazon, where she provides training in field methods and protocols for safe, ethical catch-and-release programs for animals.  

Recent publications

Watsa, M., and Wildlife Disease Surveillance Focus Group. Rigorous wildlife disease surveillance. Science. 369(6500):145–147 (2020).

Watsa, M., Erkenswick, G., Pomerantz, A., Prost, S. Portable sequencing as a teaching tool in conservation and biodiversity research. PLoS Biol. 18 (4) (2020). 

Reindert Nijland, Wageningen University, Netherlands
Reindert Nijland

Title

Endangered European sturgeon detection through non-amplified eDNA sequencing 

Abstract

The European sturgeon (Acipenser sturio) is critically endangered and no natural breeding population exists. Currently, a reintroduction program is running. We are developing environmental DNA (eDNA) based monitoring to track the reintroduction of the European sturgeon in the rivers and estuaries in the Netherlands. Supported by the ORG.one program, we sequenced the full genome of A. sturio. Initial experiments with eDNA from the tank, housing the sturgeon, demonstrated that this genome data enables direct, unamplified detection of sturgeon eDNA. Ultimately, we will create a biodiversity monitoring system based on eDNA sampling and real-time analyses, including in situ eDNA sequencing.

Biography

Reindert Nijland is a molecular marine ecologist with a focus on the North Sea. He works as an Assistant Professor in the Marine Animal Ecology group at Wageningen University, and enjoys sequencing anything, anywhere, to understand change in marine ecosystems.

Recent publications

Doorenspleet, K. et al. High resolution species detection: accurate long read eDNA metabarcoding of North Sea fish using Oxford Nanopore sequencing. bioRxiv. doi:10.1101/2021.11.26.470087 (2021).

van Kruistum, H. et al. Parallel genomic changes drive repeated evolution of placentas in live-bearing fish. Mol Biol Evol. 38(6):2627–2638 (2021). 

Auditorium
12:10 - 12:20 BST 13:10 - 13:20 CET 7:10 - 7:20 EST
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STUDIO INTERVIEWS

online

Exclusive live speaker interviews from the previous session straight from the London Calling stage

Auditorium
12:15 - 13:00 BST 13:15 - 14:00 CET 7:15 - 8:00 EST
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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

Live lounge
12:50 - 13:05 BST 13:50 - 14:05 CET 7:50 - 8:05 EST
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SHOWCASE STAGE

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Glen Gowers & Bupe Mwambingu, Basecamp Research, UK
Glen Gowers & Bupe Mwambingu

Title

Responsible exploration of our planet's biodiversity towards discovery-enabled biodesign 

Abstract

By partnering with biodiversity hotspots and biotechnology companies across the globe, Basecamp Research is addressing the systemic challenges that limit commercial biodiscovery to date. Through equitable benefit sharing arrangements around the world, Basecamp Research is combining distributed data collection capabilities with purpose-built graph architecture, which gives them a comprehensive and unique view of Earth's metagenome, allowing complex design problems to be addressed with ease. The team at Basecamp Research spans an enormous range of expertise, from explorers and diplomats to data scientists and biotech pioneers.

Biography

Glen is a co-founder of Basecamp Research. Prior to this, Glen was scientific lead on the Return to Vatnajökull Expedition (2019), which sought to become the first team to conduct fully off-grid DNA sequencing in a polar-style environment. Glen has a master’s in biochemistry from the University of Oxford and a Ph.D. in bioengineering from Imperial College, London. Bupe is a biodiversity partnerships manager at Basecamp Research. Trained as a forensic scientist, Bupe is also an elite member of an international emergency disaster response team. Bupe strives to develop international collaborations with benefit-sharing principles around the world and upskilling community STEM skills through education and conservation initiatives.  

Recent publications

Gowers, G. F. et al. Entirely off-grid and solar-powered DNA sequencing of microbial communities during an ice cap traverse expedition. Genes. 10(11): 902 (2019). 

Live lounge
13:15 - 14:05 BST 14:15 - 15:05 CET 8:15 - 9:05 EST
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TRANSCRIPTOMICS BREAKOUT

online onsite

Breakouts: A series of 3 x 10 minute talks followed by a 15-minute panel discussion

Nicola Hall, University of Oxford, UK
Nicola Hall

Title

Multiplexed, long-read CaptureSeq identifies full-length transcript isoforms in the human brain

Abstract

The architecture of full-length human transcript isoforms remains largely unknown, particularly for large and highly spliced genes. We therefore combined CaptureSeq target enrichment with sample barcoding and long-read nanopore sequencing to characterise the full-length transcript isoforms of >1,400 genes in human post-mortem tissue. We focused on voltage-gated calcium channel genes, which are promising psychiatric drug targets but are also expressed in the cardiovascular system. Isoforms identified as enriched in the brain vs. the cardiovascular system could be brain-selective drug targets. The information gained from our approach has the potential to improve transcriptomic annotations and may also identify novel therapeutic targets.  

Biography

Nicola Hall is a postdoctoral researcher at the University of Oxford, Department of Psychiatry. She is using her background in molecular biology and RNA sequencing to investigate gene expression in the human brain. Her current work focuses on the tissue-specific alternative splicing of genes implicated in schizophrenia and bipolar disorder, using targeted sequencing to characterise transcripts. Nicola completed her Ph.D. in 2017 at the University of Oxford, Department of Biochemistry.

Recent publications

Hall, N. A. L., Carlyle, B. C., Haerty, W., Tunbridge, E. M. Roadblock: improved annotations do not necessarily translate into new functional insights. Genome Biol. 22(1):320 (2021). 

Josie Gleeson, The University of Melbourne, Australia
Josie Gleeson

Title

Accurate expression quantification from nanopore direct RNA sequencing with NanoCount

Abstract

Sequencing full-length native RNAs using long-read direct RNA sequencing (DRS) has the potential to overcome many limitations of other sequencing methods that require RNA fragmentation, cDNA synthesis, or PCR. We developed NanoCount for fast, accurate transcript isoform quantification in DRS and demonstrate it outperforms similar methods. Using synthetic controls and human SH-SY5Y cell differentiation into neuron-like cells, we show that DRS accurately quantifies RNA expression and identifies differential expression of genes and isoforms. Our results demonstrate enhanced DRS isoform quantification with NanoCount and establish the ability of DRS to identify biologically relevant differential expression of genes and isoforms.  

Biography

As a Ph.D. candidate in the Clark Laboratory at the University of Melbourne, Josie uses long-read sequencing data to develop new computational tools and characterise neuropsychiatric risk genes. She currently has a focus in the transcriptomics field, applying direct RNA sequencing data from Oxford Nanopore Technologies to human cell types.

Recent publications

Gleeson, J, et al. Accurate expression quantification from nanopore direct RNA sequencing with NanoCount. Nucleic Acids Res. 50(4) (2022). 

Chenchen Zhu, Stanford University, USA
Chenchen Zhu

Title

Systematic assessment of long-read RNA-Seq datasets and its application in transcriptome analysis

Abstract

Recent advances in long-read sequencing enables the direct measurement of transcripts, which requires full-length libraries that differ from short-read RNA-Seq. A systematic understanding of the distinct characteristics of long-read RNA-Seq is much needed. Here, we assess nanopore sequencing data for various library properties. Our analysis shows that truncation in 5’ and 3’ UTR regions and shifts in splice sites are common, imposing a major challenge for accurate transcript analysis. By taking these biases into account, we improve transcript identification and quantification for nanopore sequencing and validate using synthetic controls. These insights will facilitate future transcriptome analysis using nanopore sequencing.

Biography

Chenchen is Postdoc Fellow in Michael Snyder's lab at Stanford University. His work focuses on understanding transcriptional regulation at bulk and single-cell levels. He is also integrating multiomics datasets to identify key regulators that link genotype to complex phenotype. Chenchen has been using nanopore sequencing to study transcript isoforms and splicing changes associated with human diseases. He is keen to develop new methods that take full advantage of long-read sequencing to make new discoveries in biology.

Recent publications

Zhu, C. et al. Single-molecule, full-length transcript isoform sequencing reveals disease-associated RNA isoforms in cardiomyocytes. Nat Commun. 12(1):4203 (2021). 

Bowie room
13:15 - 14:05 BST 14:15 - 15:05 CET 8:15 - 9:05 EST
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DATA ANALYSIS TOOLS

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Eoghan Harrington, Genomic Applications Fellow, Oxford Nanopore Technologies
Eoghan Harrington

Abstract

Sockeye: nanopore-only demultiplexing of single-cell reads

Abstract

The combination of single-cell isolation methods, novel barcoding schemes, and sequencing-based readouts has led to an explosion in the number of single-cell genomic assays available. These assays can be combined to create a multi-modal snapshot of cell state, providing unprecedented insight into the heterogeneity associated with different cell and tissue types, developmental trajectories, and different disease states. Multiple studies have now shown that nanopore sequencing of 10x libraries can be used in tandem with short-read sequencing to provide a more complete view of the transcriptome, revealing transcript isoforms and associated genotypes inaccessible to short reads alone. Several tools have been developed to analyse nanopore-sequenced 10x transcriptome libraries; however, they currently assume access to paired short-read data. Given the throughput and accuracy improvements of the Oxford Nanopore platform, this is no longer necessary for many analyses. Here, we present Sockeye — a bioinformatic pipeline that identifies 10x cell barcodes and UMIs without the use of short-read data, outputting files compatible with common downstream analyses.

Biography

Eoghan Harrington is a Genomic Applications Fellow working out of Oxford Nanopore’s New York City location. He brings over a decade of experience in genome sequencing to bear on his role in the Genomic Applications Group, a multi-disciplinary team tasked with finding novel uses for Oxford Nanopore’s devices and communicating them to a wide audience. 

Rupesh Kesharwani , Human Genome Sequencing Center, Baylor College of Medicine, USA
Rupesh Kesharwani

Title

STRspy-ing hidden variation in forensic DNA profiles with the MinION

Abstract

The high variability characteristic of short tandem repeat (STR) markers is harnessed for human identification in forensic genetic analyses. Despite the power and reliability of current typing techniques, sequence-level information, both within and around STRs, are masked in the length-based profiles generated. Here, we evaluate the forensic applicability of nanopore sequencing using reads produced on the MinION device and analyzed with STRspy, a novel method capable of producing length- and sequence-based STR allele designations. STRspy generated accurate genotypes across all autosomal STR loci amplified at 30 PCR cycles with 100% concordance and even achieves high concordance at 15 PCR cycles.

Biography

Rupesh Kesharwani is a senior bioinformatics programmer at Baylor College of Medicine (BCM), USA. His research focuses on developing bioinformatics workflows for NGS platforms, including RNA-Seq, Iso-Seq, as well as STR DNA profiling in forensic investigation. Dr. Kesharwani worked as an application computational scientist at the Jackson lab in the US for three years before joining BCM. In 2012, Rupesh won an international scholarship to study in Italy, where he earned his Ph.D. and post-doc from the University of Pavia. During his research, he focused on understanding the molecular mechanism of miRNome and transcriptome in cardiac aging.

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).

Mc Cartney, A. M. et al. An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates. F1000Res. 10:246 (2021).

Kesharwani, R. K., Chiesa, M., Bellazzi, R., and Colombo, G. CBS-miRSeq: A comprehensive tool for accurate and extensive analyses of microRNA-sequencing data. Comput Biol Med. 110:234–243 (2019). 
 

The Clash Room
13:15 - 14:05 BST 14:15 - 15:05 CET 8:15 - 9:05 EST
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HUMAN CLINICAL RESEARCH

online onsite

Breakouts: A series of 3 x 10 minute talks followed by a 15-minute panel discussion

Ivo Gut, CNAG-CRG, Spain
Ivo Gut

Title

Novel method for multiplexed, full-length single-molecule sequencing of human mitochondrial DNA using Cas9-mediated enrichment 

Abstract

Traditional methods to reconstruct the mitochondrial DNA (mtDNA) sequence are challenged. They fail to determine variant phase, to capture multiple deletions, and to cover the mitochondrial genome evenly. Here, we describe a method to target, multiplex, and sequence at high coverage full-length human mitochondrial genomes as native single molecules, utilizing the RNA-guided DNA endonuclease Cas9. Combining Cas9 induced breaks that define the mtDNA beginning and end of the sequencing reads, as barcodes, we achieve high demultiplexing specificity and delineation of the full-length of the mtDNA, regardless of the structural variant pattern. Data analysis is done with a newly developed pipeline with our software baldur, which efficiently detects single nucleotide heteroplasmy to below 1%, physically determines phase, and accurately disentangles complex deletions. Our workflow is a unique tool for studying mtDNA variation in health and disease, and will accelerate mitochondrial research.

Biography

Dr. Gut is Director of the Centro Nacional de Análisis Genómico (CNAG-CRG), one of the largest genome sequencing centers in Europe, which handles around 400 projects per year, many from study design, to sequencing, and bioinformatic analysis. He is the author of more than 400 research papers, 11 reviews, and 12 book chapters, cited over 55,000 times, inventor of 26 patents or patent applications, founder of 4 biotech start-ups, and serves on numerous international advisory boards. 

Anne Kristine Schack, University of Copenhagen & gMendel, Denmark
Anne Kristine Schack

Title

A novel assay based on Oxford Nanopore technology for potential mass screening of Klinefelter syndrome

Abstract

Klinefelter syndrome (KS) is the most common and most underdiagnosed sex chromosomal abnormality, with a prevalence of 1 in 500 male births, leading to a variety of clinical features including infertility. Multiple studies demonstrate that if treated in a timely manner (e.g. with hormonal therapy and early fertility management) boys affected with KS can have a normal life, with a 25% chance to achieve fertility. The key element in successful treatment of KS is a timely diagnosis. Here, we present research demonstrating a cost-effective, end-to-end assay with potential diagnostic utility for postnatal detection of KS based on Oxford Nanopore technology. The research suggests the technology could be applied for detection of any other genetic disorder.

Biography

Anne Kristine Schack is an all-year-round open-water swimmer with a master’s degree in microbiology from the University of Copenhagen. She is currently a researcher at gMendel and is completing her Ph.D. at the University of Copenhagen. 

Steven Verbruggen, OHMX.bio, Belgium
Steven Verbruggen

Title

HLA typing using targeted third-generation sequencing methods

Abstract

Detailed typing of the extremely variable human leukocyte antigens (HLA) is necessary to check for transplantation compatibility and to investigate auto-immune disorders. Nanopore sequencing allows detailed typing with reduced levels of sequencing artefacts, costs, and workload. The longer reads also reduce the complexity of the downstream data analysis. On top of that, targeted sequencing strategies for nanopore sequencing allows specific enrichment of long reads in the different HLA regions without using PCR. Two approaches of targeted sequencing were demonstrated to yield major advantages for HLA typing: CRISPR/Cas9 enrichment and adaptive sampling.

Biography

After graduating as a biomolecular bioscience engineer, Steven Verbruggen continued with a Ph.D. in bioinformatics, focusing on multiomics data analysis. After obtaining his doctoral degree, he started shaping the bioinformatics side of the start-up company OHMX.bio, a service provider that helps customers solve their biological questions over different omics fields using cutting-edge technologies. Within 
OHMX.bio, there is a strong focus towards nanopore sequencing. In addition, Steven is also still affiliated as a researcher to Ghent University (Belgium). 

Blondie room
14:10 - 14:55 BST 15:10 - 15:55 CET 9:10 - 9:55 EST
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FLOW CELL LOADING

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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

Live lounge
14:20 - 14:40 BST 15:20 - 15:40 CET 9:20 - 9:40 EST
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SECRET CINEMA

onsite ondemand
Alvin Ng, Early Cancer Institute, University of Cambridge, CRUK Cambridge Institute, UK
Alvin Ng

Title

Early detection of Barrett’s esophagus and esophageal adenocarcinoma using Oxford Nanopore long-read sequencing 

Abstract

Esophageal adenocarcinoma (EAC) has a poor five-year survival rate of <20%. Its precursor lesion Barrett's oesophagus (BE) provides an ideal opportunity to detect and treat cancer transformation at an earlier stage. We sequenced BE biopsies and EAC tumours, using Oxford Nanopore long reads, to detect genetic alterations arising in early and late disease stages. We identified complex rearrangements and carried out de novo assembly of the extrachromosomal DNA (ecDNA) reads from BE and EAC. In a same patient with EAC and adjacent BE, we reconstructed an ecDNA harbouring the ERBB2 oncogene, associated with more severe disease and progression to EAC.

Biography

Dr. Alvin Ng is a computational postdoctoral scientist in the Fitzgerald lab. Alvin developed his expertise in cancer genomics during his Ph.D. at Duke-NUS in Singapore. His current research aims to understand the biological processes leading to genetic instability and to detect large-scale rearrangements in gastrointestinal cancers. He aims to use those findings to develop translational approaches to detect genetic lesions in patients with the premalignant disease of Barrett’s esophagus, who are at a higher risk of developing esophageal cancer.

Recent publications

Ng, A. W. T. et al. Rearrangement processes and structural variations show evidence of selection in oesophageal adenocarcinomas. Commun Biol. 5(1):335 (2022). 

Anna Dolnik, Charité University Medicine Berlin, Germany
Anna Dolnik

Title

Combined CRISPR/Cas9 targeted enrichment and whole-genome sequencing allows real-time stratification of acute myeloid leukemia (AML) 

Abstract

Prompt testing of European LeukemiaNet molecular markers is pivotal for the risk stratification and treatment of AML patients. We have established a two-step 72-hour assay. First, based on targeted enrichment using a CRISPR/Cas9 system, relevant target regions such as FLT3, t(8;21), inv(16), and MLL translocations can be well covered (~44-fold coverage). Secondary whole-genome sequencing results in ~2-fold genome coverage with a copy number variation resolution of 0.1 Mbp. While additional testing of this AML panel within round-robin tests are warranted, introduction of this real-time sequencing approach could ultimately lead to improved leukemia diagnostics and patient-management.

Biography

Anna Dolnik is a post-doc at the Charité University Medicine Berlin, Germany. In 2016, Anna first obtained experience in Oxford Nanopore technology through resequencing of novel fusion genes found in acute myeloid leukemia (AML) with complex karyotype. Since the end of 2018, the lab routinely use a GridION for better characterization of hematologic malignancies. The focus of Anna’s research is clonal evolution in AML, identification of cancer driving genes, and characterization of complex changes in cancer genomes by whole-genome sequencing. 

Secret cinema
14:20 - 14:35 BST 15:20 - 15:35 CET 9:20 - 9:35 EST
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MINI THEATRE: Using nanopore sequencing to ensure the quality of mRNA vaccines

online onsite
Tim Mercer, AIBN/The University of Queensland, Australia
Tim Mercer

Abstract

Billions of mRNA vaccine doses have been manufactured during the COVID-19 pandemic. The removal of contaminating RNAs and inclusion of modified nucleotides reduces the innate immune response and improves the translation and performance of mRNA vaccines. Here we show how nanopore sequencing can analyse the manufacture and quality of mRNA vaccines. Nanopore sequencing enables quantitative analysis of mRNA vaccine sequences, length, and purity, including detection of off-target RNA impurities. Direct RNA sequencing can also measure the incorporation of modified nucleotides and 5’ capping of mRNA vaccines. Together, this shows how nanopore sequencing can inform best manufacturing practices, routinely monitor batch quality, and provide a detailed characterisation of the final mRNA vaccine product.

Biography

Tim Mercer is a Group Leader at the AIBN, The University of Queensland (www.mercerlab.org), and Director of BASE, a leading Australian facility for manufacturing and research into mRNA vaccines and therapies (www.basefacility.org.au). Tim Mercer and his team are developing new manufacturing processes, analytical methods, and next-generation RNA technologies to realise the potential of synthetic mRNA vaccines and therapies in treating disease. 

Blondie room
15:10 - 15:25 BST 16:10 - 16:25 CET 10:10 - 10:25 EST
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LIGHTNING TALKS

online onsite
Nick Vereecke, PathoSense BV, Belgium
Nick Vereecke

Title

Emergence of new multi-resistant Brachyspira hyodysenteriae strains in Belgian pigs, revealed by high-quality whole-genome sequencing 

Abstract

Swine dysentery (SD) caused by Brachyspira hyodysenteriae results in economic losses in swine producing countries worldwide. Increased number of SD outbreaks raised fear in Belgium as treatment would be hampered due to increased (multi-)resistance against commonly used antibiotics. Therefore, 90 Belgian B. hyodysenteriae strains (2018–2020) were analyzed with agar dilution testing and high-quality whole-genome sequencing. While multi-resistance was observed in 39.5% of strains, the presence of genetic hallmarks (e.g. tva(A)) raised the question on re-evaluation of phenotypic antimicrobial testing cut-offs in respect to the use of these hallmarks in rapid genomic antimicrobial resistance testing in the near future.

Biography

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

Recent publications

Bokma, J. and Vereecke, N. et al. Evaluation of nanopore sequencing as a diagnostic tool for the rapid identification of Mycoplasma bovis from individual and pooled respiratory tract samples. J Clin Microbiol. 59(12) (2021).  

Bokma, J and Vereecke, N. et al. Genome-wide association study reveals genetic markers for antimicrobial resistance in Mycoplasma bovis. Microbiol Spectr. 9(2) (2021).  

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

Luna van der Loos, Ghent University, Belgium
Luna van der Loos

Title

Salinity structures the microbiome of the green seaweed Ulva

Abstract

The green seaweed, Ulva, is a model system to study seaweed–bacteria interactions, but the impact of environmental drivers on holobiont dynamics is little understood. In this study, we investigated Ulva-associated bacteria across the Atlantic–Baltic Sea salinity gradient, along a 2,000 km coastline with a total of 481 samples. Our results demonstrate that Ulva-associated bacterial composition was strongly structured by both salinity and host species, contradicting earlier statements that Ulva-associated bacterial communities are taxonomically highly variable across individuals and largely stochastically defined. Characteristic bacterial communities associated with distinct salinity regions may therefore facilitate the host’s adaptation across the environmental gradient.

Biography

Luna van der Loos is a marine biologist who studies seaweed ecology, biodiversity, and physiology. Her Ph.D. focuses on the effect of the environment on seaweed–bacteria interactions, particularly the green seaweed Ulva. With nanopore sequencing, Luna characterizes Ulva-associated microbiomes across natural salinity gradients, in aquaculture facilities, and successional patterns through time. Current and future nanopore-related work includes sequencing the full genome of Ulva species and their bacterial partners.

Recent publications

van der Loos, L. M. et al. Salinity and host drive Ulva associated bacterial communities across the Atlantic‐Baltic Sea gradient. Molecular Ecology. doi: 10.1111/mec.16462 (2022).

van der Loos, L. M., D’hondt, S., Willems, A., and De Clerck, O. Characterizing algal microbiomes using long-read nanopore sequencing. Algal Research. 59:102456 (2021). 

Auditorium
15:25 - 16:15 BST 16:25 - 17:15 CET 10:25 - 11:15 EST
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ONLINE BREAKOUT: METHYLATION

online
Daniel Snell​, The Francis Crick Institute, UK
Daniel Snell​

Title

ReadFish enables characterisation of genome editing outcomes at the dosage compensation locus, RSX, in opossum fibroblasts

Abstract

In the short-tailed grey opossum, a metatherian mammal, the non-coding RNA RSX is a candidate for mediating sex chromosome dosage compensation by X chromosome inactivation. Here, we used CRISPR-Cas genome editing to ablate expression of RSX in a female opossum fibroblast cell line. In order to characterise the nature of the edits in this highly repetitive locus, we utilised ReadFish, an implementation of target enrichment on the MinION. We validated the exact size of edits in seven sub-clonal cell lines, achieving up to 36x coverage of the RSX locus and five-fold enrichment, relative to the whole X chromosome.

Biography

Daniel studied neuroscience as an undergraduate, before embarking on medical studies at UCL. He joined the MBPh.D. programme in order to integrate a Ph.D. within his medical studies, which he completed under the supervision of James Turner at the MRC National Institute for Medical Research. During both his Ph.D. and subsequent post-doctoral work, Daniel has been fascinated by the mammalian sex chromosomes; and most recently, he has begun a technology development role within the Advanced Sequencing Facility at The Francis Crick Institute. 

Eveliina Hanski, University of Oxford, UK
Eveliina Hanski

Title

From laboratory to the wild: a non-invasive, MinION-based method for determining the epigenetic age of mice

Abstract

We present a non-invasive method for determining epigenetic age in mice. Using faecal samples as a source of DNA, we measured methylation rates across four genes associated with age. We built an epigenetic clock using lab mice and used it to age wild mice with unknown chronological age. We show that the rate of epigenetic aging is consistent in lab mice but highly variable in wild mice, underlining the potential effect of genetics and/or environment on epigenetic aging. The method allows investigation of the drivers of epigenetic age over time not only in the laboratory but also in the wild.

Biography

Eveliina Hanski is a Ph.D. candidate working on host–microbiota interactions in humans and mice. In her mouse work, she uses both laboratory and wild mice. She is particularly interested in age-related dynamics in the gut microbiota, which has led her to work on a method for acquiring epigenetic age estimates from faecal samples. 

Eduardo Eyras​, Australian National University, Australia
Eduardo Eyras​

Title

RNA methylation detection at single-molecule resolution uncovers isoform-specific modifications during mouse brain development

Abstract

We describe a new computational tool that enables, for the first time, the identification of RNA modifications in individual nanopore read signals at single-nucleotide resolution and in any sample. Using extensive benchmarking with data from synthetic and natural RNA, we demonstrate a higher accuracy than other methods at detecting m6A and m5C transcriptomic sites and quantifying their stoichiometry levels. Application to mouse embryonic samples uncovers isoform-specific modifications during brain development that are altered in a mouse model of autism. Our strategy can be expanded to other modifications to unveil the full span of the epitranscriptome in normal and disease conditions.

Biography

Eduardo Eyras is an internationally recognised expert in the development of computational methods to study RNA biology. His significant contributions to the field include describing the conservation of RNA splicing across mammals, pioneering the use of machine learning to uncover mechanisms of RNA processing, and producing the first comprehensive catalogue of RNA splicing alterations and their functional impacts in cancer. Eyras currently leads an interdisciplinary research group developing innovative methods to study transcriptomes using nanopore sequencing technologies.

Recent publications

Acera Mateos P. et al. Identification of m6A and m5C RNA modifications at single-molecule resolution from nanopore sequencing. bioRxiv. 484124 (2022).

De la Rubia, I. et al. Reference-free reconstruction and quantification of transcriptomes from nanopore long-read sequencing. bioRxiv. 939942 (2020). 

Blondie room
15:25 - 15:50 BST 16:25 - 16:50 CET 10:25 - 10:50 EST
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Genetic dissection of structural variants in study subjects with antithrombin deficiency by nanopore sequencing

online onsite
Belén de la Morena Barrio, University of Murcia/CIBERER, Spain
Belén de la Morena Barrio

Abstract

The characterization of structural variants (SVs) is challenging. In antithrombin deficiency (ATD), MLPA detects SVs in >8% of cases but does not characterize the SV. We run long-range PCR, NGS, CGH array, and/or nanopore sequencing in 35 study subjects with SVs detected by MLPA, showing the limitations and strengths of these methods. Nanopore sequencing identified all SVs independently of size or type, resolved conflictive results, identified the first complex SV involved in this disorder, and determined the mechanism involved in all these SVs. Moreover, nanopore sequencing also detected a retrotransposon insertion in two cases with ATD and unknown molecular base. Our study underscores the utility of nanopore sequencing to identify and fully characterize SVs.

Biography

Belén de la Morena Barrio graduated in Pharmacy in 2015. In 2021, she obtained an International Ph.D. in Medicine from the University of Murcia. She has published 17 articles, with six as first author. Currently, Belén has a postdoctoral contract at the University of Murcia/CIBERER, Spain. Her research is focused on the use of nanopore sequencing for the identification of new molecular mechanisms involved in rare diseases. She has also launched Longseq, a company offering nanopore sequencing services.

Recent publications

de la Morena-Barrio, B. et al. Molecular dissection of structural variations involved in antithrombin deficiency. J Mol Diagn. doi: 10.1016/j.jmoldx.2022.01.009 (2022). 

Auditorium Human genomics
15:50 - 16:15 BST 16:50 - 17:15 CET 10:50 - 11:15 EST
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Comprehensive structural variant detection: from population to mosaic level

online onsite
Fritz Sedlazeck , Baylor College of Medicine, USA
Fritz Sedlazeck

Abstract

Constant advancements of Oxford Nanopore technology both in cost and error rates are transforming it into a workhorse of genomics analysis, capable of identifying SNVs, structural variants, and methylation. We developed Sniffles2, a successor to SV-detection method Sniffles. Sniffles2 increases both accuracy (e.g. genotype, insertion detection) and speed, and has more advanced functionality (e.g. population and somatic SV calling) to further promote new insights into the organism or diseases. In addition, we will report on novel development together with Oxford Nanopore to further improve our characterization of genomic variations across single cells at scale and provide insights into the current understanding of disease-driving genomic variations.

Biography

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

Recent publications

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

Auditorium Structural variation
16:15 - 16:25 BST 17:15 - 17:25 CET 11:15 - 11:25 EST
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STUDIO INTERVIEWS

online

Exclusive live speaker interviews from the previous session straight from the London Calling stage

Auditorium
16:20 - 16:55 BST 17:20 - 17:55 CET 11:20 - 11:55 EST
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POSTER NETWORKING

online onsite

Join poster presenters in person and online, ask questions, network with your peers, and vote for your favourite poster

Posters
16:20 - 16:55 BST 17:20 - 17:55 CET 11:20 - 11:55 EST
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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

Live lounge
16:25 - 16:45 BST 17:25 - 17:45 CET 11:25 - 11:45 EST
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SECRET CINEMA

onsite ondemand
Alejandro Gener, Public Health Laboratories, Los Angeles County Department of Public Health, USA
Alejandro Gener

Title

Assembly deconvolution resolves SARS-CoV-2 haplotypes in Delta-Omicron co-infections 

Abstract

SARS-CoV-2 baseline surveillance requires read-mapping onto a reference, yielding individual assemblies. This process obscures any intra-host viral sequence heterogeneity. Delta/Omicron strains co-circulated in Los Angeles during the winter of 2021. We sequenced two samples referred to us from our clinical laboratory partners. Their assemblies exhibited ambiguities indicative of co-infection. We screened loci of aligned read datasets to rapidly identify and/or rule out suspected Delta-Omicron coinfections. We developed a reference-based assembly deconvolution method to resolve each consensus sequence from suspected co-infecting viruses. Our experience illustrates the benefit of having raw sequencing data and/or aligned reads available in addition to genome assemblies.

Biography

Alejandro (Alex) Gener is a postdoctoral Bioinformatics Fellow at the Los Angeles County Public Health Laboratories, funded by the Association of Public Health Laboratories and the US Centers for Disease Control and Prevention. His current responsibilities include SARS-CoV-2 and recently Candida auris genomic surveillance. He is a non-traditional physician-scientist in-training, earning his Ph.D. at Baylor College of Medicine, where he defined an HIV-1 mRNA Atlas. Prior to that, he completed three out of four years of medical school at Universidad Central del Caribe.    

Recent publications

Gener, A. R. Anticipating HIV drug resistance with appropriate sequencing methods, AIDS. 36(1): 147–148 (2022).  

David Brandt, Center for Biotechnology, Bielefeld University, Germany
David Brandt

Title

Nanopore sequencing of native adeno-associated virus (AAV) single-stranded DNA using a transposase-based rapid protocol 

Abstract

Next-generation sequencing of single-stranded DNA (ssDNA) enables transgene characterization of gene therapy vectors such as adeno-associated virus (AAV), but current library generation uses complicated and potentially biased second-strand synthesis. We report that libraries for nanopore sequencing of ssDNA can be conveniently created without second-strand synthesis using a transposase-based protocol. We show for bacteriophage M13 ssDNA that the MuA transposase has unexpected residual activity on ssDNA, explained in part by transposase action on transient double-stranded hairpins. In the case of AAV, library creation is additionally aided by genome hybridization. We demonstrate the power of direct sequencing combined with nanopore long reads by characterizing AAV vector transgenes.

Biography

In 2011, David Brandt started his bachelor’s studies of Molecular Biotechnology and continued with his master’s studies in Genome-based Systems Biology at Bielefeld University, Germany. Since 2017, David has been working as a research associate at the Center for Biotechnology, Bielefeld, Germany (Kalinowski Lab), with a focus on bioinformatics and next-generation sequencing of viruses and organisms all across the tree of life.

Recent publications

Brandt, D. et al. Multiple occurrences of a 168-nucleotide deletion in SARS-CoV-2 ORF8, unnoticed by standard amplicon sequencing and variant calling pipelines. Viruses. 13(9):1870 (2021).

Radukic, M., Brandt, D., Haak, M., Müller, K., and Kalinowski, J. Nanopore sequencing of native 
adeno-associated virus (AAV) single-stranded DNA using a transposase-based rapid protocol. NAR Genom Bioinform. 2(4) (2020). 

Secret cinema
16:40 - 16:55 BST 17:40 - 17:55 CET 11:40 - 11:55 EST
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SHOWCASE STAGE

onsite
Ashley Beck, Carroll College, USA
Ashley Beck

Title

Applying nanopore sequencing in the undergraduate classroom for environmental microbiome analysis

Abstract

Exposing students to cutting-edge genomic tools in a real-world context is essential to prepare them as future global problem solvers. Nanopore sequencing provides an excellent platform for integrating education and research, and has been applied in undergraduate labs at Carroll College in Helena, Montana, USA. Students have investigated environmental impacts on microbial diversity using MinION technology, with projects focusing on a mining-contaminated river, a lead-contaminated smelter site, and local drinking water. The presented work highlights their 16S composition results and also reports on the student experience through survey analysis, identifying key themes regarding technical ability and perception of research.  

Biography

Ashley Beck is an Assistant Professor of Genetics in the Biology Department at Carroll College where she is dedicated not only to educating the next generation of scientists but also providing extensive research training for interested students. Her research focuses on understanding microbial community interactions and their response to environmental pressures through metabolic modeling, and she has recently begun exploring nanopore technology as a means to investigate the complexity of natural microbiomes. 

Reindert Nijland, Wageningen University, Netherlands
Reindert Nijland

Title

Nanopore sequencing for biodiversity assessment in an educational setting

Abstract

The European sturgeon (Acipenser sturio) is critically endangered and no natural breeding population exists. Currently, a reintroduction program is running. We are developing environmental DNA (eDNA) based monitoring to track the reintroduction of the European sturgeon in the rivers and estuaries in the Netherlands. Supported by the ORG.one program, we sequenced the full genome of A. sturio. Initial experiments with eDNA from the tank, housing the sturgeon, demonstrated that this genome data enables direct, unamplified detection of sturgeon eDNA. Ultimately, we will create a biodiversity monitoring system based on eDNA sampling and real-time analyses, including in situ eDNA sequencing.

Biography

Reindert Nijland is a molecular marine ecologist with a focus on the North Sea. He works as an Assistant Professor in the Marine Animal Ecology group at Wageningen University, and enjoys sequencing anything, anywhere, to understand change in marine ecosystems.

Recent publications

Doorenspleet, K. et al. High resolution species detection: accurate long read eDNA metabarcoding of North Sea fish using Oxford Nanopore sequencing. bioRxiv. doi:10.1101/2021.11.26.470087 (2021).

van Kruistum, H. et al. Parallel genomic changes drive repeated evolution of placentas in live-bearing fish. Mol Biol Evol. 38(6):2627–2638 (2021). 

Live lounge
17:05 - 17:30 BST 18:05 - 18:30 CET 12:05 - 12:30 EST
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Portable real-time sequencing to safeguard critically endangered wildlife

online onsite
Marissa Le Lec, University of Otago, New Zealand
Marissa Le Lec

Abstract

An increasing number of wild species are on the brink of extinction, rendering them vulnerable to inbreeding and catastrophic events. Here, we leveraged in situ real-time sequencing to safeguard the kākāpō, a critically endangered parrot endemic to New Zealand. We established in situ DNA extraction, nanopore sequencing, and data analysis on a remote sanctuary island to provide conservationists rapid access to genomic monitoring approaches. We assessed the success rate of artificial insemination through parentage analyses of kākāpō chicks, determined their sex for adjusting healthcare requirements, and monitored recurring Aspergillosis outbreaks. This approach has opened completely new avenues for safeguarding endangered species and for rapidly adjusting their conservation management.

Biography

Marissa is a final-year Ph.D. student at the University of Otago in New Zealand. Her current and future research aspirations centre around the application of cutting-edge genomics to monitor biodiversity or inform conservation, as well as better understanding evolution in small populations.  

Recent publications

Cheng, H. et al. Haplotype-resolved assembly of diploid genomes without parental data. Nat Biotechnol. doi: 10.1038/s41587-022-01261-x. online ahead of print. (2022)

Oberle, A. et al. 16S rRNA long-read nanopore sequencing is feasible and reliable for endometrial microbiome analysis. Reprod Biomed Online. 42(6):1097-1107 (2021). 

Lara Urban, Helmholtz Munich, Germany
Lara Urban

Abstract

An increasing number of wild species are on the brink of extinction, rendering them vulnerable to inbreeding and catastrophic events. Here, we leveraged in situ real-time sequencing to safeguard the kākāpō, a critically endangered parrot endemic to New Zealand. We established in situ DNA extraction, nanopore sequencing, and data analysis on a remote sanctuary island to provide conservationists rapid access to genomic monitoring approaches. We assessed the success rate of artificial insemination through parentage analyses of kākāpō chicks, determined their sex for adjusting healthcare requirements, and monitored recurring Aspergillosis outbreaks. This approach has opened completely new avenues for safeguarding endangered species and for rapidly adjusting their conservation management.

Biography

Lara just started her own research group as a Principal Investigator at Helmholtz Munich, AI for Health and the Helmholtz Pioneer Campus, where her team will focus on applying genomics and AI for the benefit of planetary health. During her Ph.D. at the University of Cambridge and EMBL-EBI, she previously developed methodology in the fields of statistical genomics and deep learning, to then apply this expertise in the context of biodiversity conservation as a Humboldt Fellow in New Zealand.

Recent publications

Urban, L. et al. Freshwater monitoring by nanopore sequencing. Elife. 10:e61504 (2021).

Cheng, H. et al. Haplotype-resolved assembly of diploid genomes without parental data. Nat Biotechnol. doi: 10.1038/s41587-022-01261-x. online ahead of print. (2022)

Oberle, A. et al. 16S rRNA long-read nanopore sequencing is feasible and reliable for endometrial microbiome analysis. Reprod Biomed Online. 42(6):1097-1107 (2021). 

Auditorium Population genomics
17:30 - 17:55 BST 18:30 - 18:55 CET 12:30 - 12:55 EST
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De novo assembly of immunoglobulin loci linked to full-length single-cell transcriptome of antigen-specific plasmablasts

online onsite
Christian Stevens, Icahn School of Medicine at Mount Sinai, USA
Christian Stevens

Abstract

In this study, following an MMR booster, plasmablasts and memory B cells were collected and characterized via scRNA-Seq. In individual cells, we successfully identified and paired full-length heavy and light chains. A subset were synthesized and their antigen-binding potency was evaluated against live virus. Additionally, we sequenced the donor’s germline V/D/J/C genes making up their personalized immune repertoire, with implications for identifying genes in these loci important for mounting a robust immune response. We also found expression differences in genes known to affect the glycosylation phenotype and effector function of antibodies. Our pipeline significantly expands the possibilities of personalized immunology.  

Biography

Christian is an MD/Ph.D. candidate in the lab of Benhur Lee. His work has focused on emerging zoonotic viruses, such as Nipah virus and SARS-CoV-2, viral engineering to deliver gene editing tools, and expanding the bioinformatics capacity in the Lee lab. He also has an interest in science policy and communication, and working to understand how physician-scientists can best serve as successful advocates. 

Auditorium Immunology
17:55 - 18:00 BST 18:55 - 19:00 CET 12:55 - 13:00 EST
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Closing remarks

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


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

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

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

Auditorium
18:00 - 18:10 BST 19:00 - 19:10 CET 13:00 - 13:10 EST
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STUDIO INTERVIEWS

online

Exclusive live speaker interviews from the previous session straight from the London Calling stage

Auditorium