Application of nanopore sequencing in clinical haematology
Professor Schuh completed academic and clinical haematology training in Oxford and in 2006, she was appointed clinical lead for haematology laboratories, including molecular diagnostics, and has also been the clinical lead for chronic lymphocytic leukaemia and other lymphoproliferative disorders for the NHS Thames Valley Cancer Network. Over the past twelve years she has led over 30 early and late phase clinical trials in leukaemia as a principle or national chief investigator. A number of these led to NICE approvals and have changed clinical practice for patients in the UK and worldwide. As a result, she was recently appointed as the Chair of Chronic Lymphocytic Leukaemia Research in the UK by the National Cancer Research Institute. In addition to other national and international roles, she has also chaired the UK CLL Forum since 2016 that promotes training and education, and she has led the UK's guidelines writing group for CLL Therapy on behalf of the British Society of Haematology. Her second research interest is with the development, evaluation and implementation of new technologies for Precision Diagnostics, especially genomics. Her group published the first ever longitudinal study of the changes in the genomic landscape of patients undergoing treatment for leukaemia. She is the lead for the Genomics England Clinical Interpretation Partnership for haematological malignancies. Professor Schuh has received grants from the NIHR, Wellcome Trust, Technology Strategy Board, Cancer Research UK and Bloodwise and she has authored or co-authored over 80 peer-reviewed publications in the last five years.
The Ohio State University
Oxford Nanopore Technologies
Clive is Chief Technology Officer at Oxford Nanopore Technologies. On the Executive team, he is responsible for all of the Company’s product-development activities. Clive leads the specification and design of the Company’s nanopore-based sensing platform, including strand DNA/RNA sequencing and protein-sensing applications with a strong focus on scientific excellence and successful adoption by the scientific community.
Clive joined Oxford Nanopore Technologies from the Wellcome Trust Sanger Institute (Cambridge, UK) where he played a key role in the adoption and exploitation of next-generation DNA sequencing platforms. This involved helping to set up the world’s largest single installation of Illumina (formerly Solexa) Genome Analyzers in a production sequencing environment, initially used to pioneer the 1000 Genomes Project. From early 2003 he was Director of Computational Biology and IT at Solexa Ltd, where he was central to the development and commercialisation of the Genome Analyzer (GA). Solexa was sold to Illumina for $650m in early 2007 after the successful placement and adoption of 12 instruments. The Solexa technology, now commercialised by Illumina, is the market-leading DNA sequencing technology driving the renaissance in DNA-based discovery.
He has a strong background in computer science and genetics/molecular biology and manages interdisciplinary teams including mechanical engineering, electronics, physics, surface chemistry, electrophysiology, software engineering and applications (of the technology). Clive applies modern agile management techniques to the entire product-development lifecycle. Clive has also held various management and consulting positions at GlaxoWellcome, Oxford Glycosciences and other EU- and US-based organisations. He has worked at the interface between computing and science, ranging from genetics to proteomics. He holds degrees in Genetics and Computational Biology from the University of York.
Oxford Nanopore Technologies
Dan Turner is Vice President of Applications at Oxford Nanopore Technologies and is a highly experienced scientist who has worked in the field of next-generation sequencing for the last 11 years. Dan provides scientific 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 illustrate the benefits of these technologies to the wider world. Before joining Oxford Nanopore Technologies, Dan was Head of Sequencing Technology Development at the Wellcome Trust Sanger Institute, and prior to this he held postdoctoral positions at the Sanger Institute and Cornell University Medical College in Manhattan.
Telomere-to-telomere assembly of a complete human X chromosome
Release of the first human genome assembly was a landmark achievement, and after nearly two decades of improvements, the current human reference genome (GRCh38) is the most accurate and complete vertebrate genome ever produced. However, no one chromosome has yet been finished end to end, and hundreds of gaps persist across the genome. These unresolved regions include segmental duplications, ribosomal rRNA gene arrays, and satellite arrays that harbor unexplored variation of unknown consequence. We aim to finish these remaining regions and generate the first truly complete assembly of a human genome.
Here we announce a whole-genome de novo assembly that surpasses the continuity of GRCh38, along with the first complete, telomere-to-telomere assembly of a human X chromosome. In total, we collected 40X coverage of ultra-long Oxford Nanopore sequencing for the CHM13hTERT cell line, including 44 Gb of sequence in reads >100 kb and a maximum read length exceeding 1 Mb. This unprecedented coverage of ultra-long reads enabled the resolution of most repeats in the genome, including large fractions of the centromeric satellite arrays and short arms of the acrocentrics. A de novo assembly combining this nanopore data with 70X of existing PacBio data achieved an NG50 contig size of 75 Mb (compared to 56 Mb for GRCh38), with some chromosomes broken only at the centromere. Using this assembly as a basis, we chose to manually finish the X chromosome. The few unresolved segmental duplications were assembled using ultra-long reads spanning the individual copies, and the ~2.3 Mbp X centromere was assembled by identifying unique variants within the array and using these to anchor overlapping ultra-long reads. These results demonstrate that it is now possible to finish entire human chromosomes without gaps, and our future work will focus on completing and validating the remainder of the genome.
Karen H. Miga, PhD, is an Assistant Research Scientist at UCSC. Dr. Miga’s research program combines innovative computational and experimental approaches to produce the high-resolution sequence maps of human centromeric and pericentromeric DNAs.
Identification of new somatic structural variants and cancer driver genes using long-read nanopore sequencing
Third generation DNA sequencing technologies have been transforming genome medicine and cancer research, producing evidences for structural variations (SV’s) being the common and major driver of complex diseases and tumorigenesis. By taking advantage of the un-parallelled power of long-read and high-throughput capability of the Oxford Nanopore PromethION platform, we investigated the role of SV’s in cancer development. We sequenced DNA obtained from colorectal cancer biopsy and corresponding normal tissue-samples of Han Chinese. Using a comprehensive SV-calling pipeline that consists of ngmlr-sniffle, dynamic filtering, database search and comparison, manual curation, and break point mapping, we obtained high quality SV call sets. By using PCA, population structure, and frequency spectrum analyses, we identified a set of SV’s that are tumor specific. In addition to somatic point mutations in mismatch repair genes that are well known for causing colorectal cancers, we observed complex somatic SV’s that show evidence of chromothriptic rearrangements, the hallmark of the late stage tumors, that were focally localized to a terminal region of a chromosome in colorectal cancer samples. One of the complex somatic rearrangements was linked to the amplification of the gene that is essential for DNA recombination. Furthermore, we also observed a direct link between the expansion of microsatellites and SV’s, suggesting the microsatellite instability might drive the formation of SV’s and cause genome instability in colorectal cancers. Collectively, our results present the power of the Oxford Nanopore PromethION platform for high resolution analysis of SV’s in the human genome, which can lead to a better understanding of the molecular, biochemical, and cellular events that govern tumor progression.
As Director of the Grandomics Genome Institute, Min works with a talented group of scientists and technologists who develop new genomic solutions to enhance the strengths of the Oxford Nanopore platform for genome science and genome medicine. His team integrates existing and new methods to create a comprehensive pipeline to produce complete animal and plant genomes with a minimum number of gaps. His team also studies the origin, mechanisms, and roles of SV’s in adaptive evolution, complex diseases, and tumorigenesis.
Revealing mRNA alternative splicing complexity in the human brain
Nicola Hall is a postdoctoral researcher at the University of Oxford in Department of Psychiatry with the Tunbridge group. She is using her background in molecular biology and RNA sequencing to investigate gene expression in the human brain. Her current work focuses on alternative splicing of the calcium channel CACNA1C, implicated in schizophrenia and bipolar disorder. Nicola completed her PhD in 2017 at the University of Oxford in the Department of Biochemistry.
University of Nottingham
Using direct RNA sequencing to detect RNA structures in transcriptomes
Yue Wan received her BSc in Cell Biology and Biochemistry from the University of California, San Diego and her PhD in Cancer Biology from Stanford University under the mentorship of Howard Y. Chang. During her PhD, she developed the first high-throughput method for probing RNA structures genome-wide. Yue is a recipient of the NSS-PhD scholarship from the Agency for Science, Technology and Research (A*STAR) in Singapore and is currently a Principle Investigator in the Genome Institute of Singapore. She is a Society in Science- Branco Weiss Fellow, EMBO Young Investigator and CIFAR-Azrieli Global Scholar, as well as a recipient of the Young Scientist Award and L’Oreal-UNESCO for Women in Science, Singapore National Fellowship. She is interested in studying functional RNA structures and understanding their roles in regulating cellular biology.