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Accelerating Time to Discovery with Whole Exome Sequencing on UK Biobank’s Research Analysis Platform
UK Biobank, a large-scale biomedical database and research resource containing in-depth genetic and health information from half a million UK participants, is holding this webinar with DNAnexus, the Regeneron Genetics Center (RGC) and NVIDIA to discuss the recent exome sequencing project, the commitment to practical equitable data access, and the DNAnexus developed UKB Research Analysis Platform.

UK Biobank undergoes ongoing data collection, coupled with linkage to electronic health records, that has generated over 800,000 data files and more than 10 million variants. RGC rapidly sequenced and analyzed 450,000 UK Biobank exomes, using a bioinformatics protocol comprising entirely open-source tools including BWA-MEM, GLnexus, and Google’ DeepVariant. The scale and speed of this analysis (20,000 samples/week) was enabled by GPU-accelerated secondary analysis tool NVIDIA Clara Parabricks running Google’s DeepVariant, and by the DNAnexus platform. As part of the data release, UK Biobank, NVIDIA, RGC, and DNAnexus are collaborating to provide the entirety of this workflow to all users of the UK Biobank Research Analysis Platform.

In this webinar, UK Biobank, RGC, NVIDIA & DNAnexus will review the exact analysis pipeline used to quickly generate the 450,000 reference data set, and are offering UK Biobank researchers a free 6 month trial license to NVIDIA Clara Parabricks to help them replicate this accelerated workflow. The webinar goal is both to provide an overview of this analysis pipeline and to enable all UK Biobank researchers the opportunity to fully harmonize their own data, at any scale, with the UK Biobank exome data.

You agree to share your data with DNAnexus and NVIDIA. Your information will be handled in accordance with our Privacy Policy: https://www.dnanexus.com/privacy

Your information will be handled in accordance with NVIDIA's Privacy Policy. https://www.nvidia.com/en-us/about-nvidia/privacy-policy/

Feb 17, 2022 08:00 AM in Pacific Time (US and Canada)

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Speakers

Mark Effingham
Deputy CEO @UK Biobank
Mark is Deputy CEO of UK Biobank and brings broad experience of technical strategy, IT delivery and domain expertise in health informatics and big data. Mark is a Chartered IT Professional and Fellow of the British Computer Society. He holds a PhD and MSc from the University of Birmingham.
Tim Harkins
Product Manager, Genomics @NVIDIA
Tim Harkins, Ph.D. has been a team member of some of the more disruptive genomic technologies from microarrays to real-time PCR to next generation sequencing. With nearly 70 peer reviewed publications across the genomics industry, Tim has helped develop new assays and new technologies from single cell methylation to studying the mutational landscape of various cancers to metagenomic studies to helping decode new genomes like salamanders, domesticated dogs, and wild strawberries, to mention just a few. With over 20 years of industry experience, Tim has worked across both R&D and commercial teams to bring these platforms and applications to the market.
Will Salerno
Senior Director of Genome & Sequencing Informatics @Regeneron Genetics Center
William Salerno, Ph.D. is the Senior Director of Genome Sequencing Informatics at the Regeneron Genetics Center (RGC), which is a uniquely integrated research initiative that seeks to improve patient care by using genomic approaches to speed drug discovery and development. The Genome & Sequencing Informatics group at RGC performs all primary and secondary analysis of the RGC's genomic data. At 500k+ samples a year, the RGC operates at a scale and pace that demands unparalleled rigor in production and uncomfortably bold innovation in NGS methods development and compute infrastructure. Before RGC, Salerno was an assistant professor and director of genome informatics at Baylor College of Medicine. He received his BA in Integrated Science, Mathematics from Northwestern and his PhD from Baylor College of Medicine in Biochemistry and Bioinformatics.
Ben Busby
Director, Solutions Science @DNAnexus
Ben Busby works to make biomedical data science a more productive environment to work in for bioinformaticians and biomedical data scientists. At DNAnexus he does this by prototyping both scientific data integration as well as complex compute environments for users of the UKBioBank, as well as many other folks throughout academia, industry and government. Ben also develops prototype software in machine learning, omics, imaging, pharmacogenomics and NLP with his group, as well as in a number of biomedical hackathons he runs and participates in around the world. Prior to DNAnexus, Ben consulted for Johns Hopkins University, Ariel Precision Medicine, Deloitte, and NCBI, as well as founding the Bioinformatics and Data Science department at the FAES Graduate School on the NIH campus.
Moderator: Harry Clifford
Senior Product Architect, Genomics @NVIDIA
As senior product architect for genomics at NVIDIA, Harry works at the interface between engineering and product development, leveraging NVIDIA’s expertise in AI, high performance computing (HPC), and data analytics stacks to address genomics workflows with accelerated high-accuracy solutions. His background is in bioinformatics and functional genomics, including a PhD from the University of Oxford, post-doctoral experience in the biopharma industry and at the University of Cambridge, and entrepreneurial experience in the biotech sector. Harry was listed in Forbes’ “30 Under 30” after co-founding precision oncology company CCG.ai (acquired by Dante Labs), a Y Combinator and Merck Accelerator-backed start-up delivering decision support via deep learning and advanced analytical software.