In this lecture Professor Carlos Bustamante from Stanford University describes the importance of expanding population genetic studies beyond a Northern European ancestry based approach into multi and trans-ethnic study designs.
Jeong-Sun Seo of Macrogen and Seoul National University College of Medicine reports on sequencing many Asian genomes to better understand genetic variation in that population. He shows that identifying certain structural variants may explain diseases that disproportionately affect Asian people.
In his talk from the AGBT 2015 PacBio workshop, Craig Venter detailed plans to sequence 1 million genomes and gather extensive phenotypic data to make sense of them. Included: generating 30 reference genomes to represent ethnogeographic diversity; the need for long-range continuity in sequencing; and truly predictive genomics.
PacBio customers and thought leaders discuss the role SMRT sequencing is playing in comprehensive genomics: past, present, and future. Featuring J. Craig Venter, Gene Myers, Deanna Church, Jeong-Sun Seo and W. Richard McCombie.
Yunfei Guo, from the University of Southern California, presents his ASHG 2015 poster on a de novo assembly of a diploid Asian genome. The uniform coverage of long-read sequencing helped access regions previously unresolvable due to high GC bias or long repeats. The assembly allowed scientists to fill some 400 gaps in the latest human reference genome, including some as long as 50 kb.
Michael Schatz of Cold Spring Harbor Laboratory and Johns Hopkins University discusses the challenges in detecting structural variations (SVs) in high throughput sequencing data, especially more complex SVs such as a duplication nested within an inversion. To overcome these challenges, Dr. Schatz and his team have been applying long-read sequencing to analyze SVs in a range of samples from small microbial genomes, through mid-sized plant and animal genomes, to large mammalian genomes. The increased read lengths, which currently average over 10kbp and some approach 100kbp, make it possible to span more complex SVs and accurately assess SVs in repetitive regions,…
Euan Ashley speaks about precision medicine and said clinical-grade analysis has been limited by complex regions in the human genome. His key theme,”Precision medicine needs to be accurate medicine,” was illustrated with several examples where short-read sequencing or traditional clinical sequencing methods failed to be accurate. Also included: targeted RNA sequencing and gene phasing with long-read sequencing.
Adam Ameur talks about a range of applications for which SMRT Sequencing had been useful in the SciLifeLab. Examples include analyzing a DNA translocation in chronic myeloid leukemia samples; studying the HPV genome; and sequencing the FADS region to understand fatty acid production.
Karyn Meltz Steinberg presents the first high quality African reference genome assembly of the Yoruban individual, NA19240, produced from SMRT Sequencing data. She said PacBio sequencing offers significant improvement over short-read sequence data for high-quality assemblies.
Melissa Laird Smith from Icahn Institute at Mt. Sinai reviews her work studying the genetic background of immune response by characterizing population diversity at the immunoglobulin heavy chain locus. Webinar registration required.
In this ASHG 2016 poster video, Martin Pollard from the Wellcome Trust Sanger Institute and the University of Cambridge describes an ambitious project to better represent natural variation in the complex MHC region by sequencing the locus in thousands of people from various populations in Africa. A pilot project in five populations has already revealed a lot of diversity in the region, which is important for human disease, vaccine response, and organ transplantation. Pollard says SMRT Sequencing is the only technology that can deliver the full-length haplotypes necessary to identify complete variation in this highly polymorphic complex. Plus: plans to…
PacBio bioinformatician Aaron Wenger presents this ASHG 2016 poster demonstrating human structural variation detection at varying coverage levels with SMRT Sequencing on the Sequel System. Results were compared to truth sets for well-characterized genomes. Results indicate that even low coverage of SMRT Sequencing makes it possible to detect hundreds of SVs that are missed in high-coverage short-read sequencing data.
Valerie Schneider of the National Center for Biotechnology Information discuss how the Genome Reference Consortium (GRC) is bringing more ethnic diversity to the latest human reference assembly (GRCh38) by adding patches and alternate loci scaffolds. Scientists working with population graphs are among the early adopters of these new alternate loci scaffolds. She also discusses work underway at the McDonnell Genome Institute at Washington University to generate a set of high-quality, de novo whole genomes from a wide variety of populations. The new ethnic genomes “are also intended to stand on their own as complements to the reference so users can…
Andrew Carroll, Director of Science at DNAnexus, presents how to greatly improve the accuracy of SV-calling by using long-read PacBio sequencing and fast and easy-to-run cloud-optimized apps like PBHoney, Parliament, and Sniffles.
Jonas Korlach spoke about recent SMRT Sequencing updates, such as latest Sequel System chemistry release (1.2.1) and updates to the Integrative Genomics Viewer that’s now update optimized for PacBio data. He presented the recent data release of structural variation detected in the NA12878 genome, including many more insertions and deletions than short-read-based technologies were able to find.