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ASHG 2017 Day 1: Structural Variation, Reference Genomes, and More Diversity

Wednesday, October 18, 2017

The annual meeting of the American Society of Human Genetics kicked off with a splash yesterday in Orlando, Fla. The PacBio team was thrilled that the opening talks in the presidential address and plenary session included a significant focus on increasing diversity in genetic studies to better characterize underrepresented populations. Nancy Cox, ASHG president, highlighted a number of excellent efforts to address this but noted, “Compared with what we need, what we’ve done so far is really just a drop in the bucket.” As regular blog readers know, we work closely with groups around the world to build population-specific reference genomes and improve structural variant calling for all groups, so her message really resonated with us.

The other headline event for us yesterday was a joint workshop from the Genome Reference Consortium and Genome in a Bottle consortium, called “Getting the Most from the Reference Assembly and Reference Materials.” In the GRC portion of the event, talks from NCBI’s Valerie Schneider and McDonnell Genome Institute’s Tina Graves-Lindsay were particularly interesting for our team. Schneider offered a brief overview of GRC projects and a deeper dive into accomplishments and challenges in improving the human reference genome. As she noted, the latest build is GRCh38, which is a combination of sequences from some 70 people; she and her team continue to patch the assembly, correcting mistakes and adding new representations of genetic variation without changing existing coordinates. Graves-Lindsay spoke about the need to generate more high-quality human genome sequences for better characterization of people from all ancestries, and reported on efforts to do just that. The GRC has now used SMRT Sequencing, among other tools, to produce data for 10 diploid and two haploid genomes as a means of adding allelic diversity to the reference. Two chromosome-level assemblies reflect just how complete and contiguous these resources are. They plan to produce FALCON-unzip assemblies for all samples to increase quality and usefulness even further.

In its section of the workshop, GIAB covered reference materials, variant benchmarking, and more. Among the speakers, Baylor’s Fritz Sedlazeck and NIST’s Justin Zook gave talks that were especially meaningful for us. Sedlazeck, who has developed several important algorithms for working with long-read sequencing data and calling structural variants, encouraged the community to support large population studies focused on structural variation. He also announced a new project that will entail whole genome sequencing for 100 individuals using SMRT Sequencing and linked-read sequencing, with the goal of detecting and phasing structural variants. In his talk, Zook spoke about bringing the principles of metrology to genomics, and said that GIAB benchmarks are already widely used for clinical validation. His team is now focused on particularly challenging genetic regions and variants and recently released a structural variant call set.

The excitement continues today with our workshop, Population and Clinical Genetics Studies Using Long-read SMRT Sequencing. Please join us on the lower level of Hilton Orlando, Orange Ballroom D (connected to the Orange County Convention Center) at 12:30 p.m. for lunch and learning with Han Brunner, M.D., Charles Lee, Ph.D., FACMG, Karen McFarland, Ph.D., and our own Chief Scientific Officer Jonas Korlach, Ph.D.

Stay tuned for more updates as we report back daily on the great science being presented at ASHG.

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