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Tuesday, June 11, 2019

Genome in a Bottle Consortium Describes Human Genome Structural Variation Benchmark

UPDATE: The paper has been published in Nature Biotechnology A preprint released this week from the Genome in a Bottle (GIAB) Consortium describes a benchmark set of structural variants (SVs), differences ≥50 bp, in the genome of a human male named HG002. The GIAB benchmark is the first to allow measuring precision (false positives) and recall (false negatives) of different approaches to detecting structural variants. The GIAB Consortium also developed a tool, Truvari, to support evaluation of variant call sets against the benchmark. Earlier GIAB benchmarks, first released in 2014 and last updated in 2017, have led to enormous improvements…

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Wednesday, March 6, 2019

GIAB Expands Variant Call Sets with SMRT Sequencing Results

Genome in a Bottle Consortium You may have missed last week’s Advances in Genome Biology & Technology conference in sunny Marco Island, Fla., but you definitely shouldn’t miss the two posters presented there by Justin Zook and Justin Wagner from NIST’s Genome in a Bottle (GIAB) consortium. The GIAB team has made critical progress in generating high-quality human genome reference materials and benchmarks that have helped to improve the accuracy and reproducibility of variant calling across laboratories. The latest results advance that work with an expansion of the benchmark set to include additional small (single-nucleotide variant and indel) variants and…

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Wednesday, October 18, 2017

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

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…

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