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Towards a Comprehensive Variation Benchmark for Medically-Relevant Autosomal Genes

C.E. Credits: P.A.C.E. CE Florida CE
Speaker
  • Computer Scientist, NIST
    Biography

      Justin Wagner is a Computer Scientist on the NIST Human Genomics team developing whole human genome benchmarks for the Genome in a Bottle (GIAB) consortium. He has contributed to GIAB benchmarks including an expansion of the GIAB small variant benchmark using long and linked read sequencing, a targeted diploid assembly benchmark of the Major Histocompatibility Complex, and a benchmark that is under-development for a subset of medically-relevant and difficult-to-characterize genes.


    Abstract

    The Genome in a Bottle Consortium has published benchmarks for variant calling, but some challenging medically-relevant genes have been partially or fully excluded due to mapping challenges, structural variation, and issues in the reference genomes. Here, we use a trio-based, long-read, phased diploid assembly to form phased small variant and structural variant benchmarks for 273 out of 396 autosomal genes covered <90% by mapping-based benchmarks. We curated >1000 variants to exclude errors in the assembly, mostly in homopolymers and highly homozygous regions, and to ensure the benchmark accurately identifies false positives and false negatives across call sets. The new benchmark for challenging medically relevant genes will improve the characterization of challenging variants, leading to better insights for clinical genomics in the near future.

    Learning Objectives:

    1. Learn about applications of long read sequencing technologies for variant detection in medical genes

    2. Clarify use of Genome in a Bottle benchmarks and how a medical gene focused benchmark improves clinical application


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