Year: 2020
Type: article
Abstract: Most human genomes are characterized by aligning individual reads to the reference genome, but accurate long reads and linked reads now enable us to construct accurate, phased de novo assemblies. We focus on a medically important, highly variable, 5 million base-pair (bp) region where diploid assembly is particularly useful - the Major Histocompatibility Complex (MHC). Here, we develop a human genome benchmark derived from a diploid assembly for the openly-consented Genome in a Bottle sample HG002. We assemble a single contig for each haplotype, align them to the reference, call phased small and structural variants, and define a small variant benchmark for the MHC, covering 94% of the MHC and 22368 variants smaller than 50 bp, 49% more variants than a mapping-based benchmark. This benchmark reliably identifies errors in mapping-based callsets, and enables performance assessment in regions with much denser, complex variation than regions covered by previous benchmarks.
Source: Nature Communications
Authors: Chen-Shan Chin, Justin Wagner, Qiandong Zeng, Erik Garrison, Shilpa Garg, Arkarachai Fungtammasan, Mikko Rautiainen, Sergey Aganezov, Melanie Kirsche, Samantha Zarate, Michael C. Schatz, Chunlin Xiao, William J. Rowell, Charles Markello, Jesse Farek, Fritz J. Sedlazeck, Vikas Bansal, Byunggil Yoo, Neil Miller, Xin Zhou, Andrew Carroll, Alvaro Martinez Barrio, Marc Salit, Tobias Marschall, Alexander T. Dilthey, Justin M. Zook
Institutions: DNAnexus (United States), National Institute of Standards and Technology, Material Measurement Laboratory, LabCorp (United States), University of California, Santa Cruz, Harvard University, Max Planck Institute for Informatics, Saarland University, Johns Hopkins University, Cold Spring Harbor Laboratory, National Institutes of Health, National Center for Biotechnology Information, Pacific Biosciences (United States), Baylor College of Medicine, University of California San Diego, Children's Mercy Hospital, Stanford University, Google (United States), 10X Genomics (United States), Heinrich Heine University Düsseldorf
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $5,380
OpenAlex ID: W3089079506