Skip to main content
U.S. flag

An official website of the United States government

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you’ve safely connected to the .gov website. Share sensitive information only on official, secure websites.

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls

Published

Author(s)

Justin M. Zook, Brad Chapman, Winston Hide, Marc L. Salit

Abstract

Clinical adoption of human genome sequencing requires methods that output genotypes with known accuracy at millions or billions of positions across a genome. Because of substantial discordance among calls made by existing sequencing methods and algorithms, there is a need for a highly accurate set of genotypes across a genome that can be used as a benchmark. Here we present methods to make high-confidence, single-nucleotide polymorphism (SNP), indel and homozygous reference genotype calls for NA12878, the pilot genome for the Genome in a Bottle Consortium. We minimize bias toward any method by integrating and arbitrating between 14 data sets from five sequencing technologies, seven read mappers and three variant callers. We identify regions for which no confident genotype call could be made, and classify them into different categories based on reasons for uncertainty. Our genotype calls are publicly available on the Genome Comparison and Analytic Testing website to enable real-time benchmarking of any method.
Citation
Nature Biotechnology
Volume
32

Keywords

Human whole genome sequencing, DNA sequencing, Reference Materials, Reference Data

Citation

Zook, J. , Chapman, B. , Hide, W. and Salit, M. (2014), Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls, Nature Biotechnology, [online], https://doi.org/10.1038/nbt.2835 (Accessed March 19, 2024)
Created February 16, 2014, Updated February 21, 2019