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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
biochemistry, genetics and molecular biology
Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls
Nature Biotechnology, Volume 32, No. 3, Year 2014
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Description
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. © 2014 Nature America, Inc.
Authors & Co-Authors
Zook, Justin M.
United States, Gaithersburg
National Institute of Standards and Technology
Chapman, Brad A.
United States, Boston
Harvard T.h. Chan School of Public Health
Hofmann, Oliver M.
United States, Boston
Harvard T.h. Chan School of Public Health
Hide, Winston A.
United States, Boston
Harvard T.h. Chan School of Public Health
Salit, Marc L.
United States, Gaithersburg
National Institute of Standards and Technology
Statistics
Citations: 499
Authors: 5
Affiliations: 3
Identifiers
Doi:
10.1038/nbt.2835
ISSN:
10870156
Research Areas
Genetics And Genomics