Skip Navigation
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Your Environment. Your Health.

Publication Detail

Title: Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel.

Authors: Delaneau, Olivier; Marchini, Jonathan; 1000 Genomes Project Consortium; 1000 Genomes Project Consortium

Published In Nat Commun, (2014 Jun 13)

Abstract: A major use of the 1000 Genomes Project (1000 GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000 GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants.

PubMed ID: 25653097 Exiting the NIEHS site

MeSH Terms: Algorithms*; Alleles; Gene Frequency; Genome, Human*; Genome-Wide Association Study*; Haplotypes; Humans; Microarray Analysis/statistics & numerical data*; Polymorphism, Single Nucleotide

Back
to Top