Journal article
Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel
Nature communications, Vol.5(1), pp.3934-3934
06/13/2014
DOI: 10.1038/ncomms4934
PMCID: PMC4338501
PMID: 25653097
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.
Details
- Title: Subtitle
- Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel
- Creators
- Olivier Delaneau - Department of Statistics, University of Oxford, Oxford OX1 3TG, UKJonathan Marchini - 1] Department of Statistics, University of Oxford, Oxford OX1 3TG, UK Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK1000 Genomes Project Consortium
- Contributors
- Jacob J Michaelson (Contributor) - University of Iowa, Roy J. Carver Department of Biomedical Engineering
- Resource Type
- Journal article
- Publication Details
- Nature communications, Vol.5(1), pp.3934-3934
- Publisher
- England
- DOI
- 10.1038/ncomms4934
- PMID
- 25653097
- PMCID
- PMC4338501
- ISSN
- 2041-1723
- eISSN
- 2041-1723
- Grant note
- 096599 / Wellcome Trust P20 MD006899 / NIMHD NIH HHS R01 HG002898 / NHGRI NIH HHS U01 HG006513 / NHGRI NIH HHS G0801823 / Medical Research Council P30 ES013508 / NIEHS NIH HHS BB/I02593X/1 / Biotechnology and Biological Sciences Research Council R01 CA166661 / NCI NIH HHS
- Language
- English
- Date published
- 06/13/2014
- Academic Unit
- Roy J. Carver Department of Biomedical Engineering; Communication Sciences and Disorders; Psychiatry; Iowa Neuroscience Institute
- Record Identifier
- 9984070274102771
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