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

Delaneau, O., Marchini, J., 1000 Genomes Project, C., Lehrach, H., Sudbrak, R., Amstislavskiy, V. S., et al. (2014). Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel. Nature Communications, 5: 5:3934. doi:10.1038/ncomms4934.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0025-B4D5-F Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0027-B04A-E
Genre: Journal Article

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 Creators:
Delaneau, O., Author
Marchini, J., Author
1000 Genomes Project, Consortium1, Author
Lehrach, H.1, 2, Author              
Sudbrak, R.1, Author
Amstislavskiy, V. S.1, Author
Lienhard, M.1, 3, Author              
Mertes, F.1, 2, Author              
Sultan, M.1, Author
Timmermann, B.1, 4, Author              
Yaspo, M. L.1, 5, Author              
Herwig, R.1, 3, Author              
Affiliations:
1The 1000 Genomes Project Consortium, ou_persistent22              
2Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433550              
3Bioinformatics (Ralf Herwig), Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479648              
4Sequencing (Head: Bernd Timmermann), Scientific Service (Head: Christoph Krukenkamp), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479670              
5Gene Regulation and Systems Biology of Cancer (Marie-Laure Yaspo), Independent Junior Research Groups (OWL), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_2117287              

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 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.

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Language(s): eng - English
 Dates: 2014-06-13
 Publication Status: Published online
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Method: Peer
 Identifiers: DOI: 10.1038/ncomms4934
ISSN: 2041-1723 (Electronic)
 Degree: -

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Project name : 1000 Genome Project
Grant ID : 01GS08201
Funding program : -
Funding organization : BMBF

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Title: Nature Communications
  Abbreviation : Nat. Commun.
Source Genre: Journal
 Creator(s):
Affiliations:
Publ. Info: London : Nature Publishing Group
Pages: - Volume / Issue: 5 Sequence Number: 5:3934 Start / End Page: - Identifier: ISSN: 2041-1723
CoNE: https://pure.mpg.de/cone/journals/resource/2041-1723