Journal article
Imputation of coding variants in African Americans: better performance using data from the exome sequencing project
Bioinformatics (Oxford, England), Vol.29(21), pp.2744-2749
11/01/2013
DOI: 10.1093/bioinformatics/btt477
PMCID: PMC3799474
PMID: 23956302
Abstract
Although the 1000 Genomes haplotypes are the most commonly used reference panel for imputation, medical sequencing projects are generating large alternate sets of sequenced samples. Imputation in African Americans using 3384 haplotypes from the Exome Sequencing Project, compared with 2184 haplotypes from 1000 Genomes Project, increased effective sample size by 8.3-11.4% for coding variants with minor allele frequency <1%. No loss of imputation quality was observed using a panel built from phenotypic extremes. We recommend using haplotypes from Exome Sequencing Project alone or concatenation of the two panels over quality score-based post-imputation selection or IMPUTE2's two-panel combination.
yunli@med.unc.edu.
Supplementary data are available at Bioinformatics online.
Details
- Title: Subtitle
- Imputation of coding variants in African Americans: better performance using data from the exome sequencing project
- Creators
- Qing DuanEric Yi Liu - University of North Carolina at Chapel HillPaul L AuerGuosheng Zhang - University of North Carolina at Chapel HillEthan M LangeGoo JunChris BizonShuo JiaoSteven BuyskeNora FranceschiniChris S CarlsonLi HsuAlex P ReinerUlrike PetersJeffrey HaesslerKeith CurtisChristina L WasselJennifer G RobinsonLisa W MartinChristopher A HaimanLoic Le MarchandTara C MatiseLucia A HindorffDana C CrawfordThemistocles L AssimesHyun Min KangGerardo HeissRebecca D JacksonCharles KooperbergJames G WilsonGonçalo R AbecasisKari E NorthDeborah A NickersonLeslie A LangeYun Li
- Resource Type
- Journal article
- Publication Details
- Bioinformatics (Oxford, England), Vol.29(21), pp.2744-2749
- Publisher
- England
- DOI
- 10.1093/bioinformatics/btt477
- PMID
- 23956302
- PMCID
- PMC3799474
- ISSN
- 1367-4803
- eISSN
- 1367-4811
- Grant note
- U01 HG004803 / NHGRI NIH HHS U01HG004798 / NHGRI NIH HHS U01HG004790 / NHGRI NIH HHS U01HG004803 / NHGRI NIH HHS RC2 HL-103010 / NHLBI NIH HHS N01WH32100-2 / WHI NIH HHS RC2 HL102923 / NHLBI NIH HHS N01WH32115 / WHI NIH HHS N01WH24152 / WHI NIH HHS U01 HG004798 / NHGRI NIH HHS N01WH42107-26 / WHI NIH HHS RC2 HL-102926 / NHLBI NIH HHS N01WH44221 / WHI NIH HHS U01HG004801 / NHGRI NIH HHS RC2 HL102925 / NHLBI NIH HHS RC2 HL103010 / NHLBI NIH HHS RC2 HL-102923 / NHLBI NIH HHS U01 HG004802 / NHGRI NIH HHS RC2 HL102924 / NHLBI NIH HHS N01WH32122 / WHI NIH HHS RC2 HL102926 / NHLBI NIH HHS R01 HG006703 / NHGRI NIH HHS RC2 HL-102925 / NHLBI NIH HHS R01 HG006292 / NHGRI NIH HHS N01WH32118-32119 / WHI NIH HHS N01WH32108-9 / WHI NIH HHS U01HG004802 / NHGRI NIH HHS N01WH42129-32 / WHI NIH HHS U01 HG004790 / NHGRI NIH HHS N01WH22110 / WHI NIH HHS RC2 HL-102924 / NHLBI NIH HHS N01WH32111-13 / WHI NIH HHS U01 HG004801 / NHGRI NIH HHS N01WH32105-6 / WHI NIH HHS
- Language
- English
- Date published
- 11/01/2013
- Academic Unit
- Epidemiology; Internal Medicine
- Record Identifier
- 9983995016302771
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