Pulse lineResearch With Heart Logo

Imputation of coding variants in African Americans: better performance using data from the exome sequencing project.

TitleImputation of coding variants in African Americans: better performance using data from the exome sequencing project.
Publication TypeJournal Article
Year of Publication2013
AuthorsDuan Q, Liu EYi, Auer PL, Zhang G, Lange EM, Jun G, Bizon C, Jiao S, Buyske S, Franceschini N, Carlson CS, Hsu L, Reiner AP, Peters U, Haessler J, Curtis K, Wassel CL, Robinson JG, Martin LW, Haiman CA, Le Marchand L, Matise TC, Hindorff LA, Crawford DC, Assimes TL, Kang HMin, Heiss G, Jackson RD, Kooperberg C, Wilson JG, Abecasis GR, North KE, Nickerson DA, Lange LA
Secondary AuthorsLi Y
JournalBioinformatics
Volume29
Issue21
Pagination2744-9
Date Published2013 Nov 01
ISSN1367-4811
KeywordsAfrican Americans, Exome, Gene Frequency, Genetic Variation, Genome, Human, Genome-Wide Association Study, Haplotypes, Humans, Phenotype, Polymorphism, Single Nucleotide, Sequence Analysis, DNA
Abstract

SUMMARY: 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

CONTACT: yunli@med.unc.edu.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

DOI10.1093/bioinformatics/btt477
Alternate JournalBioinformatics
PubMed ID23956302
PubMed Central IDPMC3799474
Grant ListRC2 HL102923 / HL / NHLBI NIH HHS / United States
R01 HG006292 / HG / NHGRI NIH HHS / United States
N01WH42129-32 / WH / WHI NIH HHS / United States
RC2 HL102926 / HL / NHLBI NIH HHS / United States
R01 HG006703 / HG / NHGRI NIH HHS / United States
RC2 HL-102926 / HL / NHLBI NIH HHS / United States
U01 HG004790 / HG / NHGRI NIH HHS / United States
U01 HG004802 / HG / NHGRI NIH HHS / United States
N01WH32100-2 / WH / WHI NIH HHS / United States
RC2 HL-102923 / HL / NHLBI NIH HHS / United States
N01WH32108-9 / WH / WHI NIH HHS / United States
U01HG004803 / HG / NHGRI NIH HHS / United States
U01HG004802 / HG / NHGRI NIH HHS / United States
N01WH42107-26 / WH / WHI NIH HHS / United States
RC2 HL-102924 / HL / NHLBI NIH HHS / United States
RC2 HL102924 / HL / NHLBI NIH HHS / United States
N01WH32122 / WH / WHI NIH HHS / United States
U01 HG004803 / HG / NHGRI NIH HHS / United States
U01HG004798 / HG / NHGRI NIH HHS / United States
N01WH32105-6 / WH / WHI NIH HHS / United States
N01WH32111-13 / WH / WHI NIH HHS / United States
RC2 HL-102925 / HL / NHLBI NIH HHS / United States
N01WH32118-32119 / WH / WHI NIH HHS / United States
U01HG004801 / HG / NHGRI NIH HHS / United States
RC2 HL103010 / HL / NHLBI NIH HHS / United States
U01HG004790 / HG / NHGRI NIH HHS / United States
U01 HG004798 / HG / NHGRI NIH HHS / United States
N01WH32115 / WH / WHI NIH HHS / United States
N01WH44221 / WH / WHI NIH HHS / United States
N01WH22110 / WH / WHI NIH HHS / United States
RC2 HL-103010 / HL / NHLBI NIH HHS / United States
RC2 HL102925 / HL / NHLBI NIH HHS / United States
N01WH24152 / WH / WHI NIH HHS / United States
U01 HG004801 / HG / NHGRI NIH HHS / United States