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Comparison of HapMap and 1000 Genomes Reference Panels in a Large-Scale Genome-Wide Association Study.

TitleComparison of HapMap and 1000 Genomes Reference Panels in a Large-Scale Genome-Wide Association Study.
Publication TypeJournal Article
Year of Publication2017
Authorsde Vries PS, Sabater-Lleal M, Chasman DI, Trompet S, Ahluwalia TS, Teumer A, Kleber ME, Chen M-H, Wang J J, Attia JR, Marioni RE, Steri M, Weng L-C, Pool R, Grossmann V, Brody JA, Venturini C, Tanaka T, Rose LM, Oldmeadow C, Mazur J, Basu S, Frånberg M, Yang Q, Ligthart S, Hottenga JJ, Rumley A, Mulas A, de Craen AJM, Grotevendt A, Taylor KD, Delgado GE, Kifley A, Lopez LM, Berentzen TL, Mangino M, Bandinelli S, Morrison AC, Hamsten A, Tofler G, de Maat MPM, Draisma HHM, Lowe GD, Zoledziewska M, Sattar N, Lackner KJ, Völker U, McKnight B, Huang J, Holliday EG, McEvoy MA, Starr JM, Hysi PG, Hernandez DG, Guan W, Rivadeneira F, McArdle WL, P Slagboom E, Zeller T, Psaty BM, Uitterlinden AG, de Geus EJC, Stott DJ, Binder H, Hofman A, Franco OH, Rotter JI, Ferrucci L, Spector TD, Deary IJ, März W, Greinacher A, Wild PS, Cucca F, Boomsma DI, Watkins H, Tang W, Ridker PM, Jukema JW, Scott RJ, Mitchell P, Hansen T, O'Donnell CJ, Smith NL, Strachan DP
Secondary AuthorsDehghan A
JournalPLoS One
Volume12
Issue1
Paginatione0167742
Date Published2017
ISSN1932-6203
KeywordsGenome-Wide Association Study, HapMap Project, Humans
Abstract

An increasing number of genome-wide association (GWA) studies are now using the higher resolution 1000 Genomes Project reference panel (1000G) for imputation, with the expectation that 1000G imputation will lead to the discovery of additional associated loci when compared to HapMap imputation. In order to assess the improvement of 1000G over HapMap imputation in identifying associated loci, we compared the results of GWA studies of circulating fibrinogen based on the two reference panels. Using both HapMap and 1000G imputation we performed a meta-analysis of 22 studies comprising the same 91,953 individuals. We identified six additional signals using 1000G imputation, while 29 loci were associated using both HapMap and 1000G imputation. One locus identified using HapMap imputation was not significant using 1000G imputation. The genome-wide significance threshold of 5×10-8 is based on the number of independent statistical tests using HapMap imputation, and 1000G imputation may lead to further independent tests that should be corrected for. When using a stricter Bonferroni correction for the 1000G GWA study (P-value

DOI10.1371/journal.pone.0167742
Alternate JournalPLoS One
PubMed ID28107422
PubMed Central IDPMC5249120
Grant ListHHSN268201100012C / HL / NHLBI NIH HHS / United States
RC2 MH089951 / MH / NIMH NIH HHS / United States
R01 HL103612 / HL / NHLBI NIH HHS / United States
HHSN268201100009I / HL / NHLBI NIH HHS / United States
R01 NS017950 / NS / NINDS NIH HHS / United States
R01 MH081802 / MH / NIMH NIH HHS / United States
R01 HL120393 / HL / NHLBI NIH HHS / United States
HHSN268201100010C / HL / NHLBI NIH HHS / United States
UL1 RR025005 / RR / NCRR NIH HHS / United States
HHSN268201100008C / HL / NHLBI NIH HHS / United States
U01 HL080295 / HL / NHLBI NIH HHS / United States
HHSN268201100005G / HL / NHLBI NIH HHS / United States
HHSN268201100008I / HL / NHLBI NIH HHS / United States
R01 HL043851 / HL / NHLBI NIH HHS / United States
R01 HL059367 / HL / NHLBI NIH HHS / United States
HHSN268201100007C / HL / NHLBI NIH HHS / United States
R01 MD009164 / MD / NIMHD NIH HHS / United States
HHSN268200800007C / HL / NHLBI NIH HHS / United States
HHSN268201100011I / HL / NHLBI NIH HHS / United States
HHSN268201100011C / HL / NHLBI NIH HHS / United States
R01 HL086694 / HL / NHLBI NIH HHS / United States
R01 HL087652 / HL / NHLBI NIH HHS / United States
U01 HG004402 / HG / NHGRI NIH HHS / United States
UL1 TR000124 / TR / NCATS NIH HHS / United States
N01HC55222 / HL / NHLBI NIH HHS / United States
MR/K026992/1 / / Medical Research Council / United Kingdom
N01HC85086 / HL / NHLBI NIH HHS / United States
R01 HL105756 / HL / NHLBI NIH HHS / United States
U01 DK062418 / DK / NIDDK NIH HHS / United States
P30 DK063491 / DK / NIDDK NIH HHS / United States
HHSN268201100006C / HL / NHLBI NIH HHS / United States
HHSN268201200036C / HL / NHLBI NIH HHS / United States
R01 AG033193 / AG / NIA NIH HHS / United States
HHSN268201100005I / HL / NHLBI NIH HHS / United States
K24 DK080140 / DK / NIDDK NIH HHS / United States
U24 MH068457 / MH / NIMH NIH HHS / United States
UM1 CA182913 / CA / NCI NIH HHS / United States
R01 CA047988 / CA / NCI NIH HHS / United States
R01 HL080467 / HL / NHLBI NIH HHS / United States
N01HC85082 / HL / NHLBI NIH HHS / United States
HHSN268201100009C / HL / NHLBI NIH HHS / United States
N01HC85083 / HL / NHLBI NIH HHS / United States
HHSN268201100005C / HL / NHLBI NIH HHS / United States
N01HC25195 / HL / NHLBI NIH HHS / United States
HHSN268201100007I / HL / NHLBI NIH HHS / United States
/ / Wellcome Trust / United Kingdom
BB/F019394/1 / / Biotechnology and Biological Sciences Research Council / United Kingdom
N01HC85079 / HL / NHLBI NIH HHS / United States
F32 AR059469 / AR / NIAMS NIH HHS / United States
R01 AG023629 / AG / NIA NIH HHS / United States
R01 HL087641 / HL / NHLBI NIH HHS / United States
N01HC85080 / HL / NHLBI NIH HHS / United States
N01HC85081 / HL / NHLBI NIH HHS / United States