TY - JOUR
T1 - Pathway analysis of genome-wide data improves warfarin dose prediction.
AU - Daneshjou, Roxana
AU - Tatonetti, Nicholas P.
AU - Karczewski, Konrad J.
AU - Sagreiya, Hersh
AU - Bourgeois, Stephane
AU - Drozda, Katarzyna
AU - Burmester, James K.
AU - Tsunoda, Tatsuhiko
AU - Nakamura, Yusuke
AU - Kubo, Michiaki
AU - Tector, Matthew
AU - Limdi, Nita A.
AU - Cavallari, Larisa H.
AU - Perera, Minoli
AU - Johnson, Julie A.
AU - Klein, Teri E.
AU - Altman, Russ B.
N1 - Funding Information:
Geoffery M. Cooper, for allowing us to use the Cooper. et. al. warfarin data. The International Warfarin Pharmacogenetic Consortium. RD was funded by the Howard Hughes Medical Institute Medical Fellows, Stanford School of Medicine Medical Scholars Grant, and the Stanford School of Medicine Medical Scientist Training Program, NPT was funded by DOESCGF. JKB is a member of the Wisconsin Network for Health Research and funded by grant UL155025011. LHC is funded by American Heart Association Midwest Affiliate Grant-In-Aid (10GRNT3750024) and the University of Illinois Hans Vahlteich Pharmacy Endowment Award. NAL was funded by the National Heart Lung and Blood Institute (RO1HL092173) and the National Institute of Neurological Disorders and Stroke (K23NS45598). MP is funded by K23 HL089808-01A2. MT is funded by Wisconsin Network for Health Research. RBA is funded by. NIH/NIGMS R24 GM61374, BioX2 NSF Grant (CNS-0619926). Declarations The publication costs for this article were funded by the above grants.
PY - 2013
Y1 - 2013
N2 - Many genome-wide association studies focus on associating single loci with target phenotypes. However, in the setting of rare variation, accumulating sufficient samples to assess these associations can be difficult. Moreover, multiple variations in a gene or a set of genes within a pathway may all contribute to the phenotype, suggesting that the aggregation of variations found over the gene or pathway may be useful for improving the power to detect associations. Here, we present a method for aggregating single nucleotide polymorphisms (SNPs) along biologically relevant pathways in order to seek genetic associations with phenotypes. Our method uses all available genetic variants and does not remove those in linkage disequilibrium (LD). Instead, it uses a novel SNP weighting scheme to down-weight the contributions of correlated SNPs. We apply our method to three cohorts of patients taking warfarin: two European descent cohorts and an African American cohort. Although the clinical covariates and key pharmacogenetic loci for warfarin have been characterized, our association metric identifies a significant association with mutations distributed throughout the pathway of warfarin metabolism. We improve dose prediction after using all known clinical covariates and pharmacogenetic variants in VKORC1 and CYP2C9. In particular, we find that at least 1% of the missing heritability in warfarin dose may be due to the aggregated effects of variations in the warfarin metabolic pathway, even though the SNPs do not individually show a significant association. Our method allows researchers to study aggregative SNP effects in an unbiased manner by not preselecting SNPs. It retains all the available information by accounting for LD-structure through weighting, which eliminates the need for LD pruning.
AB - Many genome-wide association studies focus on associating single loci with target phenotypes. However, in the setting of rare variation, accumulating sufficient samples to assess these associations can be difficult. Moreover, multiple variations in a gene or a set of genes within a pathway may all contribute to the phenotype, suggesting that the aggregation of variations found over the gene or pathway may be useful for improving the power to detect associations. Here, we present a method for aggregating single nucleotide polymorphisms (SNPs) along biologically relevant pathways in order to seek genetic associations with phenotypes. Our method uses all available genetic variants and does not remove those in linkage disequilibrium (LD). Instead, it uses a novel SNP weighting scheme to down-weight the contributions of correlated SNPs. We apply our method to three cohorts of patients taking warfarin: two European descent cohorts and an African American cohort. Although the clinical covariates and key pharmacogenetic loci for warfarin have been characterized, our association metric identifies a significant association with mutations distributed throughout the pathway of warfarin metabolism. We improve dose prediction after using all known clinical covariates and pharmacogenetic variants in VKORC1 and CYP2C9. In particular, we find that at least 1% of the missing heritability in warfarin dose may be due to the aggregated effects of variations in the warfarin metabolic pathway, even though the SNPs do not individually show a significant association. Our method allows researchers to study aggregative SNP effects in an unbiased manner by not preselecting SNPs. It retains all the available information by accounting for LD-structure through weighting, which eliminates the need for LD pruning.
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U2 - 10.1186/1471-2164-14-s3-s11
DO - 10.1186/1471-2164-14-s3-s11
M3 - Article
C2 - 23819817
AN - SCOPUS:84885410983
VL - 14 Suppl 3
JO - Unknown Journal
JF - Unknown Journal
ER -