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Epistasis between SNPs in genes involved in lipoprotein metabolism influences high- and low-density lipoprotein cholesterol levels

Authors
Kim, SunshinShin, CholCho, Nam H.Koh, InSongKo, Jeong-JaeKwack, KyuBum
Issue Date
Dec-2014
Publisher
SPRINGER
Keywords
Epistatic interaction; Lipoprotein; Metabolism; Single nucleotide polymorphism (SNP); SNPwinter
Citation
GENES & GENOMICS, v.36, no.6, pp 809 - 817
Pages
9
Indexed
SCIE
SCOPUS
KCI
Journal Title
GENES & GENOMICS
Volume
36
Number
6
Start Page
809
End Page
817
URI
https://scholarworks.korea.ac.kr/kumedicine/handle/2020.sw.kumedicine/8704
DOI
10.1007/s13258-014-0216-7
ISSN
1976-9571
2092-9293
Abstract
Although genome-wide association (GWA) studies have provided valuable insights into the genetic architecture of human disease, they have elucidated relatively little of the heritability of complex traits. A significant part of the missing heritability might be explained by rare combinations of common SNPs. We hypothesized that epistasis among 15 genes (148 SNPs) involved in lipoprotein metabolism would influence HDL-cholesterol (HDL-C) and LDL-cholesterol (LDL-C) levels. Using SNPwinter software with the various epistatic models, we identified 58 association signals with HDL-C levels for SNPs in eleven genes and 118 associations with LDL-C for SNPs in fourteen genes. These associations were discovered in the urban Ansan cohort (n = 4,102) and replicated in a rural cohort (n = 3,434), the Ansung. We found replicated associations with new genes (SOAT1, APOB, HMGCR, and FDFT1 for HDL-C, and SOAT1, FDFT1, LPL, SQLE, ABCA1, LRP1, SCARB1, and PLTP for LDL-C), in addition to those (CETP, LIPC, LPL, ABCA1, PLTP, SCARB1, and LRP1 for HDL-C, and CETP, LIPC, LDLR, APOB, CYP7A1, and HMGCR for LDL-C) identified by GWA studies, through investigating pairwise interactions between candidate genes of biological and clinical importance. Interestingly, we found that some genes were more likely to be involved in epistatic interactions (ABCA1 and LIPC for HDL-C, and ABCA1, SCARB1, and LIPC for LDL-C).
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Shin, Chol
Ansan Hospital (Department of Pulmonary, Allergy, and Critical Care Medicine, Ansan Hospital)
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