title: Mining the LIPG allelic spectrum reveals the contribution of rare and common regulatory variants to HDL cholesterol.
abstract: Genome-wide association studies (GWAS) have successfully identified loci associated with quantitative traits, such as blood lipids. Deep resequencing studies are being utilized to catalogue the allelic spectrum at GWAS loci. The goal of these studies is to identify causative variants and missing heritability, including heritability due to low frequency and rare alleles with large phenotypic impact. Whereas rare variant efforts have primarily focused on nonsynonymous coding variants, we hypothesized that noncoding variants in these loci are also functionally important. Using the HDL-C gene LIPG as an example, we explored the effect of regulatory variants identified through resequencing of subjects at HDL-C extremes on gene expression, protein levels, and phenotype. Resequencing a portion of the LIPG promoter and 5' UTR in human subjects with extreme HDL-C, we identified several rare variants in individuals from both extremes. Luciferase reporter assays were used to measure the effect of these rare variants on LIPG expression. Variants conferring opposing effects on gene expression were enriched in opposite extremes of the phenotypic distribution. Minor alleles of a common regulatory haplotype and noncoding GWAS SNPs were associated with reduced plasma levels of the LIPG gene product endothelial lipase (EL), consistent with its role in HDL-C catabolism. Additionally, we found that a common nonfunctional coding variant associated with HDL-C (rs2000813) is in linkage disequilibrium with a 5' UTR variant (rs34474737) that decreases LIPG promoter activity. We attribute the gene regulatory role of rs34474737 to the observed association of the coding variant with plasma EL levels and HDL-C. Taken together, the findings show that both rare and common noncoding regulatory variants are important contributors to the allelic spectrum in complex trait loci.
authors.affiliation: Institute for Translational Medicine and Therapeutics, Institute for Diabetes, Obesity, and Metabolism, and Cardiovascular Institute, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America.
authors.forename: Sumeet A
authors.initials: SA
authors.lastname: Khetarpal
authors.forename: Andrew C
authors.initials: AC
authors.lastname: Edmondson
authors.forename: Avanthi
authors.initials: A
authors.lastname: Raghavan
authors.forename: Hemanth
authors.initials: H
authors.lastname: Neeli
authors.forename: Weijun
authors.initials: W
authors.lastname: Jin
authors.forename: Karen O
authors.initials: KO
authors.lastname: Badellino
authors.forename: Serkalem
authors.initials: S
authors.lastname: Demissie
authors.forename: Alisa K
authors.initials: AK
authors.lastname: Manning
authors.forename: Stephanie L
authors.initials: SL
authors.lastname: DerOhannessian
authors.forename: Megan L
authors.initials: ML
authors.lastname: Wolfe
authors.forename: L Adrienne
authors.initials: LA
authors.lastname: Cupples
authors.forename: Mingyao
authors.initials: M
authors.lastname: Li
authors.forename: Sekar
authors.initials: S
authors.lastname: Kathiresan
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Rader
mesh_terms: D020121:5' Untranslated Regions; D000328:Adult; D000368:Aged; D000483:Alleles; D008076:Cholesterol, HDL / Q000097:blood / Q000235:genetics* / Q000378:metabolism*; D005260:Female; D015870:Gene Expression; D005787:Gene Frequency; D005809:Genes, Regulator / Q000235:genetics; D055106:Genome-Wide Association Study; D005838:Genotype; D006239:Haplotypes / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D061307:Human Umbilical Vein Endothelial Cells; D006801:Humans; D008049:Lipase / Q000097:blood / Q000235:genetics* / Q000378:metabolism*; D050356:Lipid Metabolism / Q000235:genetics*; D008297:Male; D008875:Middle Aged; D016297:Mutagenesis, Site-Directed; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D011401:Promoter Regions, Genetic
chemical_list: D020121:5' Untranslated Regions; D008076:Cholesterol, HDL; C410382:LIPG protein, human; D008049:Lipase