Genome-wide association studies identified novel loci for non-high-density lipoprotein cholesterol and its postprandial lipemic response

Ping An, Robert J. Straka, Toni I. Pollin, Mary F. Feitosa, Mary K. Wojczynski, E. Warwick Daw, Jeffrey R. O'Connell, Quince Gibson, Kathleen A. Ryan, Paul N. Hopkins, Michael Y. Tsai, Chao Qiang Lai, Michael A. Province, Jose M. Ordovas, Alan R. Shuldiner, Donna K. Arnett, Ingrid B. Borecki

Research output: Contribution to journalArticlepeer-review

10 Scopus citations


Non-high-density lipoprotein cholesterol(NHDL) is an independent and superior predictor of CVD risk as compared to low-density lipoprotein alone. It represents a spectrum of atherogenic lipid fractions with possibly a distinct genomic signature. We performed genome-wide association studies (GWAS) to identify loci influencing baseline NHDL and its postprandial lipemic (PPL) response. We carried out GWAS in 4,241 participants of European descent. Our discovery cohort included 928 subjects from the Genetics of Lipid-Lowering Drugs and Diet Network Study. Our replication cohorts included 3,313 subjects from the Heredity and Phenotype Intervention Heart Study and Family Heart Study. A linear mixed model using the kinship matrix was used for association tests. The best association signal was found in a tri-genic region at RHOQ-PIGF-CRIPT for baseline NHDL (lead SNP rs6544903, discovery p = 7e-7, MAF = 2 %; validation p = 6e-4 at 0.1 kb upstream neighboring SNP rs3768725, and 5e-4 at 0.7 kb downstream neighboring SNP rs6733143, MAF = 10 %). The lead and neighboring SNPs were not perfect surrogate proxies to each other (D′ = 1, r2 = 0.003) but they seemed to be partially dependent (likelihood ration test p = 0.04). Other suggestive loci (discovery p < 1e-6) included LOC100419812 and LOC100288337 for baseline NHDL, and LOC100420502 and CDH13 for NHDL PPL response that were not replicated (p > 0.01). The current and first GWAS of NHDL yielded an interesting common variant in RHOQ-PIGF-CRIPT influencing baseline NHDL levels. Another common variant in CDH13 for NHDL response to dietary high-fat intake challenge was also suggested. Further validations for both loci from large independent studies, especially interventional studies, are warranted.

Original languageEnglish
Pages (from-to)919-930
Number of pages12
JournalHuman Genetics
Issue number7
StatePublished - Jul 2014

Bibliographical note

Funding Information:
Acknowledgments the authors thank the other investigators, the staff and the participants of the GOlDn study, the HaPI Heart study and the Family Heart study. the GOlDn study support was provided by the nHlBI grant U01 Hl072524. the FamHs was supported by nIH Grants r01 Hl087700 and r01 Hl088215 (Michael a. Province, PI) from nHlBI, and r01 DK8925601 and r01 075681 (Ingrid B. Borecki, PI) from nIDDK. the investigators thank the GOlDn and FamHs participants and staff for their valuable contributions. the HaPI Heart study was supported by nIH research Grants U01 Hl072515, r01 Hl104193, U01 Hl084756 and the Mid atlantic nutrition and Obesity research Center Grant P30 DK072488. We thank the staff at the amish research Clinic for their outstanding efforts and our amish research volunteers for their long-standing partnership in research.

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)


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