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This article is part of the supplement: The Framingham Heart Study 100,000 single nucleotide polymorphisms resource

Open Access Research

A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study

Sekar Kathiresan123, Alisa K Manning14, Serkalem Demissie14, Ralph B D'Agostino15, Aarti Surti2, Candace Guiducci2, Lauren Gianniny2, Nöel P Burtt2, Olle Melander6, Marju Orho-Melander7, Donna K Arnett8, Gina M Peloso14, Jose M Ordovas9 and L Adrienne Cupples14*

Author Affiliations

1 National Heart Lung and Blood Institute's Framingham Heart Study, Framingham, MA, USA

2 Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA

3 Cardiovascular Disease Prevention Center, Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA

4 School of Public Health, Boston University, Boston, MA, USA

5 Department of Mathematics and Statistics, Boston University, Boston, MA, USA

6 Department of Clinical Sciences, Hypertension and Cardiovascular Diseases, University Hospital Malmö, Lund University, Malmö, Sweden

7 Diabetes and Endocrinology, University Hospital Malmö, Lund University, Malmö, Sweden

8 Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA

9 Nutrition and Genomics Laboratory, Jean Mayer-USDA Human Nutrition Research Center at Tufts University, Boston, MA, USA

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BMC Medical Genetics 2007, 8(Suppl 1):S17  doi:10.1186/1471-2350-8-S1-S17

Published: 19 September 2007



Blood lipid levels including low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), and triglycerides (TG) are highly heritable. Genome-wide association is a promising approach to map genetic loci related to these heritable phenotypes.


In 1087 Framingham Heart Study Offspring cohort participants (mean age 47 years, 52% women), we conducted genome-wide analyses (Affymetrix 100K GeneChip) for fasting blood lipid traits. Total cholesterol, HDL-C, and TG were measured by standard enzymatic methods and LDL-C was calculated using the Friedewald formula. The long-term averages of up to seven measurements of LDL-C, HDL-C, and TG over a ~30 year span were the primary phenotypes. We used generalized estimating equations (GEE), family-based association tests (FBAT) and variance components linkage to investigate the relationships between SNPs (on autosomes, with minor allele frequency ≥10%, genotypic call rate ≥80%, and Hardy-Weinberg equilibrium p ≥ 0.001) and multivariable-adjusted residuals. We pursued a three-stage replication strategy of the GEE association results with 287 SNPs (P < 0.001 in Stage I) tested in Stage II (n ~1450 individuals) and 40 SNPs (P < 0.001 in joint analysis of Stages I and II) tested in Stage III (n~6650 individuals).


Long-term averages of LDL-C, HDL-C, and TG were highly heritable (h2 = 0.66, 0.69, 0.58, respectively; each P < 0.0001). Of 70,987 tests for each of the phenotypes, two SNPs had p < 10-5 in GEE results for LDL-C, four for HDL-C, and one for TG. For each multivariable-adjusted phenotype, the number of SNPs with association p < 10-4 ranged from 13 to 18 and with p < 10-3, from 94 to 149. Some results confirmed previously reported associations with candidate genes including variation in the lipoprotein lipase gene (LPL) and HDL-C and TG (rs7007797; P = 0.0005 for HDL-C and 0.002 for TG). The full set of GEE, FBAT and linkage results are posted at the database of Genotype and Phenotype (dbGaP). After three stages of replication, there was no convincing statistical evidence for association (i.e., combined P < 10-5 across all three stages) between any of the tested SNPs and lipid phenotypes.


Using a 100K genome-wide scan, we have generated a set of putative associations for common sequence variants and lipid phenotypes. Validation of selected hypotheses in additional samples did not identify any new loci underlying variability in blood lipids. Lack of replication may be due to inadequate statistical power to detect modest quantitative trait locus effects (i.e., <1% of trait variance explained) or reduced genomic coverage of the 100K array. GWAS in FHS using a denser genome-wide genotyping platform and a better-powered replication strategy may identify novel loci underlying blood lipids.