Research Project:
NUTRITION, CARDIOVASCULAR HEALTH, AND GENOMICS
Location: Human Nutrition Research Center on Aging
Title: A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study
Authors
| Kathiresan, Sekar - MA GENERAL HOSPITAL | | Manning, Alisa - FRAMINGHAM HEART STUDY | | Demissie, Serkalem - FRAMINGHAM HEART STUDY | | D'Agostino, Ralph - FRAMINGHAM HEART STUDY | | Surti, Aarti - BROAD INST. MIT, HARVARD | | Guiducci, Candace - BROAD INST. MIT, HARVARD | | Gianniny, Lauren - BROAD INST. MIT, HARVARD | | Burtt, Noel - BROAD INST. MIT, HARVARD | | Melander, Olle - LUND UNIV. SWITZERLAND | | Arnett, Donna - UNIV OF ALABAMA, BIRM. | | Peloso, Gina - FRAMINGHAM HEART STUDY | |
Ordovas, Jose
| | Cupples, L - FRAMINGHAM HEART STUDY | | Orho-Melander, Marju - LUND UNIV. SWITZERLAND |
Submitted to: BMC Medical Genetics
Publication Type:
Peer Reviewed Journal
Publication Acceptance Date: August 5, 2007
Publication Date: September 19, 2007
Citation: Kathiresan, S., Manning, A.K., Demissie, S., D'Agostino, R.B., Surti, A., Guiducci, C., Gianniny, L., Burtt, N., Melander, O., Arnett, D.K., Peloso, G.M., Ordovas, J.M., Cupples, L.A., Orho-Melander, M. 2007. A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study. BMC Medical Genetics. 8:1.
Interpretive Summary: Blood lipid levels including low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), and triglycerides(TG) are highly heritable. The study of large numbers of polymorphisms using what is known as genome-wide association studies, is a promising approach to find new genes related to these heritable risk factors for cardiovascular diseases. Our study was carried out in 1087 Framingham Heart Study Offspring cohort participants. Using gene chips we examined 100,000 polymorphisms distributed across the genome for associations with blood lipid levels. Some results confirmed previously reported associations with candidate genes including variation in the lipoprotein lipase gene (/LPL/) and HDL-C and TGs. However, we did not identify new genes associated with blood lipids. This may be due to insufficient statistical power to detect modest effects or reduced genomic coverage of the 100K array. Therefore, a denser genome-wide genotyping platform and a better-powered replication strategy need to be used to identify novel genes underlying blood lipids.
Technical Abstract: Abstract Background: 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.
Methods: 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 3 10%, genotypic call rate 3 80%, and Hardy-Weinberg equilibrium p3 0.001) and multivariable-adjusted residuals. We pursued a three-stage replication strategy for 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 (n6650 individuals).
Results: 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 TG or HDL (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.
Conclusions: 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.
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