A Multilocus Genotyping Assay for Candidate Markers of Cardiovascular Disease Risk
- Suzanne Cheng1,9,
- Michael A. Grow1,
- Céline Pallaud2,
- William Klitz3,
- Henry A. Erlich1,
- Sophia Visvikis2,
- John J. Chen3,4,
- Clive R. Pullinger5,
- Mary J. Malloy6,7,
- Gérard Siest2, and
- John P. Kane6,8
- 1Department of Human Genetics, Roche Molecular Systems, Inc., Alameda, California 94501 USA; 2Centre de Médecine Préventive, 54501 Vandoeuvre-lès-Nancy, France; 3School of Public Health and 4Department of Integrative Biology, University of California at Berkeley, Berkeley, California 94720 USA; 5Cardiovascular Research Institute, 6Department of Medicine, 7Department of Pediatrics, and 8Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94143 USA
Abstract
A number of chronic diseases, including cardiovascular disease, appear to have a multifactorial genetic risk component. Consequently, techniques are needed to facilitate evaluation of complex genetic risk factors in large cohorts. We have designed a prototype assay for genotyping a panel of 35 biallelic sites that represent variation within 15 genes from biochemical pathways implicated in the development and progression of cardiovascular disease. Each DNA sample is amplified using two multiplex polymerase chain reactions, and the alleles are genotyped simultaneously using an array of immobilized, sequence-specific oligonucleotide probes. This multilocus assay was applied to two types of cohorts. Population frequencies for the markers were estimated using 496 unrelated individuals from a family-based cohort, and the observed values were consistent with previous reports. Linkage disequilibrium between consecutive pairs of markers within theapoCIII, LPL, and ELAM genes was also estimated. A preliminary analysis of single and pairwise locus associations with severity of atherosclerosis was performed using a composite cohort of 142 individuals for whom quantitative angiography data were available; evaluation of the potentially interesting associations observed will require analysis of an independent and larger cohort. This assay format provides a research tool for studies of multilocus genetic risk factors in large cardiovascular disease cohorts, and for the subsequent development of diagnostic tests.
