Analysis of lipoprotein lipase haplotypes reveals associations not apparent from analysis of the constituent loci

Associations of three lipoprotein lipase gene polymorphisms, lipid profiles and coronary artery disease

Lipoprotein lipase (LPL) plays a central role in lipoprotein metabolism by hydrolyzing the core triglycerides (TGs) of circulating chylomicrons and very-low-density lipoprotein (VLDL). The effects of LPL polymorphisms on lipid levels and coronary artery disease (CAD) have been inconsistent among studies and populations. To assess the lipid profiles and distributions of three LPL gene polymorphisms in Saudi patients with CAD, the HindIII, PvuII and Ser447Ter polymorphisms in the LPL gene were analyzed in 226 patients with CAD and 110 controls. Polymerase chain reaction-restriction fragment length polymorphism was used to detect LPL gene polymorphisms. The plasma lipid profiles of the patients were determined using standard enzymatic methods. Patients in the CAD group had significantly higher triglyceride (TG), total cholesterol (TC) and low-density lipoprotein cholesterol (LDL-C) levels than controls irrespective of the HindIII, PvuII or Ser447Ter genotype. Compared to the findings in controls, the HindIII TT, PvuII TC and Ser447Ter CC genotypes were associated with significantly reduced high-density lipoprotein cholesterol (HDL-C) levels in patients with CAD (P<0.0001). In summary, there are associations between LPL gene variants and high plasma TG, TC and LDL-C levels as well as low HDL-C levels.

A method for the assessment of disease associations with single-nucleotide polymorphism haplotypes and environmental variables in case-control studies

The rough draft of the human genome map has been used to identify most of the functional genes in the human genome, as well as to identify nucleotide variations, known as "single-nucleotide polymorphisms" (SNPs), in these genes. By use of advanced biotechnologies, researchers are beginning to genotype thousands of SNPs from biological samples. Among the many possible applications, one of them is the study of SNP associations with complex human diseases, such as cancers or coronary heart diseases, by using a case-control study design. Through the gathering of environmental risk factors and other lifestyle factors, such a study can be effectively used to investigate interactions between genes and environmental factors in their associations with disease phenotype. Earlier, we developed a method to statistically construct individuals' haplotypes and to estimate the distribution of haplotypes of multiple SNPs in a defined population, by use of estimating-equation techniques. Extending this idea, we describe here an analytic method for assessing the association between the constructed haplotypes along with environmental factors and the disease phenotype. This method is also robust to the model assumptions and is scalable to a large number of SNPs. Asymptotic properties of estimations in the method are proved theoretically and are tested for finite sample sizes by use of simulations. To demonstrate the use of the method, we applied it to assess the possible association between apolipoprotein CIII (six coding SNPs) and restenosis by using a case-control data set. Our analysis revealed two haplotypes that may reduce the risk of restenosis.