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Papers In Press, published online ahead of print February 1, 2007
J. Lipid Res., doi:10.1194/jlr.M600372-JLR200

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Journal of Lipid Research, Vol. 48, 434-443, February 2007
Copyright © 2007 by American Society for Biochemistry and Molecular Biology

High-density genotyping and functional SNP localization in the CETP gene

John F. Thompson^1,*, Linda S. Wood^*, Eve H. Pickering, Bryan DeChairo and Craig L. Hyde

^* Pharmacogenomics, Pfizer Global Research and Development, Groton, CT 06340
Statistical Applications, Pfizer Global Research and Development, Groton, CT 06340
Molecular Profiling, Pfizer Global Research and Development, Groton, CT 06340

The online version of this article (available at http://www.jlr.org) contains supplemental data in the form of one figure and one table.

Published, JLR Papers in Press, November 15, 2006.

¹ To whom correspondence should be addressed. e-mail: john.f.thompson{at}pfizer.com

The cholesteryl ester transfer protein gene (CETP) has been the subject of hundreds of genetic analyses that typically focus on a small number of polymorphisms within a single ethnic group. Furthermore, the extent of DNA beyond the transcribed sequence from which single nucleotide polymorphisms (SNPs) may influence CETP expression has not been well defined. To better understand the role of natural variation in modulating CETP and high density lipoprotein-cholesterol (HDL-C) levels, dense genotyping of CETP and regions up to 15 kb on either side of the gene was carried out on >2,000 individuals. A complex, nonlinear set of linkage disequilibrium bins was found, with many bins interspersed along the DNA sequence and spread over large regions of the gene. Bins assigned based on large numbers of individuals matched the small subset of SNPs that had been assigned to bins previously with a small number of individuals. Associations of known functional SNPs with HDL-C were found, but there were suggestions that there are additional functional SNPs not characterized previously. Narrowing of the set of likely functional SNPs was accomplished by comparing associations observed in different ethnic groups. The promoter SNP most highly associated with HDL-C that is likely to be functional, position –4,502, alters a consensus transcription factor binding site.

Supplementary key words genetics • high density lipoprotein • single nucleotide polymorphism • cholesteryl ester transfer protein

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