Association testing by DNA pooling: an effective initial screen.

Aruna Bansal; Dirk van den Boom; Stefan Kammerer; Christiane Honisch; Gail Adam; Charles R Cantor; Patrick Kleyn; Andi Braun

doi:10.1073/pnas.262671399

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Association testing by DNA pooling: an effective initial screen.

Aruna Bansal·Dirk van den Boom·Stefan Kammerer·Christiane Honisch·Gail Adam·Charles R Cantor·Patrick Kleyn·Andi Braun

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Abstract

With an ever-increasing resource of validated single-nucleotide polymorphisms (SNPs), the limiting factors in genome-wide association analysis have become genotyping capacity and the availability of DNA. We provide a proof of concept of the use of pooled DNA as a means of efficiently screening SNPs and prioritizing them for further study. This approach reduces the final number of SNPs that undergo full, sample-by-sample genotyping as well as the quantity of DNA used overall. We have examined 15 SNPs in the cholesteryl ester transfer protein (CETP) gene, a gene previously demonstrated to be associated with serum high-density lipoprotein cholesterol levels. The SNPs were amplified in two pools of DNA derived from groups of individuals with extremely high and extremely low serum high-density lipoprotein cholesterol levels, respectively. P values <0.05 were obtained for 14 SNPs, supporting the described association. Genotyping of the individual samples showed that the average margin of error in frequency estimate was approximately 4% when pools were used. These findings clearly demonstrate the potential of pooling techniques and their associated technologies as an initial screen in the search for genetic associations.

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Adolescent Adult Aged Alleles Carrier Proteins Cholesterol Ester Transfer Proteins Cholesterol, HDL Female Gene Pool Glycoproteins Haplotypes Humans Middle Aged Polymorphism, Single Nucleotide Journal Article

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Aruna Bansal, Dirk van den Boom, Stefan Kammerer, Christiane Honisch, Gail Adam, Charles R Cantor, Patrick Kleyn, Andi Braun. 2002-12-10. Association testing by DNA pooling: an effective initial screen.. https://doi.org/10.1073/pnas.262671399

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