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Methods

Survey of allelic expression using EST mining

McGill University and Genome Quebec Innovation Centre, Montreal, Quebec H3A 1A, Canada

Cis-acting allelic variation in gene regulation is a source of phenotypic variation. Consequently, recent studies have experimentally screened human genes in an attempt to initiate a catalog of genes possessing cis-acting variants. In this study, we use human EST data in dbEST as the source of allelic expression data, and the HapMap database to provide expected allele frequencies in human populations. We demonstrate a greater concordance of allele frequencies estimated from human ESTs in dbEST with those derived from the CEPH HapMap sample representing Caucasians from northern and western Europe, than population samples obtained in Asia and Africa. Deviations between allele frequencies observed in EST databases and the ones obtained from the CEPH HapMap samples may result from common heritable cis-acting variants altering the relative allele distribution in RNA. We provide in silico as well as experimental evidence that this strategy does allow significant enrichment of genes harboring common heritable cis-acting polymorphisms in linkage disequilibrium with expressed alleles.

Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.4023805. Freely available online through the Genome Research Immediate Open Access option.

¹ Corresponding author.
E-mail tomi.pastinen1{at}staff.mcgill.ca; fax (514) 398-2622.

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