title: Targeted screening of cis-regulatory variation in human haplotypes.
abstract: Regulatory cis-acting variants account for a large proportion of gene expression variability in populations. Cis-acting differences can be specifically measured by comparing relative levels of allelic transcripts within a sample. Allelic expression (AE) mapping for cis-regulatory variant discovery has been hindered by the requirements of having informative or heterozygous single nucleotide polymorphisms (SNPs) within genes in order to assign the allelic origin of each transcript. In this study we have developed an approach to systematically screen for heritable cis-variants in common human haplotypes across >1,000 genes. In order to achieve the highest level of information per haplotype studied, we carried out allelic expression measurements by using both intronic and exonic SNPs in primary transcripts. We used a novel RNA pooling strategy in immortalized lymphoblastoid cell lines (LCLs) and primary human osteoblast cell lines (HObs) to allow for high-throughput AE. Screening hits from RNA pools were further validated by performing allelic expression mapping in individual samples. Our results indicate that >10% of expressed genes in human LCLs show genotype-linked AE. In addition, we have validated cis-acting variants in over 20 genes linked with common disease susceptibility in recent genome-wide studies. More generally, our results indicate that RNA pooling coupled with AE read-out by second generation sequencing or by other methods provides a high-throughput tool for cataloging the impact of common noncoding variants in the human genome.
authors.affiliation: Department of Human Genetics, McGill University, Montréal H3A 1B1, Canada.
authors.forename: Dominique J
authors.initials: DJ
authors.lastname: Verlaan
authors.forename: Bing
authors.initials: B
authors.lastname: Ge
authors.forename: Elin
authors.initials: E
authors.lastname: Grundberg
authors.forename: Rose
authors.initials: R
authors.lastname: Hoberman
authors.forename: Kevin C L
authors.initials: KC
authors.lastname: Lam
authors.forename: Vonda
authors.initials: V
authors.lastname: Koka
authors.forename: Joana
authors.initials: J
authors.lastname: Dias
authors.forename: Scott
authors.initials: S
authors.lastname: Gurd
authors.forename: Nicolas W
authors.initials: NW
authors.lastname: Martin
authors.forename: Hans
authors.initials: H
authors.lastname: Mallmin
authors.forename: Olof
authors.initials: O
authors.lastname: Nilsson
authors.forename: Eef
authors.initials: E
authors.lastname: Harmsen
authors.forename: Ken
authors.initials: K
authors.lastname: Dewar
authors.forename: Tony
authors.initials: T
authors.lastname: Kwan
authors.forename: Tomi
authors.initials: T
authors.lastname: Pastinen
mesh_terms: D000483:Alleles; D002460:Cell Line; D002874:Chromosome Mapping; D005091:Exons; D015870:Gene Expression; D053263:Gene Regulatory Networks; D005816:Genetic Complementation Test; D014644:Genetic Variation; D015894:Genome, Human; D055106:Genome-Wide Association Study; D006239:Haplotypes; D006801:Humans; D007438:Introns; D008214:Lymphocytes / Q000378:metabolism; D010006:Osteoblasts / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide