Global patterns of cis variation in human cells revealed by high-density allelic expression analysis Export

@article{citeulike:5971220, abstract = {Cis-acting variants altering gene expression are a source of phenotypic differences. The cis-acting components of expression variation can be identified through the mapping of differences in allelic expression (AE), which is the measure of relative expression between two allelic transcripts. We generated a map of AE associated SNPs using quantitative measurements of AE on Illumina Human1M BeadChips. In 53 lymphoblastoid cell lines derived from donors of European descent, we identified common cis variants affecting 30\% (2935/9751) of the measured RefSeq transcripts at 0.001 permutation significance. The pervasive influence of cis-regulatory variants, which explain 50\% of population variation in AE, extend to full-length transcripts and their isoforms as well as to unannotated transcripts. These strong effects facilitate fine mapping of cis-regulatory SNPs, as demonstrated by dissection of heritable control of transcripts in the systemic lupus erythematosus–associated C8orf13-BLK region in chromosome 8. The dense collection of associations will facilitate large-scale isolation of cis-regulatory SNPs.}, author = {Ge, Bing and Pokholok, Dmitry K. and Kwan, Tony and Grundberg, Elin and Morcos, Lisanne and Verlaan, Dominique J. and Le, Jennie and Koka, Vonda and Lam, Kevin C. L. and Gagne, Vincent and Dias, Joana and Hoberman, Rose and Montpetit, Alexandre and Joly, Marie-Michele and Harvey, Edward J. and Sinnett, Daniel and Beaulieu, Patrick and Hamon, Robert and Graziani, Alexandru and Dewar, Ken and Harmsen, Eef and Majewski, Jacek and Goring, Harald H. H. and Naumova, Anna K. and Blanchette, Mathieu and Gunderson, Kevin L. and Pastinen, Tomi}, citeulike-article-id = {5971220}, citeulike-linkout-0 = {http://dx.doi.org/10.1038/ng.473}, citeulike-linkout-1 = {http://dx.doi.org/10.1038/ng.473}, day = {18}, doi = {10.1038/ng.473}, issn = {1061-4036}, journal = {Nature Genetics}, keywords = {allelic\_expression, bioinformatics, genetics, methods}, month = {October}, number = {11}, pages = {1216--1222}, posted-at = {2009-10-20 20:48:36}, priority = {5}, publisher = {Nature Publishing Group}, title = {Global patterns of cis variation in human cells revealed by high-density allelic expression analysis}, url = {http://dx.doi.org/10.1038/ng.473}, volume = {41}, year = {2009} }

TY - JOUR ID - citeulike:5971220 L3 - citeulike-article-id:5971220 N2 - Cis-acting variants altering gene expression are a source of phenotypic differences. The cis-acting components of expression variation can be identified through the mapping of differences in allelic expression (AE), which is the measure of relative expression between two allelic transcripts. We generated a map of AE associated SNPs using quantitative measurements of AE on Illumina Human1M BeadChips. In 53 lymphoblastoid cell lines derived from donors of European descent, we identified common cis variants affecting 30% (2935/9751) of the measured RefSeq transcripts at 0.001 permutation significance. The pervasive influence of cis-regulatory variants, which explain 50% of population variation in AE, extend to full-length transcripts and their isoforms as well as to unannotated transcripts. These strong effects facilitate fine mapping of cis-regulatory SNPs, as demonstrated by dissection of heritable control of transcripts in the systemic lupus erythematosus–associated C8orf13-BLK region in chromosome 8. The dense collection of associations will facilitate large-scale isolation of cis-regulatory SNPs. IS - 11 JF - Nature Genetics SN - 1061-4036 EP - 1222 TI - Global patterns of cis variation in human cells revealed by high-density allelic expression analysis PB - Nature Publishing Group VL - 41 SP - 1216 KW - allelic_expression KW - bioinformatics KW - genetics KW - methods AU - Ge, Bing AU - Pokholok, Dmitry AU - Kwan, Tony AU - Grundberg, Elin AU - Morcos, Lisanne AU - Verlaan, Dominique AU - Le, Jennie AU - Koka, Vonda AU - Lam, Kevin AU - Gagne, Vincent AU - Dias, Joana AU - Hoberman, Rose AU - Montpetit, Alexandre AU - Joly, Marie-Michele AU - Harvey, Edward AU - Sinnett, Daniel AU - Beaulieu, Patrick AU - Hamon, Robert AU - Graziani, Alexandru AU - Dewar, Ken AU - Harmsen, Eef AU - Majewski, Jacek AU - Goring, Harald AU - Naumova, Anna AU - Blanchette, Mathieu AU - Gunderson, Kevin AU - Pastinen, Tomi PY - 2009/10/18/ UR - http://dx.doi.org/10.1038/ng.473 ER -