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


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2009-11

AUTHORS

Bing Ge, Dmitry K Pokholok, Tony Kwan, Elin Grundberg, Lisanne Morcos, Dominique J Verlaan, Jennie Le, Vonda Koka, Kevin C L Lam, Vincent Gagné, Joana Dias, Rose Hoberman, Alexandre Montpetit, Marie-Michele Joly, Edward J Harvey, Daniel Sinnett, Patrick Beaulieu, Robert Hamon, Alexandru Graziani, Ken Dewar, Eef Harmsen, Jacek Majewski, Harald H H Göring, Anna K Naumova, Mathieu Blanchette, Kevin L Gunderson, Tomi Pastinen

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. More... »

PAGES

1216-1222

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/ng.473

DOI

http://dx.doi.org/10.1038/ng.473

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1035940427

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/19838192


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