Influence of human genome polymorphism on gene expression.
Genetic variation, through its effects on gene expression, plays a crucial role in phenotypic variation and disease susceptibility. Recent studies from our group and others have integrated a number of resources and technologies to assess several aspects of genome variation affecting gene expression. Some of these large-scale mapping studies involving expression quantitative traits have recently been reviewed [Gibson, G. and Weir, B. (2005) The quantitative genetics of transcription. Trends Genet., 21, 616-623; de Koning, D.J. and Haley, C.S. (2005) Genetical genomics in humans and model organisms. Trends Genet., 21, 377-381], with particular attention to the statistical issues. In this review, we compare allele-specific expression studies in human samples (primarily lymphoblastoid cell lines from the CEPH HapMap panel), as a prelude to a discussion on study design issues and sources of variation, in order to propose the steps required to build a detailed map of cis-acting regulatory variation in the human genome. Obtaining panels of tissues from large numbers of individuals remains an important limitation. We also conclude that there is insufficient knowledge as to the feasibility of comprehensive studies of trans-acting variation in the human genome.
Pastinen
Tomi
T
Genome Quebec Innovation Centre, McGill University, Room 7105, 740 Dr Penfield Avenue, Montreal, Que., Canada H3A 1A4.
Ge
Bing
B
Hudson
Thomas J
TJ
D000483:Alleles; D002874:Chromosome Mapping; D005786:Gene Expression Regulation; D015894:Genome, Human; D006239:Haplotypes; D006801:Humans; D008954:Models, Biological; D008957:Models, Genetic; D011110:Polymorphism, Genetic; D040641:Quantitative Trait Loci