Authors
Greg Gibson, Youssef Idaghdour, Wendy Czika, Kelci Miclaus, Sang H. Lee, Peter M. Visscher, and Russell D. Wolfinger
Summary
Studies of the genetics of gene expression reveal expression SNPs (eSNP) that explain variation in transcript abundance. Here we report a step-by-step protocol of a whole genome gene expression association mapping procedure using JMP Genomics (SAS Institute, Cary, NC) as described in ref. 1. The method accounts for population structure, ethnicity, relatedness and other variables and was applied on a sample of 194 individuals from a city and two villages in southern Morocco representing two ethnicities and a wide range of family relationships. Gene expression genome-wide association testing between 516,792 SNPs from Illumina Human 610-Quad beadchips with expression measurements at 22,300 probes from Illumina HumanHT12 beadchips was performed. Filtering via Pearson correlation tests between expression and SNP genotypes was used prior to testing with more complex models that contained several fixed effects and relatedness between individuals as a random effect. These models were run using processes implemented in JMP Genomics 4.1 released by SAS in December 2009.Further details
The protocol was published on Protocol Exchange on 15 December 2009. To see the entire protocol, click on the source link.Advertisement
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