Computational protocol: Novel Crohn Disease Locus Identified by Genome-Wide Association Maps to a Gene Desert on 5p13.1 and Modulates Expression of PTGER4

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Protocol publication

[…] The database genome-wide expression analysis data was provided by W. Cookson (Imperial College, London, United Kingdom). Briefly, expression data were generated from RNA extracted from EBV-transformed cells from 378 genotyped offspring in nuclear families. Annotations for individual transcripts on the Affymetrix arrays were extracted from the Affymetrix NetAffx database (http://www.affymetrix.com). Data from the gene expression experiment was normalized together using the RMA (Robust Multi-Array Average) package [,] to remove any technical or spurious background variation. An inverse normalization transformation step was also applied to each trait to avoid any outliers. A variance components method was used to estimate heritability of each trait using Merlin-regress (RandomSample option) [, ]. For PTGER4, we obtained a mean quantitative expression value of −0.017 and a variance of 0.722 while the heritability estimate for PTGER4 estimated using the sibship data was 0.844. Association analysis was applied with Merlin (FASTASSOC option). We estimated an additive effect for SNPs and tested its significance using a score test that adjusts for familiality and takes into account uncertainty in the inference of missing genotypes. […]

Pipeline specifications

Software tools NetAffx, Merlin
Application Protein sequence analysis
Organisms Homo sapiens