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Fig. 1 | BMC Medical Genetics

Fig. 1

From: Genome-wide rare copy number variation screening in ulcerative colitis identifies potential susceptibility loci

Fig. 1

Analysis Workflow. Affymetrix 6.0 data sets for the German (discovery) sample as well as WTCCC2 (UK replication) sample were processed with Affymetrix power tools (APT). Sample cleaning was based on identity by state (IBS) and principal component analysis (PCA) to exclude non-Caucasian samples as well as relatives. The remaining data sets were converted into the CNVineta format. 151 CNVs overrepresented in cases were identified after screening for rare CNVs in the German discovery sample, of which 14 deletion and 10 duplications remained after manual inspection. These 24 CNVs were further evaluated in two independent replication samples, one German and one British (WTCCC2). Dup7p22.1 and Dup8q24.3 were relevant only in UK (Affy6.0) sample, while Del13q32.1 was replicated only in the German (TaqMan) sample. Fine mapping for the deletion was done by Sanger sequencing, while custom array-CGH was used for the two duplications. The status of the 3 relevant CNVs was further evaluated in a Norwegian sample (Affy6.0), a Lithuanian sample (TaqMan) and a control sample of various European individuals from previous published studies. Details of the in silico controls (origins, genotyping platform and probe coverage for the three CNV regions) are found in Additional file 1: Table S2. M.A.R.V (Mega Analysis of Rare Variants) approach was used for combining data from different panels

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