Genome-wide copy number variant data for inflammatory bowel disease in a caucasian population

Frenkel S1, Bernstein CN2, Jin YW1, Sargent M2, Kuang Q1, Jiang W1,3, Wei J4, Thiruvahindrapuram B4, Scherer SW4,5, Hu P1,3,6. Data Brief. 2019 Jul 2;25:104203. doi: 10.1016/j.dib.2019.104203. eCollection 2019 Aug.


Author information

Department of Biochemistry and Medical Genetics, The George and Fay Yee Centre for Healthcare Innovation, University of Manitoba, Winnipeg, MB, Canada.

Department of Internal Medicine, The University of Manitoba IBD Clinical and Research Centre, University of Manitoba, Winnipeg, MB, Canada.

Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.

The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.

Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.

Department of Electrical and Computer Engineering, University of Manitoba, Winnipeg, MB, Canada.


Genome-wide copy-number association studies offer new opportunities to identify the mechanisms underlying complex diseases, including chronic inflammatory, psychiatric disorders and others. We have used genotyping microarrays to analyse the copy-number variants (CNVs) from 243 Caucasian individuals with Inflammatory Bowel Disease (IBD). The CNV data was obtained by using multiple quality control measures and merging the results of three different CNV detection algorithms: PennCNV, iPattern, and QuantiSNP. The final dataset contains 4,402 CNVs detected by two or three algorithms independently with high confidence. This paper provides a detailed description of the data generation and quality control steps. For further interpretation of the data presented in this article, please see the research article entitled 'Copy number variation-based gene set analysis reveals cytokine signalling pathways associated with psychiatric comorbidity in patients with inflammatory bowel disease'.

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