Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls

Abstract

Copy number variants (CNVs) account for a major proportion of human genetic polymorphism and have been predicted to have an important role in genetic susceptibility to common disease. To address this we undertook a large, direct genome-wide study of association between CNVs and eight common human diseases. Using a purpose-designed array we typed approximately 19,000 individuals into distinct copy-number classes at 3,432 polymorphic CNVs, including an estimated approximately 50% of all common CNVs larger than 500 base pairs. We identified several biological artefacts that lead to false-positive associations, including systematic CNV differences between DNAs derived from blood and cell lines. Association testing and follow-up replication analyses confirmed three loci where CNVs were associated with disease-IRGM for Crohn's disease, HLA for Crohn's disease, rheumatoid arthritis and type 1 diabetes, and TSPAN8 for type 2 diabetes-although in each case the locus had previously been identified in single nucleotide polymorphism (SNP)-based studies, reflecting our observation that most common CNVs that are well-typed on our array are well tagged by SNPs and so have been indirectly explored through SNP studies. We conclude that common CNVs that can be typed on existing platforms are unlikely to contribute greatly to the genetic basis of common human diseases.

Box Figure 1

Box Figure 2

Box Figure 3

Figure 1. Flow-chart showing which CNVs are included on the array

The chart shows the reasons for CNVs being removed from consideration (the column of arrows and text to the right of the figure) from those originally targeted on the array and the number of CNVs remaining at each stage of filtering.

Figure 2. Illustrative CNVs

Histograms of three multiallelic CNVs (one per row) previously reported to be associated with autoimmune diseases: Beta-Defensin (CNVR3771.10), CCL3L1 (CNVR7077.12) and FCGR3B (CNVR383.1), showing 6, 5, and 4 fitted copy number classes respectively. The histogram of normalised intensity ratios is shown for one control and the three autoimmune collections. Histograms are overlaid by the fitted distribution used to model each class (variously the red, blue, light green, cyan, magenta and dark green curves). In all such figures, the area under the fitted curve of a particular colour is the same for all collections at the same CNV.

Figure 3. Genome-wide association results

Distribution of −log10(p) along the 23 chromosomes where p is the p-value for the one degree-of-freedom test of association for each disease. The x-axis shows the chromosomes numbered from 1 (on the left) to X (on the right). CNVs included in these plots were filtered on the basis of a clustering quality score (see SoM for details) and manual inspection of the most significant associations. The two apparent associations on chromosome 2 for rheumatoid arthritis and type 1 diabetes result from a dispersed duplication in which the variation is actually located within the HLA locus (see Box).