Supplementary Figure 13: Copy number variant identified by RNA-seq data.

Unusual clustering of allele-specific reads from Vti1b led to identification of a ∼250-kb duplication. (a) Allele-specific and (b) total read counts for Vti1b. For two crosses (PWK/PhJ × CAST/EiJ and WSB/EiJ × CAST/EiJ), allele-specific read counts for biological replicates formed two clusters (red circles) for several consecutive genes on chromosome 12. The pattern was consistent across genes, with an overrepresentation of CAST/EiJ alleles in certain animals, coinciding with an overall higher level of total gene expression. This highly unusual pattern suggested a CAST/EiJ duplication in this region. (c) Further analysis of RNA-seq data suggested a CAST duplication affecting at least five genes (colored in red). A total of 12 DNA samples (n = 6 presumed three copy, n = 6 presumed two copy) were then examined with a high-density SNP array. Probe intensity data were used to identify duplication spanning at least 239 kb and encompassing the entire coding region of the five genes with unusual expression data. The flanking genes Pigh and Plekhh1 are expressed in the brain but do not show increased expression in mice with the duplication, suggesting that the duplication did not include regulatory sequences necessary for expression of these genes.