Additional file 2: of Dissecting TSC2-mutated renal and hepatic angiomyolipomas in an individual with ARID1B-associated intellectual disability

Exome CNV calls and heterozygous SNPs in the ARID1B or TSC2 region. Microsoft Excel spreadsheet file containing the worksheets “summary”, “CNVkit_exome-aberrations” and “LOH_ARID1BandTSC2”. The “summary” worksheet contains a detailed description of all other worksheets and the respective data columns. The “CNVkit_exome-aberrations” worksheet contains all the segments called by CNVkit 0.9.4.dev0 which have a copy numer different from 2. The “LOH_ARID1BandTSC2” worksheet contains all heterozygous single nucleotide variants called in the PBL and both kindey and liver AML samples with at least 20 bp coverage in each sample (to reduce sampling bias) with 500 k bases of the ARID1B (chr6[hg19]:156599064–158,031,913) or TSC2 (chr16[hg19]:1597990–2,638,713) gene. Fisher’s exact test from R version 3.4.3 was used to calculate p-values between the PBL and AML read coverages at each SNV position to check for significant deviation from the expected allele fraction. (XLSX 48 kb)