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)

本数据集涵盖ARID1B或TSC2基因区域的外显子组拷贝数变异（CNV）呼叫结果及杂合单核苷酸多态性位点数据。该数据集以微软Excel电子表格格式存储，内含「summary」、「CNVkit_exome-aberrations」及「LOH_ARID1BandTSC2」三个工作表。「summary」工作表对其余所有工作表及其对应的数据列进行了详细说明。「CNVkit_exome-aberrations」工作表收录了由CNVkit 0.9.4.dev0工具检测得到的所有拷贝数不等于2的基因组片段。「LOH_ARID1BandTSC2」工作表包含在外周血淋巴细胞（PBL）、肾脏及肝脏AML样本中鉴定出的全部杂合单核苷酸变异位点：所有入选位点需满足每个样本在该位点的测序覆盖度不低于20bp（以降低采样偏差），且位点处于ARID1B基因（chr6[hg19]:156599064–158031913）或TSC2基因（chr16[hg19]:1597990–2638713）上下游500kb范围内。本研究采用R语言版本3.4.3中的费希尔精确检验（Fisher’s exact test），针对每个单核苷酸变异位点的PBL与AML样本测序读段覆盖度计算p值，以验证其等位基因频率与理论预期值是否存在显著偏离。本数据集为大小48kb的XLSX格式文件。