Supplementary Table S12 from A Functional Survey of the Regulatory Landscape of Estrogen Receptor–Positive Breast Cancer Evolution

Supplementary Table S12: Summary of SNVs and INDELs identified by SIDV. S12.1: full list of SNVs and INDELs. Chromosome and position on the chromosome (hg38 coordinates) are indicated for each variant, along with the reference and detected alternative allele. Also, the table indicates the donor, and whether the variant allele was directly detected in the primary (P_CALL) and/or the metastatic material (M_CALL). S12.2: tumor purity estimation for each sample and site (P = primary; M = metastasis) is listed, along with the size of the subset of SNVs used for the purity estimation analysis. S12.3: final annotation of the SNVs after sample-specific purity correction. For each SNV, genomic coordinates, reference and alternative alleles, donor identifier, and evidence (filtered read counts) supporting the different alleles in normal (N), primary (P) and metastatic (M) samples are provided. For both primary and metastatic samples, the variant allele frequency (VAF), along with the estimated purity for the sample, the estimated copy number alterations of the region bearing the variant (CNA) and the purity-corrected VAF, or cancer-cell fraction (CCF), are indicated. S12.4: regions showing an enrichment in either amplifications (amp) or deletions (del) across the metastatic samples as compared to the matched primary samples, are indicated.