DOI: 10.5061/dryad.cg40g
title: Data from: Mutation screening of 1,237 cancer genes across six model cell lines of basal-like breast cancer

description: Basal-like breast cancer is an aggressive subtype generally characterized
 as poor prognosis and lacking the expression of the three most important
 clinical biomarkers, estrogen receptor, progesterone receptor, and HER2.
 Cell lines serve as useful model systems to study cancer biology in vitro
 and in vivo. We performed mutational profiling of six basal-like breast
 cancer cell lines (HCC38, HCC1143, HCC1187, HCC1395, HCC1954, and HCC1937)
 and their matched normal lymphocyte DNA using targeted capture and
 next-generation sequencing of 1,237 cancer-associated genes, including all
 exons, UTRs and upstream flanking regions. In total, 658 somatic variants
 were identified, of which 378 were non-silent (average 63 per cell line,
 range 37–146) and 315 were novel (not present in the Catalogue of Somatic
 Mutations in Cancer database; COSMIC). 125 novel mutations were confirmed
 by Sanger sequencing (59 exonic, 48 3’UTR and 10 5’UTR, 1 splicing), with
 a validation rate of 94% of high confidence variants. Of 36 mutations
 previously reported for these cell lines but not detected in our exome
 data, 36% could not be detected by Sanger sequencing. The base
 replacements C/G&gt;A/T, C/G&gt;G/C, C/G&gt;T/A and
 A/T&gt;G/C were significantly more frequent in the coding regions
 compared to the non-coding regions (OR 3.2, 95% CI 2.0–5.3,
 P&lt;0.0001; OR 4.3, 95% CI 2.9–6.6, P&lt;0.0001; OR 2.4, 95% CI
 1.8–3.1, P&lt;0.0001; OR 1.8, 95% CI 1.2–2.7, P = 0.024,
 respectively). The single nucleotide variants within the context of
 T[C]T/A[G]A and T[C]A/T[G]A were more frequent in the coding than in the
 non-coding regions (OR 3.7, 95% CI 2.2–6.1, P&lt;0.0001; OR 3.8, 95%
 CI 2.0–7.2, P = 0.001, respectively). Copy number estimations were derived
 from the targeted regions and correlated well to Affymetrix SNP array copy
 number data (Pearson correlation 0.82 to 0.96 for all compared cell lines;
 P&lt;0.0001). These mutation calls across 1,237 cancer-associated
 genes and identification of novel variants will aid in the design and
 interpretation of biological experiments using these six basal-like breast
 cancer cell lines.
description: 6basalBC_bams.tar.gz.splita6basalBC_bams.tar.gz, split, part a (of 16 parts, a-p, ~1GB/each). Archive contains targeted region BED file and sequencing data BAM files for 6 basal-like breast cancer cell lines (HCC38, HCC1143, HCC1187, HCC1395, HCC1954, HCC1937; each suffixed with "T") and their corresponding normal DNA sample (each suffixed with "BL"), using hg19 coordinates.6basalBC_bams.tar.gz.splitb6basalBC_bams.tar.gz, split, part b.6basalBC_bams.tar.gz.splitc6basalBC_bams.tar.gz, split, part c.6basalBC_bams.tar.gz.splitd6basalBC_bams.tar.gz, split, part d.6basalBC_bams.tar.gz.splite6basalBC_bams.tar.gz, split, part e.6basalBC_bams.tar.gz.splitf6basalBC_bams.tar.gz, split, part f.6basalBC_bams.tar.gz.splitg6basalBC_bams.tar.gz, split, part g.6basalBC_bams.tar.gz.splith6basalBC_bams.tar.gz, split, part h.6basalBC_bams.tar.gz.spliti6basalBC_bams.tar.gz, split, part i.6basalBC_bams.tar.gz.splitj6basalBC_bams.tar.gz, split, part j.6basalBC_bams.tar.gz.splitk6basalBC_bams.tar.gz, split, part k.6basalBC_bams.tar.gz.splitl6basalBC_bams.tar.gz, split, part L.6basalBC_bams.tar.gz.splitm6basalBC_bams.tar.gz, split, part m.6basalBC_bams.tar.gz.splitn6basalBC_bams.tar.gz, split, part n.6basalBC_bams.tar.gz.splito6basalBC_bams.tar.gz, split, part o.6basalBC_bams.tar.gz.splitp6basalBC_bams.tar.gz, split, part p (final part).