title: Exome-seq of human DIPG sample : Sample Pt-0227-DIPG
design: "The methodology described below is a minor modification of the approach described in ""The mutational landscape of lethal castration-resistant prostate cancer"" (Nature).  All captured DNA libraries were sequenced with the Illumina HiSeq in paired- end mode, yielding 80 base pairs from the final library fragments.  The reads were mapped as single reads to the reference human genome (NCBI build 36.1, hg18) using Bowtie.  A mismatched base (SNV) was identified as a variant when 1) it had at least six reads of support, 2) it constituted at least 10% of the coverage at that position, 3) it was observed on both strands, and 4) it fell within 50 bases of a region targeted for capture. In matched samples (samples with matched normals), a variant was called somatic if 1) there was 8x coverage in the matched normal, 2) it did not occur in the matched normal sample in more than two reads and 2% of the coverage (or 4% of the coverage if the tumor variant fraction was at least 20%), 3) if it had any support in the matched normal, and 4) it was not present in either dbSNP (v137) or the Exome Sequencing Project data set (ESP6500). In unmatched samples, a variant was called probable somatic if it affected the same codon as either a somatic point mutation observed in the matched samples or a somatic mutation from COSMIC (v66). Finally, all somatic/probable somatic variants were screened against the full set of benign samples. Variants were removed from further consideration if they appeared in any benign sample with at least three reads and 10% of the coverage. Copy number aberrations were quantified and reported for each gene as the segmented normalized log2-transformed exon coverage ratios between each tumor sample and its matched normal as described in ""Detection of Somatic Copy Number Alterations in Cancer Using Targeted Exome Capture Sequencing"" (Neoplasia).  For unmatched samples, we used the average coverage derived from the full set of benign samples as a 'normal pool;' for chromosomes X and Y only, we formed separate normal pools from the XX and XY benign samples.    If the mean exonic copy number showed a gain or loss of at least 30% and deviated from the null hypothesis by at least 2.5 s.d., we called the gene gained or lost."
attributes.tag: alignment_software
attributes.value: Bowtie