Paired Tumor-Normal Whole-Exome Sequencing

Four hundred thirty cases of paired tumor-normal whole-exome sequencing data were obtained from the Sequence Read Archive^{51 (link)}: 338 chronic lymphocytic leukemia cases from 279 patients from Landau et al,^{52 (link)} 32 cutaneous T-cell lymphoma cases from Choi et al,^{53 (link)} 51 nasopharyngeal carcinoma cases from Zheng h et al,^{54 (link)} and 8 cholangiocarcinoma cases from Ong et al.^{55 (link)} Fifteen additional cholangiocarcinoma cases were obtained from the European Nucleotide Archive^{56 (link)} from Chan-on et al.^{57 (link)} All sample identifiers used are available in the Data Supplement. These cases were processed via L-MAP. Tumor and normal samples were downloaded in the FASTQ format using fastq-dump.^{51 (link)} Alignment to hg38 was performed by using bwa (version 0.7.12)^{58 (link)} with the mem algorithm. Duplicate reads were marked and removed by using Picard Mark- Duplicates.⁵⁹ Base quality score recalibration and indel realignment were performed by using GATK,^{60 (link)} and the resulting BAM files were sliced, as above, by using SAM tools.