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NextGen Sequencing

Available NextGen Sequencing (NGS) Data

  • Whole-exome sequencing (WES); FASTQ and vcf
  • Consensus WES (variants present in all sequenced PDX models); MAF and vcf
  • RNASeq; FASTQ and TPM
  • Germline sequence (when available); FASTQ and vcf
  • Cancer-Associated Genes; table of reported variants from WES

NGS Generation

  • While the sequencing pipeline removes mouse reads per the posted PDMR Genomics SOPs, some murine contribution from the NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) host will likely remain.
  • The pathology, WES, RNASeq, etc. provided for each model in the PDMR database are derived from representative samples of that model. Recipients should characterize the PDX models during expansion for their experiments to ensure they remain consistent over time.
  • Patient germline sequence has been included at the patient-level in the database, and somatic calls have been made, for a limited set of models. These were generated from either a peripheral mononuclear blood fraction or purified cancer-associated fibroblasts (CAFs).
  • For all other models, somatic mutations could not be removed from the model sequences.

File naming structure

  • Sequence file names include the version of the pipeline used for sequencing.
  • The most recent pipeline version of the sequence files are linked in the PDMR database.
  • If you are obtaining data files through bulk downloads from the FTP site, be sure to use the most recent pipeline version for analysis. For example, an RNASeq file with version “v2.0” should be used instead of a file with “v1.2” for the same PDX.
  • NOTE: the README file lists previously posted sequence files that should be removed from any subsequent analysis.
  • Reviewed:

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