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NCI Patient-Derived Models Repository (PDMR) - An NCI Precision Oncology Initiative Resource
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Last Updated: 10/28/19

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 SOP, some murine contribution will likely remain. Review the SOPs for details (https://pdmr.cancer.gov/sops/default.htm#h04).
    • The host mouse model used is NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG); the reference sequence can be found on the SOP page.
  • The provided PDX pathology, WES, RNASeq, etc in the PDMR database are representative of the models. Recipients should perform their own analysis on PDXs they grow out to characterize them.
  • For a limited set of models, germline sequence has been included from either the patient’s peripheral mononuclear blood fraction or purified cancer-associated fibroblasts (CAFs). In these cases, the germline sequence files are posted at the patient-level in the database and somatic calls have been made. For all other models, there has been no removal of somatic mutations from the sequences as tissue for germline sequencing was not obtained.

File naming structure

  • Sequence file names include the specific version of the pipeline used for sequencing. Details on file nomenclature and versioning can be found in the following SOP: https://pdmr.cancer.gov/content/docs/MCCRD_NGS_filename_structure.pdf
  • The most recent pipeline version of the sequence files are linked in the PDMR database. However, if you are doing bulk downloads of data files 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.
    Graphic showing file naming structure
  • Please note the following README file lists previously posted sequence files that should be removed from any subsequent analysis: ftp://dctdftp.nci.nih.gov/pub/pdm/README_SequenceFiles_Public.txt