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The Bioinformatic Analysis section provides support for translational research. Omic data is pulled from clinical test providers including Caris and Tempus, as well as from the ORIEN/AVATAR tumor normal exome sequencing project.

The Bioinformatic Analysis section processes these datasets and uploads them into a Patient Molecular Repository, an HCI cBioPortal instance, and a GQuery omics data server for IRB-permitted data mining.

For germline datasets, ACMG incidental finding genes are screened for likely pathogenic variants. The Genetic Counseling Shared Resource reviews these cases and, where appropriate, contacts the treating physician for a follow-up clinical diagnostic.

Workflows: Alignment, QC, Variant Calling, Copy Number, Translocation, MSI/TMB, LoH, RSEM/FeatureCounts...

Omic Data Sources - 10,228 HCI Patients as of May 2023:

      3163 ORIEN/ AVATAR – T/N Exome T Transcriptome
      546 Caris – T only ~600 gene panel
      2194 Tempus – T/N ~600 gene panel
      4325 Genetic Counseling RSR germline testing

The HCI Patient Molecular Repository (PMR) is a structured data store on AWS : s3://hcibioinfo-patient-molecular-repo  It contains all of the available molecular test datasets from Tempus, Caris, and the ORIEN AVATAR program from HCI patients.  

  • PMR ID/
    • Data Source/
      • Vendor ID/
        • Analysis Directories/
  • (Example) HyR2pf8YCC/ 
    • Avatar/
      • A038489_SL527003_SL530338_SL531140/ (OrienID_NormExoID_TumExoID_TumRnaID)
        • Alignment/
        • Fastq/
        • ClinicalReport/
        • RNAAnalysis/
        • SampleConcordance/
        • SomaticVariantCalls/
        • CopyAnalysis/
        • GermlineVariantCalling/
    • Tempus/
      • TL-20-7A8F09/ (TempusTestID)
        • Ditto
    • Caris/
      • TN21-118970_2021-04-24/ (CarisTestID_IssueDate)
        • Ditto

Tools For Working With the PMR:

Screenshot of the cBioPortal web page