The Cancer Bioinformatics (CBI) Shared Resource provides support for preclinical and translational research. Omic data is pulled from clinical test providers including Caris, Tempus, Ambry, and Invitae as well as from the ORIEN/AVATAR tumor normal exome sequencing project.

CBI processes these datasets and uploads them into a Patient Molecular Repository (PMR), an HCI cBioPortal instance, and a GQuery omics data server for IRB-permitted data mining.

Supported Services:

• Automated germline variant screening for ACMG incidental finding. The Inherited Cancer Research Shared Resource reviews these cases and, where appropriate, contacts the treating physician for a follow-up clinical diagnostic.
• Automated joint Clinical and Molecular patient cohort queries for clinical trial recruitment.
• Support for molecular tumor boards using cBioPortal. 

Workflows: Json/Xml Clinical Report Abstraction, Alignment, QC, Variant Calling, Copy Number, Translocation, MSI/TMB, LoH, RSEM/FeatureCounts...

See All Workflows

Available Omic Data Sources - 16,6K HCI Patients, 357TB, 1.1M files as of Nov 2025:

• 3,699 ORIEN/ AVATAR – T/N Exome T Transcriptome
• 922 Caris – T only ~600 gene panel
• 4,232 Tempus – T/N ~600 gene panel
• 2,005  Ambry - N testing, 1-30 gene panel
• 6,796  Invitae - N testing, 1-30 gene panel

The HCI Patient Molecular Repository (PMR) is a structured data store on AWS (s3://hcibioinfo-patient-molecular-repo). It contains molecular testing datasets, both raw sequencing and harmonized analysis, 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:

• cBioPortal - A local instance of the cBioPortal web platform for querying the molecular datasets in the PMR and their associated clinical attributes.
• GQuery - a command line tool for identifying datasets in the PMR that contain particular molecular attributes such as somatic or germline variant, copy number, and gene fusions. Go to the GQuery project and run the GQueryCLI application pointing it to the GQuery indexed data sources on CHPC (/uufs/chpc.utah.edu/common/PE/hci-bioinformatics1/TNRunner/GQuery/)
• PMRSearch - a command line tool for finding datasets in the PMR that match particular clinical attributes from the vendor json and xml reports. Download the USeq package and run the PatientMolecularRepoSearch application.
• SubjectMatchMaker - a command line tool for linking PMR IDs to MRNs, HCI Person IDs, and patient PHI.
• AWS CLI - Use the official AWS CLI to write the contents of the PMR to a file and then search it using grep.
• S3Copy - a command line tool for copying PMR files to another bucket or downloading them locally. Unarchives files as needed. Runs as a daemon. Go to the AwsApps project and run the S3Copy application.
• PMR Dashboard - R Shiny App for real time statistics, must be called from within the HCI network.