Bioinformatics Translational Genomics

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...

https://github.com/HuntsmanCancerInstitute/Workflows/tree/master/Hg38RunnerWorkflows

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:

• cBioPortal - A local instance of the cBioPortal web platform for querying the molecular datasets in the PMR and their associated clinical attributes, see https://uofuhealth.utah.edu/huntsman/shared-resources/gba/bioinformatics/software/cbioportal 

• 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.  See the https://github.com/HuntsmanCancerInstitute/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 (https://github.com/HuntsmanCancerInstitute/USeq) and run the PatientMolecularRepoSearch application. 

• SubjectMatchMaker - a command line tool for linking PMR IDs to MRNs, HCI Person IDs, and patient PHI.  See the https://github.com/HuntsmanCancerInstitute/SubjectMatchMaker project.

• 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. See the https://github.com/HuntsmanCancerInstitute/AwsApps project and run the S3Copy application.