Skip to main content

Launch GNomEx

Launch Seven Bridges

Launch cBioPortal

The Bioinformatic Analysis section provides support for translational research. Genomic data is pulled from clinical test providers including Foundation Medicine 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 translational research-specific GNomEx LIMS instance, 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...

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

Omic Data Sources - 13,607 HCI Patients as of Nov 2020:

      1448 ORIEN/ AVATAR – T/N Exome T Transcriptome
      2134 Foundation Medicine – T ~400 gene panel
      604 Tempus – T/N ~600 gene panel
      9421 Genetic Counseling RSR germline testing

Comprehensive Genomic Query Engine: https://github.com/HuntsmanCancerInstitute/GQuery

Optimize Hyve cBioPortal: https://hci-bio-cbioportal.hci.utah.edu

Screenshot of the cBioPortal web page