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
