Overview

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

Contact Us

Bioinformatic Analysis Director
David Nix, PhD
david.nix@hci.utah.edu
801-587-4611

Bioinformatic Analysis Associate Director
Timothy Parnell, PhD
timothy.parnell@hci.utah.edu
801-587-4312

Governance

HCI Senior Director Oversight
Alana Welm, PhD

Faculty Advisory Committee Chair
Katherine Varley, PhD

Faculty Advisory Committee Members
Richard Clark, PhD
Jason Gertz, PhD
Christopher Gregg, PhD
Philip Moos, PhD
Sean Tavtigian, PhD
Katherine Varley, PhD
Joseph Yost, PhD