Work in collaboration with Serghei Mangul and the Mangul lab on extracting off-target variation from tumor data to build prognostic biomarkers is now online.

Seeing beyond the target: Leveraging off-target reads in targeted clinical tumor sequencing to identify prognostic biomarkers.
Mangul S, Brito JJ, Groha SM, Zaitlen N, Gusev A. 2021

We develop and apply novel tools to extract omics features from off-target tumor panel reads including: rDNA, mtDNA, microbiome, and T/B cell receptor sequences. We show that these features correlate with known immune components in TCGA data, and apply them to thousands of panel sequenced tumors with clinical data to identify prognostic associations (that replicate!). This was a wonderful collaboration with the Mangul and Zaitlen labs. See also the related work on extracting germline variation from off-target data.

Figure: Hazard ratio from significant associations of SBT features with survival time.

sbt survival