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.