Our pre-print on a new approach to inferring and harnessing germline variation directly from tumor-only sequencing is online:

Constructing germline research cohorts from the discarded reads of clinical tumor sequences. Gusev A, Groha SM, Taraszka K, Semenov YR, Zaitlen N. 2021

We show that targeted tumor-only sequencing that is commonly used diagnostically (such as Foundation Medicine, Tempus, DFCI OncoPanel) can also be used to impute germline variation using off-target reads. We then apply this approach to ~25,000 clinically sequenced tumors and show accurate inference of variants, germline risk scores, and genetic ancestry. We believe this approach meaningfully broadens the utility of existing tumor studies. The full pipeline and deployable workflow are available in a repository.

ancestry ibd Figure | Schematic of the off-target imputation process