Pan-Cancer Analysis of CDK12 Loss-of-Function Alterations and Their Association with the Focal Tandem-Duplicator Phenotype

Background CDK12 loss-of-function (LOF) genomic alterations are associated with focal tandem duplications (FTDs) in ovarian and prostate cancers. Because these FTDs may produce fusion-induced neoantigens (FINAs), CDK12 alteration is a candidate biomarker for immune checkpoint inhibitor sensitivity. Here we determine the prevalence of CDK12-LOF alterations and their association with FTDs across diverse tumor types. Materials and Methods A total of 142,133 tumor samples comprising 379 cancer types were sequenced (August 2014 to April 2018) by hybrid capture-based comprehensive genomic profiling (Foundation Medicine, Cambridge, MA) as part of routine clinical care. Results were analyzed for base substitutions, short insertions/deletions, rearrangements, and copy number alterations. CDK12-LOF genomic alterations were assessed for zygosity status and association with FTDs/focal copy number gain. Results CDK12 genomic alterations were detected in 1.1% of all cases, most frequently in prostate cancer (5.6%), but were also observed at >1% frequency in 11 cancer types. Across multiple cancer types, including prostate, gastric/esophageal, ovarian, breast, and endometrial cancer, the number of FTDs was significantly increased in CDK12-LOF versus CDK12 wild-type cases. Notably, CDK12-LOF was not consistently associated with a homologous recombination deficiency genomic signature. Quantitative assessment of CDK12-associated FTDs by measurement of single copy number gains identified novel likely deleterious CDK12 kinase-domain mutations in prostate and ovarian cancers. Conclusion Detection of CDK12-LOF genomic alterations and their association with FTDs in a diverse spectrum of malignancies suggests that immunotherapy approaches targeting FINAs derived from CDK12-associated FTDs may be a broadly applicable strategy that could be explored across cancer types in a tumor-agnostic manner. Implications for Practice CDK12 inactivation in ovarian and prostate cancer results in the generation of focal tandem duplications, which can cause fusion-induced neoantigens. In prostate cancer, CDK12 alterations have demonstrated promise as a potential predictive biomarker for response to immune checkpoint blockade. This study evaluated genomic profiling data from >142,000 tumors to determine the prevalence of CDK12 loss-of-function genomic alterations across tumor types and demonstrated that CDK12 alterations are associated with the tandem-duplicator phenotype in cancer types other than ovarian and prostate cancer. The association of CDK12 alterations with focal tandem duplications across broad cancer types suggests that CDK12 inactivation warrants further investigation as a pan-cancer biomarker for immunotherapy benefit.