The increased accessibility of comprehensive molecular characterization of tumors and germline samples from cancer patients has accelerated translational discoveries and significantly impacted patient care. These approaches ultimately form the basis for precision cancer medicine, whereby ?clinically actionable? molecular data about a patient's tumor and germline genomic profile, specifically defined as diagnostic, prognostic, and predictive markers, are used at the point of care to guide treatment decision-making. While these strategies have been successful in certain use cases, the approaches to understand somatic and germline components of cancer patients are typically considered independently, and systematic characterization of the interaction between the somatic and germline genomes in the context of diagnostic and predictive clinical relevance have not yet been systematically performed across large cohorts of patients. This is in part the result of an absence of computational algorithms that are able to consider these features simultaneously, along with a lack of patient cohorts with both somatic and germline features and clinical annotations of relevant treatment responses to guide these investigations. Our previous studies have demonstrated, through innovative computational oncology approaches, how integrated germline and somatic analysis can determine diagnostic and predictive features that have immediate clinical impact in select clinical contexts. The goal of this proposal is to directly respond to Provocative Question PQ3: Do genetic interactions between germline variations and somatic mutations contribute to differences in tumor evolution or response to therapy? Our overarching hypothesis is that complex interactions between germline and somatic features within and across key DNA repair and immune pathways mediate inherited clinical risk, and selective response to existing chemotherapies and emerging immunotherapies. Specifically, in this proposal, we will leverage existing and emerging cohorts of tumor and germline whole exome/transcriptome data from patients, along with relevant phenotypic data regarding response to chemotherapies and immunotherapies, and develop innovative computational biology algorithms to systematically dissect these cohorts and determine how interactions between germline and somatic events shape clinical actionability. This proposal is unique in that it leverages the extensive and novel resources at both the Dana-Farber Cancer Institute/Harvard Cancer Center and the Broad Institute of MIT and Harvard, along with an international team of collaborators, to address the hypotheses outlined herein. The proposed specific aims are: 1) To determine inherited cancer risk in solid tumors through integrative computational biology, 2) To evaluate the impact of somatic and germline interactions on DNA repair defects and response to platinum-based chemotherapies in solid tumors, and 3) To identify somatic and germline features that coordinate to alter the immune microenvironment and impact selective response to immune checkpoint blockade in solid tumors. These studies will define key relationships between germline and somatic variants that shape tumor biology, with implications for understanding patient risk for cancer development and selective response to chemotherapy and immunotherapy. In addition, this project will establish new computational algorithms to enable widespread integrated consideration of germline and somatic features for broader use in the scientific community. Finally, this project will accelerate the clinical relevance of germline and somatic molecular profiling to enable precision cancer medicine, and serve more broadly as an innovative model for intersecting clinical oncology with computational biology.
While both somatic and germline molecular features independently harbor alterations that have prognostic and predictive clinical impact, the role of integrated somatic-germline events toward cancer initiation or selective response to therapeutics is incompletely characterized. We have created a program to develop and apply computational methods that can dissect the role of combined somatic and germline events toward clinically actionable molecular events (diagnostic or predictive) in multiple cancer types. In response to Provocative Question PQ3, this proposal will enable this program to develop a more complete understanding of the somatic and germline factors that, together, drive cancer risk, initiation, and selective response to existing and emerging therapies across solid tumors, with the plan to translate these findings revealed through this study to immediate clinical development in this area of unmet medical need.
| Conway, Jake R; Kofman, Eric; Mo, Shirley S et al. (2018) Genomics of response to immune checkpoint therapies for cancer: implications for precision medicine. Genome Med 10:93 |
| Smart, Alicia C; Margolis, Claire A; Pimentel, Harold et al. (2018) Intron retention is a source of neoepitopes in cancer. Nat Biotechnol 36:1056-1058 |
