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Integrative Somatic and Germline Computational Biology to Redefine Clinical Actionability in Solid Tumors

综合体细胞和种系计算生物学重新定义实体瘤的临床可操作性

基本信息

批准号：
9517271
负责人：
Eliezer M Van Allen
金额：
$ 40.72万
依托单位：
DANA-FARBER CANCER INST
依托单位国家：
美国
项目类别：
财政年份：
2018
资助国家：
美国
起止时间：
2018-06-01 至 2023-05-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/9517271
关键词：
Address Algorithms Alternative Splicing Area Automobile Driving Award Cancer Center Cancer Etiology Cancer Patient Clinical Clinical Oncology Communities Complex Computational Biology Computational algorithm Computing Methodologies DNA Repair DNA Repair Gene Dana-Farber Cancer Institute Data Decision Making Defect Development Diagnostic Dissection Etiology Event Evolution Genes Genetic Genetic Polymorphism Genetic Transcription Genome Genomics Germ-Line Mutation Goals Immune Immune signaling Immunotherapy Inherited Institutes Interdisciplinary Study International Investigation Malignant Neoplasms Malignant neoplasm of prostate Malignant neoplasm of urinary bladder Mediating Medical Modality Modeling Molecular Molecular Profiling Mutation Pathogenicity Pathway interactions Patient Care Patient risk Patients Pattern Platinum Process Prognostic Marker Research Research Infrastructure Resources Risk Risk Assessment Role Sampling Shapes Signal Pathway Solid Neoplasm Somatic Mutation Splice-Site Mutation Therapeutic Translating Tumor Biology Variant Work base cancer genomics cancer initiation cancer risk cancer therapy cancer type checkpoint therapy chemotherapy clinical development clinical predictors clinical risk clinically actionable clinically relevant cohort diagnostic biomarker exome experimental study genomic profiles immune checkpoint blockade innovation loss of function molecular marker novel oncology oncology program phenotypic data point of care precision oncology predictive marker prognostic programs response transcriptome treatment response tumor

项目摘要

PROJECT SUMMARY 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.

项目总结