OncDRS: An integrative clinical and genomic data platform for enabling translational research and precision medicine

Abstract

We live in the genomic era of medicine, where a patient's genomic/molecular data is becoming increasingly important for disease diagnosis, identification of targeted therapy, and risk assessment for adverse reactions. However, decoding the genomic test results and integrating it with clinical data for retrospective studies and cohort identification for prospective clinical trials is still a challenging task. In order to overcome these barriers, we developed an overarching enterprise informatics framework for translational research and personalized medicine called Synergistic Patient and Research Knowledge Systems (SPARKS) and a suite of tools called Oncology Data Retrieval Systems (OncDRS). OncDRS enables seamless data integration, secure and self-navigated query and extraction of clinical and genomic data from heterogeneous sources. Within a year of release, the system has facilitated more than 1500 research queries and has delivered data for more than 50 research studies.

Augmenting the disease ontology improves and unifies disease annotations across species

“…In addition, these changes will benefit the many tools and resources already using DO [e.g. Jax-CKB ( Patterson et al, 2016 ); Triple-Negative Breast Cancer Database ( Vitali et al, 2016 ), OncDRS ( Orechia et al, 2015 ), QueryOR ( Bertoldi et al, 2017 ), Disease Compass ( Kozaki et al, 2017 ), DisSim ( Cheng et al, 2016 ) and UniCarbKB ( Campbell and Packer, 2016 )] by increasing the amount of data these tools can import from other resources.…”

“…Such extensive collecting and aligning of different terminologies can significantly hamper studies and analyses and/or lead to conflicting conclusions if definitions among vocabularies are inconsistent. In addition, computational tools developed to take advantage of model organism data in a clinical setting must download and integrate data from multiple resources to have the greatest chance of analytical success ( Hoehndorf et al, 2015 ; Orechia et al, 2015 ; Patterson et al, 2016 ; Vitali et al, 2016 ). Having a single disease ontology with cross-references to multiple disease vocabularies incorporating both etiology- and anatomy-based views will greatly simplify and enhance the efficiency of disease-related searches within and across species.…”

Somatic mutations in CDH1 and CTNNB1 in primary carcinomas at 13 anatomic sites

“…Subjects were drawn from the Profile study of cancer genomics at DFCI [ 12 ]. Since 2011, most DFCI cancer patients have been offered the opportunity to enroll in Profile, which performs genomic sequencing of clinically-acquired neoplastic tissue specimens.…”

“…We used the Profile study of cancer genomics at Dana-Farber Cancer Institute (DFCI; Boston, MA) [ 12 ] to evaluate whether mutations in key EMT genes might contribute to the detachment of cancer cells from primary tumors. Specifically, we examined somatic mutations in CDH1 and CTNNB1 in thousands of clinical primary carcinomas from 13 anatomic sites.…”

Precision medicine applications in prostate cancer

“…In order to put precision medicine into practice, clinicians and scientists need to be able to readily access clinical and genomic data of patients, and some search tools include Oncology Data Retrieval Systems (OncDRS (Dana Farber Cancer Institute, Cambridge, MA)) and GeneMed (National Cancer Institute, Bethesda, MD). 97 , 98 Physicians can utilize OncDRS to quickly search and obtain clinical and genomic data of patients with cancer, and such information can be used to tailor treatment and design clinical trials. Within a year of release, OncDRS aided data retrieval for more than 50 publications.…”