TY - JOUR
T1 - G-DOC Plus - An integrative bioinformatics platform for precision medicine
AU - Bhuvaneshwar, Krithika
AU - Belouali, Anas
AU - Singh, Varun
AU - Johnson, Robert M.
AU - Song, Lei
AU - Alaoui, Adil
AU - Harris, Michael A.
AU - Clarke, Robert
AU - Weiner, Louis M.
AU - Gusev, Yuriy
AU - Madhavan, Subha
N1 - Publisher Copyright:
� 2016 Bhuvaneshwar et al.
PY - 2016
Y1 - 2016
N2 - Background: G-DOC Plus is a data integration and bioinformatics platform that uses cloud computing and other advanced computational tools to handle a variety of biomedical BIG DATA including gene expression arrays, NGS and medical images so that they can be analyzed in the full context of other omics and clinical information. Results: G-DOC Plus currently holds data from over 10,000 patients selected from private and public resources including Gene Expression Omnibus (GEO), The Cancer Genome Atlas (TCGA) and the recently added datasets from REpository for Molecular BRAin Neoplasia DaTa (REMBRANDT), caArray studies of lung and colon cancer, ImmPort and the 1000 genomes data sets. The system allows researchers to explore clinical-omic data one sample at a time, as a cohort of samples; or at the level of population, providing the user with a comprehensive view of the data. G-DOC Plus tools have been leveraged in cancer and non-cancer studies for hypothesis generation and validation; biomarker discovery and multi-omics analysis, to explore somatic mutations and cancer MRI images; as well as for training and graduate education in bioinformatics, data and computational sciences. Several of these use cases are described in this paper to demonstrate its multifaceted usability. Conclusion: G-DOC Plus can be used to support a variety of user groups in multiple domains to enable hypothesis generation for precision medicine research. The long-term vision of G-DOC Plus is to extend this translational bioinformatics platform to stay current with emerging omics technologies and analysis methods to continue supporting novel hypothesis generation, analysis and validation for integrative biomedical research. By integrating several aspects of the disease and exposing various data elements, such as outpatient lab workup, pathology, radiology, current treatments, molecular signatures and expected outcomes over a web interface, G-DOC Plus will continue to strengthen precision medicine research. G-DOC Plus is available at: https://gdoc.georgetown.edu.
AB - Background: G-DOC Plus is a data integration and bioinformatics platform that uses cloud computing and other advanced computational tools to handle a variety of biomedical BIG DATA including gene expression arrays, NGS and medical images so that they can be analyzed in the full context of other omics and clinical information. Results: G-DOC Plus currently holds data from over 10,000 patients selected from private and public resources including Gene Expression Omnibus (GEO), The Cancer Genome Atlas (TCGA) and the recently added datasets from REpository for Molecular BRAin Neoplasia DaTa (REMBRANDT), caArray studies of lung and colon cancer, ImmPort and the 1000 genomes data sets. The system allows researchers to explore clinical-omic data one sample at a time, as a cohort of samples; or at the level of population, providing the user with a comprehensive view of the data. G-DOC Plus tools have been leveraged in cancer and non-cancer studies for hypothesis generation and validation; biomarker discovery and multi-omics analysis, to explore somatic mutations and cancer MRI images; as well as for training and graduate education in bioinformatics, data and computational sciences. Several of these use cases are described in this paper to demonstrate its multifaceted usability. Conclusion: G-DOC Plus can be used to support a variety of user groups in multiple domains to enable hypothesis generation for precision medicine research. The long-term vision of G-DOC Plus is to extend this translational bioinformatics platform to stay current with emerging omics technologies and analysis methods to continue supporting novel hypothesis generation, analysis and validation for integrative biomedical research. By integrating several aspects of the disease and exposing various data elements, such as outpatient lab workup, pathology, radiology, current treatments, molecular signatures and expected outcomes over a web interface, G-DOC Plus will continue to strengthen precision medicine research. G-DOC Plus is available at: https://gdoc.georgetown.edu.
KW - Bioinformatics
KW - Cloud computing
KW - Genotype-phenotype integration
KW - Next generation sequencing
KW - Outcomes research
KW - Precision medicine
KW - Translational research
KW - Variant analysis
UR - http://www.scopus.com/inward/record.url?scp=85007489252&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85007489252&partnerID=8YFLogxK
U2 - 10.1186/s12859-016-1010-0
DO - 10.1186/s12859-016-1010-0
M3 - Article
C2 - 27130330
AN - SCOPUS:85007489252
SN - 1471-2105
VL - 17
JO - BMC bioinformatics
JF - BMC bioinformatics
IS - 1
M1 - 193
ER -
