Fall 2013 Newsletter

Data Insights Improving Human Health
September 17, 2013

ICBI Director’s Blog

Nate Silver is my new hero. His prediction (well ahead of other political analysts and media outlets) of President Obama’s victory in 2012 exemplifies the various facets of data science – data collection, pre-processing, filtering, analyzing, and presenting information – almost in real-time. His simple prediction model and detailed data presentation techniques have inspired and amazed data scientists across multiple domains such as health care, biomedical research, sports analysis, politics, astronomy, and many others. We clearly live in a data-driven economy. If you haven’t gotten enough of the statistics on big data in health care, here are a few more. U.S. health care data is growing at the rate of 30 petabytes per year. Global health data size is estimated at approximately 150 exabytes, growing at 1.2 to 2.4 EB/year. The potential value of healthcare data, either through pharmaceutical product development dollars or reimbursement gains, is estimated at $300 billion annually.

So, why should we care about all this? As biomedical researchers, we not only curate big data but also play important roles as analysts, interpreters, and decision makers. As costs of big data generation drop, techniques such as targeted and whole-genome sequencing, RNA-Seq, Chip-Seq, miRNA-Seq and others are proving to be quite useful in the identification of novel and rare anomalies associated with disease, gene expression signatures, and functions of non-coding RNAs in tissue and blood. We will take a deeper dive into one of these techniques – RNA-Seq – and review its data analysis challenges and opportunities.

2nd Annual Biomedical Informatics Symposium at Georgetown University
October 11, 2013

Please join us for the 2nd annual ICBI Biomedical Informatics Symposium at Georgetown Hotel and Conference Center on Friday, October 11, 2013!

Topics include:

Genomics/systems medicine
Big data analytics
Research infrastructure
“Omics” data integration
Data visualization
Clinical research informatics

This free, one-day event will include a variety of talks by academic, industry, and government leaders working in the clinical and translational sciences who will highlight the applications of informatics science and tools that can help to advance precision medicine. This symposium promises to bring together a dynamic community of innovators, research scientists, clinicians, program managers, educators, and students to exchange ideas, and learn new methodologies.

This event is by invitation only. If you are interested in participating, please contact us at icbi@georgetown.edu.

See here for a summary of last year’s symposium.

New Initiatives

(NIH) ICBI is part of a team that received an NIH U24 grant to build a Clinically Relevant Variants Resource (CRVR), which will generate a knowledge base of genes and variants for use in a clinical setting. ICBI is helping build the informatics structure of the CRVR along with partners at UNC Chapel Hill, Emory Genetics Laboratory, Harvard Partners, University of Utah, and Washington University – St. Louis. Collaborations include the PIR and Department of Biochemistry at GUMC.

(FDA) As part of Georgetown’s FDA CERSI (Center of Excellence in Regulatory Science and Innovation) award, the ICBI, in partnership with MedStar Health, has recently started a project to study triple negative breast cancer (TNBC) in Latinas and African American women. The objective is to identify molecular markers in TNBC patients for drug discovery research and personalized medicine. This research will provide the infrastructure, data, and tools to analyze multi-omics data from TNBC samples to help reviewers at the FDA use this framework for new targeted therapies in breast cancer. Collaborators include Sandy Swain and Raquel Nunes at MedStar Washington Hospital Center and Luciane Cavalli at Georgetown Lombardi.

(MedStar Health) ICBI is working closely with Giuseppe Giaccone at Georgetown Lombardi and Dr. Chahine at MedStar Health to establish a state-of-the-art, CLIA-certified Next Generation Sequencing based Molecular Diagnostics Laboratory at MedStar Georgetown University Hospital in collaboration with MedStar Health. ICBI will provide informatics infrastructure and data analysis and reporting support for the new diagnostics laboratory, which is expected to be operational by the end of the year.

ICBI Research Support, Consultations and Services

We are excited by the response to the ICBI research support and services initiative rolled out earlier this summer to provide informatics support to the Georgetown clinical and research community as well as external collaborators. If your group is in need of data analysis consultation or clinical research management support please contact us! We have regular office hours every other Tuesday from 10am-11am where you can drop by for a consultation in the New Research Building Room E325. Office hours will be held next on Tuesday, September 24.

Areas of consultation include: Next generation sequencing analysis, molecular profiling analysis, “Big Data” analytics, predictive modeling, systems biology analysis, network modeling and inference, computational chemistry / molecular modeling, REDCap, clinical data management, and patient cohort discovery, among others. More information can be found at http://icbi.georgetown.edu/support.

ICBI in the Community

ICBI members spoke at the following recent conferences and events:

World Biotechnology Congress, Boston, Mass. (June 3-6, 2013): Platform for Personalized Oncology: Novel Approaches for Data Integration Reveal Molecular Signatures Associated with Colorectal Cancer Relapse
National Cancer Institute’s Cancer Imaging Program Workshop, Bethesda, Md. (June 3-6, 2013): Correlating Imaging Phenotypes with Genomic Signatures
CERSI and the FDA CDER Computational Science Center,Silver Spring, Md. (July 10, 2013): Georgetown CERSI’s Innovative Analytics Platform
Georgetown Lombardi Comprehensive Cancer Center Cancer Systems Biology Seminar (July 11, 2013): “Seeing” is Believing: Understanding Protein-Ligand Interactions in Cancer Drug Discovery
Amazon Web Services Public Sector Summit, Washington, DC (Sept. 10, 2013): How Cloud Computing is Fundamentally Changing the Way We Think About Data Science

Recent Publications

Michael Harris, Krithika Bhuvaneshwar, Thanemozhi Natarajan, Laura Sheahan, Difei Wang, Mahlet G. Tadesse, Ira Shoulson, Ross Filice, Kenneth Steadman, Subha Madhavan, John Deeken. Pharmacogenomic characterization of gemcitabine response – a framework for data integration to enable personalized medicine. Pharmacogenetics and Genomics (Accepted July 2013).

Robinder Gauba, Subha Madhavan, Robert Clarke, Yuriy Gusev. Integrative knowledge-driven analysis pipeline for untargeted metabolomics. BMC Bioinformatics. (Accepted, August 2013)

Subha Madhavan, Yuriy Gusev, Thanemozhi G. Natarajan, Lei Song, Krithika Bhuvaneshwar, Robinder Gauba, Abhishek Pandey, Bassem Haddad, David Goerlitz, Amrita Cheema, Hartmut Juhl, Bhaskar Kallakury, John Marshall, Stephen Byers and Louis M. Weiner. Genome-wide multi-omics profiling of colorectal cancer identifies immune determinants strongly associated with relapse. Frontiers in Oncology (Submitted August 2013).