Professional Documents
Culture Documents
Disclaimer
Please note that some of the views presented are solely mine and do not necessarily reflect those of the Georgetown University.
Encode
1st draft of human genome finished in 2001 (~ 3 billion letters) Hundreds of higher-order genomes done or in progress. The worlds current sequencing capacity is estimated to be 13 quadrillion DNA bases a year requiring 3 or more exabytes of storage (approximately 1/100 of the entire worlds data storage) The NIH-funded 1000 Genomes Project deposited 200 terabytes of data into the GenBank archive during the projects first 6 months of operation, twice as much as had been deposited into all of GenBank for the entire 30 years preceding Million Genome projects not too far way!
Will my cancer spread? Do I need chemotherapy after surgery for my cancer type? What are the side effects of chemotherapy for me? Are there any new drugs targeted for my type of cancer? What are my chances of survival?
AMIA 2011
Cytoscape
Visualization networks
JMol/Marvin
Molecule Visualization Ingenuity Analysis
Pathways, GO, Variants
G-DOC
JBrowse
Genome Visualization
EHRs
https://gdoc.georgetown.edu
OMICS Data
Clinical
Gene Expression Markers Separate CRC Relapse Patients From Non-Relapse Cases
PC
User
Genome Data
Amazon S3 Bucket
Clinical Data
2. Pharmacogenomics
Pharmacogenomics Use?
Identify populations that should receive lower or higher doses of a drug Identify responder populations (e.g. ultrarapid metabolizers) Identify high risk groups
Personalized Rx Plan: Right Drug Right Dose Right Patient Right Time
Breast Cancer
Her2 Herceptin ER/PR Tamoxifen
Colon Cancer
EGFR Erbitux MI / 18q deletions / DCC FOLFOX
Melanoma
BRaf Zelboraf
On average 75% of patients dont respond to the cancer drug given to them
Average daily doses of 3.4 mg in Asians, 5.1 mg in whites, and 6.1 mg in blacks are representative of the literature for these ethnic groups
Johnson J A Circulation 2008;118:1383-1393 Reproduced from Dang et al,6 with permission from the Annals of Pharmacotherpy.
Source: http://www.fda.gov/Drugs/ScienceResearch/ResearchAreas/Pharmacogenetics/ucm083378.htm
Genetic Factors
Bayesian Network
Background
A Bayesian network is a probabilistic graphical model that represents a set of random variables and their conditional dependencies. Generalizations of Bayesian networks that can represent and solve decision problems under uncertainty are called influence diagrams
GeNIe software
Developed at the Decision Systems Laboratory, University of Pittsburgh. It can be used to implement graphical decisiontheoretic methods, such as Bayesian networks and influence diagrams
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3. Mobile Health
Motivation
Need to enhance patient experience in the clinic Clipboard to iPAD Standardized data collection Error detection and data validation Effective secondary use of clinical care data Collect once and use multiple times (for care, research, education) Enable clinical research Patients need to feel part of the process Making patient education fun for all involved
Electronic Data Capture To Enhance Patient Engagement In Cancer Research & Care
Patient Navigation
Risk Assessments
Clinician
Screenings
(i.e. Autism, Anxiety, Alcoholism, etc.)
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Patient Education
Tonics real time data analytics engine also allows for patient education (such as videos, links or text) to be dynamically served up based on a patients answers.
- Example: Tonic automatically screens patients for breast cancer risk and serves up a video about mammograms at the end of the questionnaire to those who are calculated as being at high risk. (Those at medium and low risk see different videos.)
Current Challenges
Educating the next generation of physicians and researchers in information sciences Clinical validation of research data Data access and policy Issues Varying data formats needing harmonization Lack of clear, universal consent forms Privacy issues around storing genomes on the cloud