Analyze Genomes: Drug Response Analysis
-
Upload
matthieu-schapranow -
Category
Healthcare
-
view
1.190 -
download
0
Transcript of Analyze Genomes: Drug Response Analysis
Analyze Genomes: Drug Response Analysis
Dr. Matthieu-P. Schapranow Future Convention, Frankfurt, Germany
Nov 23, 2015
■ Since 2009 Program Manager E-Health & Life Sciences
■ 2006-2014 Strategic Projects SAP HANA
■ Visiting Scientist at V.A., Boston, MA and Charité, Berlin
■ Ph.D. in Software Engineering
Whom you are dealing with?
Schapranow, Future Convention, 2015
Analyze Genomes: Drug Response Analysis
2
What is the Hasso Plattner Institute, Potsdam, Germany?
Schapranow, Future Convention, 2015
Analyze Genomes: Drug Response Analysis
3
Ind irect In te raction
D irect In te raction
C lin ic ian P atien tR esearcher
P harm aceu tica lC om pany
H ea lthcareP roviders
H osp ita lR esearch
C enterLabora to ry
P atien tA dvocacy
G roup
Intelligent Healthcare Networks in the 21st Century?
Schapranow, Future Convention, 2015
Analyze Genomes: Drug Response Analysis
4
Ind irect In te raction
D irect In te raction
C lin ic ian P atien tR esearcher
P harm aceu tica lC om pany
H ea lthcareP roviders
H osp ita lR esearch
C enterLabora to ry
P atien tA dvocacy
G roup
Intelligent Healthcare Networks in the 21st Century?
Schapranow, Future Convention, 2015
Analyze Genomes: Drug Response Analysis
5
Ind irect In te raction
D irect In te raction
C lin ic ian P atien tR esearcher
P harm aceu tica lC om pany
H ea lthcareP roviders
H osp ita lR esearch
C enterLabora to ry
P atien tA dvocacy
G roup
Intelligent Healthcare Networks in the 21st Century!
Schapranow, Future Convention, 2015
Analyze Genomes: Drug Response Analysis
6
IT Challenges in Life Sciences Distributed Heterogeneous Data Sources
Human genome/biological data >750GB per complete human genome >15PB in databases of leading institutes
Prescription data 1.5B records from 10,000 doctors and 10M Patients (100 GB)
Clinical trials >30k recruiting trials on ClinicalTrials.gov
Human proteome 160M data points (2.4GB) per sample >3TB raw proteome data in ProteomicsDB
PubMed database >24M unstructured data in publications
Hospital information systems >50GB structured relational data
Medical sensor data Scan of a single organ creates 10GB of raw data within 1s
Cancer patient records >160k records only at NCT
Analyze Genomes: Drug Response Analysis
Schapranow, Future Convention, 2015
7
■ Patient: 67 years, male, smoker, consumes frequently alcohol
■ Diagnosis: Squamous cell carcinoma of the oropharynx, T2N2bM0, stage IVa
1. Surgery to remove tumor
2. Tumor sample is sent to laboratory to extract DNA
3. DNA is sequenced resulting in 750 GB of raw data per sample
4. Processing of raw data to perform analysis
5. Identification of relevant driver mutations using international medical knowledge
6. Informed decision making
Use Case: Precision Medicine in Oncology Identification of Best Treatment Option for Cancer Patient
Schapranow, Future Convention, 2015
Analyze Genomes: Drug Response Analysis
8
Schapranow, Future Convention, 2015
Analyze Genomes: Drug Response Analysis
9
Schapranow, Future Convention, 2015
Analyze Genomes: Drug Response Analysis
10
Schapranow, Future Convention, 2015
we.analyzegenomes.com Real-time Analysis of Big Medical Data
11
In-Memory Database
Extensions for Life Sciences
Data Exchange, App Store
Access Control, Data Protection
Fair Use
Statistical Tools
Real-time Analysis
App-spanning User Profiles
Combined and Linked Data
Genome Data
Cellular Pathways
Genome Metadata
Research Publications
Pipeline and Analysis Models
Drugs and Interactions
Analyze Genomes: Drug Response Analysis
Drug Response Analysis
Pathway Topology Analysis
Medical Knowledge Cockpit Oncolyzer
Clinical Trial Recruitment
Cohort Analysis
...
Indexed Sources
Real-time Data Analysis and Interactive Exploration
Drug Response Analysis Data Sources
Schapranow, Future Convention, 2015
Analyze Genomes: Drug Response Analysis
Smoking status, tumor classification
and age (1MB - 100MB)
Raw DNA data and genetic variants
(100MB - 1TB)
Medication efficiency and wet lab results
(10MB - 1GB)
12
Patient-specific Data
Tumor-specific Data
Compound Interaction Data
Schapranow, Future Convention, 2015
Analyze Genomes: Drug Response Analysis
13
Showcase
Schapranow, Future Convention, 2015
Analyze Genomes: Drug Response Analysis
14 Calculating Drug Response… Predict Drug Response
Schapranow, Future Convention, 2015
Analyze Genomes: Drug Response Analysis
15
cetuximab might be more beneficial for the current case
■ Online: Visit we.analyzegenomes.com for latest research results, slides, videos, tools, and publications
■ Offline: Read more about it, e.g. High-Performance In-Memory Genome Data Analysis: How In-Memory Database Technology Accelerates Personalized Medicine, In-Memory Data Management Research, Springer,
ISBN: 978-3-319-03034-0, 2014
■ In Person: Join us for “Festival of Genomics” Jan 19-21, 2016 in London, UK
Where do you find additional information?
Schapranow, Future Convention, 2015
Analyze Genomes: Drug Response Analysis
16
■ Global Medical Knowledge (Master’s project)
■ Markers for cardiovascular diseases to
assess treatment options (DHZB)
■ Combine health data to improve health care research (AOK)
■ Pharmacogenetics (Bayer)
■ Generously supported by
Join us for upcoming projects!
Schapranow, Future Convention, 2015
Analyze Genomes: Drug Response Analysis
17
Interdisciplinary Design Thinking
Teams
You?
Keep in contact with us!
Hasso Plattner Institute Enterprise Platform & Integration Concepts (EPIC)
Program Manager E-Health August-Bebel-Str. 88
14482 Potsdam, Germany
Dr. Matthieu-P. Schapranow [email protected] http://we.analyzegenomes.com/
Schapranow, Future Convention, 2015
Analyze Genomes: Drug Response Analysis
18