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


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What is the Hasso Plattner Institute, Potsdam, Germany?



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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

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Intelligent Healthcare Networks in the 21st Century?



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C enterLabora to ry

P atien tA dvocacy

G roup

Intelligent Healthcare Networks in the 21st Century?



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C enterLabora to ry

P atien tA dvocacy

G roup

Intelligent Healthcare Networks in the 21st Century!



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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



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■  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



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we.analyzegenomes.com Real-time Analysis of Big Medical Data

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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


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



Smoking status, tumor classification

and age (1MB - 100MB)

Raw DNA data and genetic variants

(100MB - 1TB)

Medication efficiency and wet lab results

(10MB - 1GB)

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Patient-specific Data

Tumor-specific Data

Compound Interaction Data



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Showcase



14 Calculating Drug Response… Predict Drug Response



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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?



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■  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!



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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/



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