The given presentation was presented at SAPPHIRE 2017 in Orlando, FL on May 18, 2017. It highlights latest research results focusing on user-centered in-memory applications for precision medicine.

1. In-Memory Apps for Precision Medicine
Dr.-Ing. Matthieu-P. Schapranow
Hasso Plattner Institute, Potsdam, Germany
May 18, 2017

2. Use Case: Precision Oncology
Identification of Best Treatment Option for Cancer Patient
■ Patient: 48 years, female, non-smoker, smoke-free environment
■ Diagnosis: Non-Small Cell Lung Cancer (NSCLC), stage IV
■ Markers: KRAS, EGFR, BRAF, NRAS, (ERBB2)
1. Remove tumor through surgery
2. Send tumor sample to laboratory for DNA extraction
3. Sequence complete DNA of sample results in 750 GB of raw genome data
4. Process raw genome data, e.g. alignment, variant calling, and annotate
5. Identify relevant variants using international medical knowledge
6. Support decision making, e.g. link to de-identified historic cases
Dr. Schapranow,
SAPPHIRE NOW, May
18, 2017
In-Memory Apps for
Precision Medicine
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3. Dr. Schapranow,
SAPPHIRE NOW, May
18, 2017
In-Memory Apps for
Precision Medicine
3

4. Dr. Schapranow,
SAPPHIRE NOW, May
18, 2017
In-Memory Apps for
Precision Medicine
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5. Dr. Schapranow,
SAPPHIRE NOW, May
18, 2017
Our Approach: AnalyzeGenomes.com
In-Memory Computing Platform for 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
In-Memory Apps for
Precision Medicine
Drug Response
Analysis
Pathway Topology
Analysis
Medical
Knowledge CockpitOncolyzer
Clinical Trial
Recruitment
Cohort
Analysis
...
Indexed
Sources

6. Real-time Data Analysis and
Interactive Exploration
App Example:
Identification of Optimal Chemotherapy
Dr. Schapranow,
SAPPHIRE NOW, May
18, 2017
In-Memory Apps for
Precision Medicine
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
■ Honored by the 2015 PerMediCon Award

7. Dr. Schapranow,
SAPPHIRE NOW, May
18, 2017
In-Memory Apps for
Precision Medicine
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8. Showcase
Dr. Schapranow,
SAPPHIRE NOW, May
18, 2017
In-Memory Apps for
Precision Medicine
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Calculating Drug Response…Predict Drug Response

9. Dr. Schapranow,
SAPPHIRE NOW, May
18, 2017
In-Memory Apps for
Precision Medicine
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cetuximab might be more
beneficial for the current case

10. ■ Query-oriented search interface
■ Seamless integration of patient specifics, e.g. from EMR
■ Parallel search in international knowledge bases, e.g. for biomarkers, literature,
cellular pathway, and clinical trials
App Example:
Medical Knowledge Cockpit for Patients and Clinicians
In-Memory Apps for
Precision Medicine
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Dr. Schapranow,
SAPPHIRE NOW, May
18, 2017

11. Dr. Schapranow,
SAPPHIRE NOW, May
18, 2017
Medical Knowledge Cockpit for Patients and Clinicians
Pathway Topology Analysis
■ Search in pathways is limited to “is a certain
element contained” today
■ Integrated >1,5k pathways from international
sources, e.g. KEGG, HumanCyc, and WikiPathways,
into HANA
■ Implemented graph-based topology exploration and
ranking based on patient specifics
■ Enables interactive identification of possible
dysfunctions affecting the course of a therapy
before its start In-Memory Apps for
Precision Medicine
Unified access to multiple formerly
disjoint data sources
Pathway analysis of genetic
variants with graph engine
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12. Dr. Schapranow,
SAPPHIRE NOW, May
18, 2017
■ Interactively explore relevant publications, e.g. PDFs
■ Improved ease of exploration, e.g. by highlighted medical terms and relevant
concepts
Medical Knowledge Cockpit for Patients and Clinicians
Publications
In-Memory Apps for
Precision Medicine
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13. Real-time Assessment of Clinical Trial Candidates
■ Switch from trial-centric to patient-centric clinical trials
■ Real-time matching and clustering of patients and
clinical trial inclusion/exclusion criteria
■ No manual pre-screening of patients for months:
In-memory technology enables interactive pre-
screening process
■ Reassessment of already screened or already
participating patient reduces recruitment costs
In-Memory Apps for
Precision Medicine
Assessment of patients
preconditions for clinical trials
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Dr. Schapranow,
SAPPHIRE NOW, May
18, 2017

14. App Example:
Real-time Assessment of Clinical Trial Candidates
■ Supports trial design and recruitment process through
statistical data analysis
■ Real-time matching and clustering of patients and
clinical trial inclusion/exclusion criteria
■ Reassessment of already screened or participating
citizens to reduce recruitment costs
■ Integrates smoothly with the
In-Memory Apps for
Precision Medicine
Real-time assessment of
clinical trial candidates
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Dr. Schapranow,
SAPPHIRE NOW, May
18, 2017

15. Heart
Failure
Sleeping
disorder
Fibrosis
Blood
pressure
Blood
volume
Gene ex-
pression
Hyper-
trophyCalcium
meta-
bolism
Energy
meta-
bolism
Iron
deficiency
Vitamin-D
deficiency
Gender
Epi-
genetics
■ Integrated systems medicine based on
real-time analysis of healthcare data
■ Initial funding period: Mar ‘15 – Feb ‘18
■ Funded consortium partners:
Systems Medicine Model of Heart Failure (SMART)
Dr. Schapranow,
SAPPHIRE NOW, May
18, 2017
In-Memory Apps for
Precision Medicine
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A R
T
+
T
RAM
S
+
S
M

16. ■ Patient: 63 years, male, smoker, chronic heart insufficiency, stage III-IV
1. Appointment I (pre-surgery): Acquire systemic patient details, e.g.
physiological and blood markers
2. Predict outcome using clinical model with patient specifics
3. Select adequate option and conduct valve replacement
4. Equip patient with sensors to allow regular monitoring
5. Appointment II 6 wks after surgery to validate outcome
Application Example: Establish Systems Medicine Model for
Improved Treatment of Heart Failure
Dr. Schapranow,
SAPPHIRE NOW, May
18, 2017
In-Memory Apps for
Precision Medicine
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17. Control your Personal Health Data
Data Donation Pass
Dr. Schapranow,
SAPPHIRE NOW, May
18, 2017
In-Memory Apps for
Precision Medicine
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18. ■ Interdisciplinary partners collaborate on enabling interactive health research
■ Current funding period: Aug 2015 – July 2018
■ Funded consortium partners:
□ AOK
German healthcare insurance company
□ data experts group
Technology operations
□ Hasso Plattner Institute
Real-time data analysis, in-memory database technology
□ Technology, Methods, and Infrastructure for Networked Medical Research
Legal and data protection
Smart Analysis Health Research Access (SAHRA)
Dr. Schapranow,
SAPPHIRE NOW, May
18, 2017
In-Memory Apps for
Precision Medicine
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19. ■ Analysis dashboard combining
functions per use case
■ Providing expert-facing entry
point to individual apps
■ Provides application-wide
authentication / single sign on
App Example:
Analysis Dashboard
Dr. Schapranow,
SAPPHIRE NOW, May
18, 2017
In-Memory Apps for
Precision Medicine
19

20. ■ Stratification of patient cohorts using patient specifics
■ Automatic matching of similar patients and patient anamnesis
■ Interactive graphical exploration of longitudinal patient data
App Example: Stratification of Hypertension Patients
and Longitudinal Data Analysis
Dr. Schapranow,
SAPPHIRE NOW, May
18, 2017
In-Memory Apps for
Precision Medicine
20

21. ■ Online: Visit we.analyzegenomes.com for latest research
results, slides, videos, tools, and publications
■ Offline: High-Performance In-Memory Genome Data Analysis:
In-Memory Data Management Research, Springer,
ISBN: 978-3-319-03034-0, 2014
■ In Person: Visit us at the HPI booth 200!
■ Join us for Intel Tech Talks at SAPPHIRE booth 669!
□ May 17 01.00pm: A Federated In-Memory Database Computing Platform Enabling
Real-time Analysis of Big Medical Data
□ May 18 3.00pm: In-Memory Apps For Precision Medicine
Where to find additional information?
Dr. Schapranow,
SAPPHIRE NOW, May
18, 2017
In-Memory Apps for
Precision Medicine
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22. Keep in contact with us!
Dr. Schapranow,
SAPPHIRE NOW, May
18, 2017
In-Memory Apps for
Precision Medicine
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Dr. Matthieu-P. Schapranow
Program Manager E-Health & Life Sciences
Hasso Plattner Institute
August-Bebel-Str. 88
14482 Potsdam, Germany
schapranow@hpi.de
http://we.analyzegenomes.com/