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Analyze Genomes: In-memory Apps supporting Precision Medicine
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Transcript of Analyze Genomes: In-memory Apps supporting Precision Medicine
Analyze Genomes: In-Memory Apps Supporting Precision Medicine -- Real-world Experiences
Dr. Matthieu-P. Schapranow SAPPHIRE, Orlando, USA
May 19, 2016
■ 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: Join us for Intel Tech Talks at SAPPHIRE booth 625 daily!
□ May 17 12.30pm: A Federated In-Memory Database Computing Platform Enabling Real-time Analysis of Big Medical Data
□ May 18 12.30pm: In-Memory Apps for Next Generation Life Sciences Research
□ May 19 11.30am: In-Memory Apps Supporting Precision Medicine
Where to find additional information?
Schapranow, SAPPHIRE, May 19, 2016
In-Memory Apps Supporting Precision Medicine
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■ Patients
□ Individual anamnesis, family history, and background
□ Require fast access to individualized therapy
■ Clinicians
□ Identify root and extent of disease using laboratory tests
□ Evaluate therapy alternatives, adapt existing therapy
■ Researchers
□ Conduct laboratory work, e.g. analyze patient samples
□ Create new research findings and come-up with treatment alternatives
The Setting Actors in Oncology
Schapranow, SAPPHIRE, May 19, 2016
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In-Memory Apps Supporting Precision Medicine
Schapranow, SAPPHIRE, May 19, 2016
Our Approach Analyze Genomes: 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
In-Memory Apps Supporting Precision Medicine
Drug Response Analysis
Pathway Topology Analysis
Medical Knowledge Cockpit Oncolyzer
Clinical Trial Recruitment
Cohort Analysis
...
Indexed Sources
Use Case: Precision Medicine in 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. 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 Schapranow, SAPPHIRE, May 19, 2016
In-Memory Apps Supporting Precision Medicine
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Schapranow, SAPPHIRE, May 19, 2016
In-Memory Apps Supporting Precision Medicine
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Schapranow, SAPPHIRE, May 19, 2016
In-Memory Apps Supporting Precision Medicine
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App Example: From Raw DNA to Variants
■ Control center for processing of raw DNA data, such as FASTQ, SAM, and VCF
■ Personal user profile guarantees privacy of uploaded and processed data
■ Supports reproducible research process by storing all relevant process parameters
■ Implements prioritized data processing and fair use, e.g. per department or per institute
■ Supports additional service, such as data annotations, billing, and sharing for all Analyze Genomes services
■ Honored by the 2014 European Life Science Award
In-Memory Apps Supporting Precision Medicine
Standardized Modeling and runtime environment for
analysis pipelines
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Schapranow, SAPPHIRE, May 19, 2016
Real-time Data Analysis and Interactive Exploration
App Example: Identification of Optimal Chemotherapy
Schapranow, SAPPHIRE, May 19, 2016
In-Memory Apps Supporting 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
■ 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: Latest Medical Knowledge for Patients and Clinicians
In-Memory Apps Supporting Precision Medicine
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Schapranow, SAPPHIRE, May 19, 2016
Schapranow, SAPPHIRE, May 19, 2016
App Example: 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 Supporting Precision Medicine
Unified access to multiple formerly disjoint data sources
Pathway analysis of genetic variants with graph engine
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Schapranow, SAPPHIRE, May 19, 2016 ■ Personalized clinical trials, e.g. by incorporating patient specifics
■ Classification of internal/external trials based on treating institute
App Example: Latest International Clinical Trials
In-Memory Apps Supporting Precision Medicine
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Schapranow, SAPPHIRE, May 19, 2016
■ Interactively explore relevant publications, e.g. PDFs
■ Improved ease of exploration, e.g. by highlighted medical terms and relevant concepts
App Example: Latest International Publications
In-Memory Apps Supporting Precision Medicine
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■ For patients
□ Identify relevant clinical trials and medical experts
□ Become an informed patient
■ For clinicians
□ Identify pharmacokinetic correlations
□ Scan for similar patient cases, e.g. to evaluate therapy efficiency
■ For researchers
□ Enable real-time analysis of medical data, e.g. assess pathways to identify impact of detected variants
□ Combined mining in structured and unstructured data, e.g. publications,
diagnosis, and EMR data
What to Take Home? Test it Yourself: AnalyzeGenomes.com
Schapranow, SAPPHIRE, May 19, 2016
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In-Memory Apps Supporting Precision Medicine
■ 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: Join us for Intel Tech Talks at SAPPHIRE booth 625 daily!
□ May 17 12.30pm: A Federated In-Memory Database Computing Platform Enabling Real-time Analysis of Big Medical Data
□ May 18 12.30pm: In-Memory Apps for Next Generation Life Sciences Research
□ May 19 11.30am: In-Memory Apps Supporting Precision Medicine
Where to find additional information?
Schapranow, SAPPHIRE, May 19, 2016
In-Memory Apps Supporting Precision Medicine
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Keep in contact with us!
Dr. Matthieu-P. Schapranow Program Manager E-Health & Life Sciences
Hasso Plattner Institute
August-Bebel-Str. 88 14482 Potsdam, Germany
http://we.analyzegenomes.com/
Schapranow, SAPPHIRE, May 19, 2016
In-Memory Apps Supporting Precision Medicine
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