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In-Memory Apps for Precision Medicine

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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.

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In-Memory Apps for Precision Medicine

  1. 1. In-Memory Apps for Precision Medicine Dr.-Ing. Matthieu-P. Schapranow Hasso Plattner Institute, Potsdam, Germany May 18, 2017
  2. 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 2
  3. 3. Dr. Schapranow, SAPPHIRE NOW, May 18, 2017 In-Memory Apps for Precision Medicine 3
  4. 4. Dr. Schapranow, SAPPHIRE NOW, May 18, 2017 In-Memory Apps for Precision Medicine 4
  5. 5. Dr. Schapranow, SAPPHIRE NOW, May 18, 2017 Our Approach: AnalyzeGenomes.com In-Memory Computing Platform for Big Medical Data 5 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. 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) 6 Patient-specific Data Tumor-specific Data Compound Interaction Data ■  Honored by the 2015 PerMediCon Award
  7. 7. Dr. Schapranow, SAPPHIRE NOW, May 18, 2017 In-Memory Apps for Precision Medicine 7
  8. 8. Showcase Dr. Schapranow, SAPPHIRE NOW, May 18, 2017 In-Memory Apps for Precision Medicine 8 Calculating Drug Response…Predict Drug Response
  9. 9. Dr. Schapranow, SAPPHIRE NOW, May 18, 2017 In-Memory Apps for Precision Medicine 9 cetuximab might be more beneficial for the current case
  10. 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 10 Dr. Schapranow, SAPPHIRE NOW, May 18, 2017
  11. 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 11
  12. 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 12
  13. 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 13 Dr. Schapranow, SAPPHIRE NOW, May 18, 2017
  14. 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 14 Dr. Schapranow, SAPPHIRE NOW, May 18, 2017
  15. 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 15 A R T + T RAM S + S M
  16. 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 16
  17. 17. Control your Personal Health Data Data Donation Pass Dr. Schapranow, SAPPHIRE NOW, May 18, 2017 In-Memory Apps for Precision Medicine 17
  18. 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 18
  19. 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. 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. 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 21
  22. 22. Keep in contact with us! Dr. Schapranow, SAPPHIRE NOW, May 18, 2017 In-Memory Apps for Precision Medicine 22 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/

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