Presentation for mHealth Israel by Martin Hirsch, CEO, l' APHP (Greater Paris University Hospitals), Nov 20, 2016. Includes an overview of the 39 hospitals in the system, IT processes and infrastructure, Clinical Data Warehouse, Genomics / bio-informatics platform

1. Greater Paris University
Hospitals
20th November 2016 – 10 slides – 20’ – Confidential
@APHP

2. AP-HP

3. Key facts
 Our 39 hospitals attended each year 8 million sick people: outpatients,
emergency, inpatient care or home hospitalization.
 We provide a public health service for all, 24h / 24, and for us it is both a
duty and pride
 95,000 dedicated professionals at the service of patients Including 18,000
physicians and 57,000 caregivers
 Nearly 40,000 births in our 13 maternity.
 A budget of 7.3 billion euros

4. 4
 AP-HP professionals account for more than 8 000 publications in peer-
reviewed journals every year, especially in the field of clinical research.
 AP-HP led more 3,400 research projects, of witch over 100 were of
international range, accounting for 40% of medical research publications
in France.
 It maintains almost 500 international patents, with a comprehensive
licensing policy with strong outreach towards small or large businesses. It
has strong partnerships with French universities and research bodies.
AP HP’s Medical Innovation and Research

5. Our IT at a glance
 Overall IT staff of 800 (1%)
 Overall budget of 150M€/year (2%)
 Fragmented hardware (50+ datacenters) / software
(1000+) / brainware
 Strategic plan 2015-2019 :
 Increased integration & end of EHR roll-out
 Innovation (new online digital services &
leveraging data potential)
 Key systems:
HR : HR Access
Finance : SAP / Maincare
EHR : AGFA (70% roll out)
Imaging: CareStream PACS
Biology LIS: MIPS

6. Focus on Clinical Data Warehouse
Promote more clinical trials
Galvanize medical
research
Build & assess medical
decision algorithms
Identify dangerous/inefficient
medication & devices
AGFA EHR CareStream PACS
MIPS LIMS
Clinical Data Warehouse
 PostGreSQL
 Over 5M patients
 Quality data, structured
(standards) & unstructured
 To date : DRG,
demographics,
biology & text
Talend ETL jobs
Medium term goals
https://www.i2b2.org/

7.  Our short term goals:
 Invest in new ETL : towards medication, imaging,
genetics, etc.
 Build strategic partnerships to develop, assess and
push to market new diagnostic & therapeutic decision-
helping algorithms
 Create a dynamic patient consent system
 Current investment : 1M€/year.
 Key contact : christel.daniel@aphp.fr
Focus on Clinical Data Warehouse

8. Toward Genomics: bio-informatics platform
Creation of Paris Region – Seq IT, Regional medical bio-
informatics platform dedicated to analysis of raw DNA
sequencing data in order to galvanize precision medicine.
This strategic choice of investing in genetics in AP-HP arise from :
 Doctors/patients need of precision/predictive medicine based on molecular analysis
 Major technological innovation in the fields of sequencing, IT and mathematical
analysis
 An important increase in genetical analysis activity for clinical and research purposes
 A progressive transition from gene panels to exome/genome approaches
 The french government strategic plan « France Medecine Génomique 2025 » to invest
in several regional platforms in France
« The rule of thumb in the genomics community is that every dollar spent on sequencing
hardware must be matched by a comparable investment in informatics » - Source

9. Toward Genomics: bio-informatics platform
In this context, the platform aims at :
 Progressively merging genomic data storage for AP-HP 39 hospitals and other
regional hospitals
 Offering a common normalized and certified analysis processes
 Offering innovative bio-informatics tools (open source, proprietary, or custom
development)
 Animating a regional bio-informatics community
 Support and training
 Technological watch
Implementing a shared services platform to assist clinical and research
units with hardware, software and brainware resources for DNA
sequencing bio-informatics analysis

10. demultiplexing
Align & Quality check
Variant Calling
Annotation
Visualization/Selection
Medical interpretation
DNA extract & sequencing1
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3
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Toward Genomics: bio-informatics platform

11. Toward Genomics: bio-informatics platform
Key projects include :
 Common storage in extensive 400 To SAN disk
 Set up of an internal « drag & drop » portal to handle .fastq, .bam, .vcf, etc files
with relevant metadata associated, automatically or manually
 Interface with lab informatics system
 Set of a big data storage and HPC/Spark calculation cluster (initially 50 nodes /
500 core / 3 To RAM)
 Integration of genetic alteration data in clinical data warehouse to associate
with other clinical data
 Preparing AP-HP candidacy for national 2025 genomics plan
 Supporting strategic partnership with Integragen company for exome/genome
sequencing
 Development of open source tools (genetic alteration discovery, annotation,
visualization, etc.)