Integrating Patient Care & Research Information Systems «ORBIS Research»

Transcription

1 Integrating Patient Care & Research Information Systems «ORBIS Research» Dr Christel Daniel CCS Patient AP-HP October 3rd, 2013

2 Agenda ORBIS Research Functional scope Phase 1 : Clinical Data Repository Phase 2 Prototype Governance Ethics & regulatory issues Semantic interoperability Connecting to external platforms 2

3 ORBIS Research

4 ORBIS Research Proof of concept ORBIS Research As part of the Clinical Information System development & deployment Département de la Recherche Clinique et du Développement (DRCD) Centre de Compétences et de Services (CCS) SI Patient - AGFA Healthcare Process: Supporting Reasearch & Teaching activities Using clinical data from the Clinical Inforamtion System (ORBIS & other IS) in the context of research activities (biomedical research, clinical & translational research) promoted by AP-HP, other institutional promotors or industry. ORBIS Research Proof of concept Exploratory work since Octobrer 2012 Users needs & functional scope First prototype : AP-HP Clinical Data Repository (CDR) (i2b2) Governance, ethics & regulatory issues Semantic interoperability 4

5 ORBIS Research: Functional scope Phase 1 / Phase a 1b Protocol feasibility (leverage clinical data to design viable trial protocols and estimate recruitment) Data collection (1) : Clinical Trials in silico (data extraction for authorized protocols one shot) Patient recruitment (detect patients eligible for authorized trials & better utilize recruitment potential through practicing physicians) Data collection (2) (data extraction for authorized protocols ) 5

6 Clinical Information System SYSTÈME D INFORMATION PATIENT ORBIS Research - Phase 1 AP-HP Clinical Data Repository Technical architecture Clinical data Clinical Data Repository (CDR) Monocentric Care team Multicentric ORBIS DB Semantic DW Other DB I2b2 CDR Feasibility 1a I2b2 projects In silico clinical trials 1b (v1.7) 6

7 Scope of the CDR AP-HP Aligned with the deployment of ORBIS Unique AP-HP patient ID Normalization (ICD-10, CCAM, LOINC, SNOMED, etc.) Type of data : Demographics & consents Diagnoses & acts (French DRG) Structured & unstructured data Medical history, familial history, habits, allergy, immunization, problems, observations, vital signs, etc Any type of encounters Lab test results, radiology reports, anatomic pathology reports Medication (orders dispense, administration) 7

8 Scope of the CDR AP-HP (V ) Hospital APR, BCT, TNN APR, BCT, TNN Demographics X X Encounters X X Diagnoses (ICD-10) X X Acts (CCAM) X X Lab results (LOINC) X X Clinical data X (questionnaires) Anatomic pathology X (APR) 8

9 Scope of the CDR AP-HP Next steps Semantic annotation and integration of structured clinical data (forms) 9

10 Scope of the CDR AP-HP Next steps Data from monitors, sensors, devices 10

11 Scope of the CDR AP-HP Next steps Semantic annotation of unstructured data & integration to the CDR Terminology Server Terminologies Ontologies Knowledge ORBIS Content Annotation Use of terminologies in ITM for extracting/enriching medical concepts in ORBIS documents IMPAX or Qdoc Triple Store Classification/Indexation 11

12 Scope of the CDR AP-HP Next steps Integration with biobanks 12

13 First prototype: AP-HP Clinical Data Repository (CDR) (i2b2) (V ) Source data (300 Go) 1,200,000 patients (unique AP-HP ID) 1,900,000 encounters 100,000 discharge summaries 13

14 ORBIS Research Phase 1 + Phase 2 Clinical Data Repository (CDR) I2b2 Projet Pre-population of individual ecrfs and/or transferring data sets 2 Patient recruitment Dynamic data collection (new patients, new data) 3 Integrating external data 14

15 ORBIS Research Integrated Future 1. Optimizing clinical protocol designs 2. Enhanced patient recruitment 3. Optimized clinical trial data collection 4. Facilitated Serious Adverse Event reporting 15

16 Governance

17 Governance Direction Générale et Commission Médicale d Etablissement (CME) Strategic plan Planning & technical committees Département de la Recherche Clinique et du Développement (DRCD) Centre de Compétence et de Service du Système d Information patient (CCS Patient) Representatives from AP-HP hospital (URC, DIM, etc) Coordination of the use of ORBIS Research in the 38 hospitals Ethics & regulatory issues Economic issues 17

18 Moving legal ethical framework ANSM CPP ANSM Source : Lettre de la délégation à la recherche clinique (DIRC) Ile de France (2007) 18

19 Key governance principles (AP-HP) 19

20 Patient consent Opt in/out 20

21 I2b2/SHRINE 21

22 EHR4CR project EHR4CR use cases demonstrated by 11 pilots in 5 European countries Germany (WWU, FAU) France (AP-HP, U936) UK (UoD, UoG, UoM, UCL) Switzerland (HUG) Poland (MuW) 22

23 EHR4CR 33 European academic and industrial partners 11 Pharmaceutical Companies (members of EFPIA) & 22 Public Partners (Academia, Hospitals and SMEs) 23

24 Feasibility studies - Queries A research worker can drag and drop Data Elements stored in the EHR4CR metadata registry (1) as well as boolean and temporal operators (2) in order to represent formally the inclusion/exculsion criteria of the clinical trial (3)

25 Feasibility studies - Queries 25

26 Feasibility studies - Results 26

27 Key governance principles The EHR4CR platform will not hold a centralised repository of patient level EHR data across our network of registered hospitals. It will hold queries, result sets and audit logs, to enable platform governance. Patient level data will not cross national boundaries via the EHR4CR platform. Only aggregated result sets will be transferred into the platform. Patient level data will remain local to each hospital, or to each hospital plus its local research environment. 27

28 Key governance principles Feasibility studies Aggregated result sets (patient counts) will be communicated from each hospital site to the central platform for onward propagation to research entities. In order to validate the platform (only during the research phase of EHR4CR) these counts may be compared with the actual numbers screened and recruited for similar historic trials. 28

29 Key governance principles Patient recruitment/clinical trial execution EHR4CR components and services that analyse patient level data and generate patient level extracts of data will be deployed locally at each site and operate exclusively at a local level to enable identification of potential patients and, if they are suitable, their recruitment. EHR4CR will only implement the interchange of patient specific, fully identifiable, data between EHR and EDC Systems if there is explicit patient consent for this information exchange, and it will occur only locally within a single clinical research environment, and only in support of the specific clinical study to which the patient has consented. 29

30 Key governance principles Once finally deployed and in real use, platform will hold a register of research entities and hospitals with collaborative relationships and will only forward aggregated data to research entities in accordance with those relationships. An EHR4CR Code of Practice for all users of the EHR4CR platform will restrict the use of aggregated query information for mutually predefined and approved purposes such as protocol feasibility and refinement. Use of the EHR4CR platform to analyse hospitals prescribing practices or outcomes for sales/marketing or benchmarking purposes will not be permitted 30

31 Semantic interoperability

32 i2b2/shrine Hierarchy of terms 32

33 Limitations i2b2 metadata table Column C_HLEVEL C_FULLNAME C_NAME C_SYNONYM_CD C_VISUALATTRIBUTES C_TOTALNUM C_BASECODE C_METADATAXML C_FACTTABLECOLUMN C_TABLENAME C_COLUMNNAME C_COLUMNDATATYPE C_OPERATOR C_DIMCODE C_COMMENT C_TOOLTIP UPDATE_DATE DOWNLOAD_DATE IMPORT_DATE SOURCESYSTEM_CD VALUETYPE_CD Data Type NUMBER(22,0) VARCHAR2(700 BYTE) VARCHAR2(2000 BYTE) CHAR(1 BYTE) CHAR(3 BYTE) NUMBER(22,0) VARCHAR2(50 BYTE) CLOB VARCHAR2(50 BYTE) VARCHAR2(50 BYTE) VARCHAR2(50 BYTE) VARCHAR2(50 BYTE) VARCHAR2(10 BYTE) VARCHAR2(700 BYTE) CLOB VARCHAR2(900 BYTE) DATE DATE DATE VARCHAR2(50 BYTE) VARCHAR2(50 BYTE) 33

34 C_METADATAXML XML required for representing the value domain E.g allow on-the-fly unit conversion for lab tests values Property <Version> <CreationDateTime> <DataType> <Flagstouse> <Oktousevalues> <MaxStringLength> <LowofLowValue> <HighofLowValue> <LowofHighValue> <HighofHighValue> <LowofToxicValue> <HighofToxicValue> <EnumValues> <Valdescription> <UnitValues> <NormalUnits> <EqualUnits> <ConvertingUnits> <Units> <MultiplyingFactor> Description Version associated with this data Timestamp associated with this data PosFloat, Float, PosInteger, Integer, Enum, String HL = High/Low A = Abnormal Indicates if it is OK to use values (Y/N) Y indicates value is a number (numeric types) N or empty indicates value is not a number The maximum length associated with a String data type Values less than this are categorized as Very Low Values between this and LowOfLow are categorized as Low Values between this and HighOfLow are categorized as Medium Values between this and LowOfHigh are categorized as High. Values greater than this are categorized as Very High Low end of toxic value range High end of toxic value range Container of values associated with enum data type enum data type value Container for unit of measurement value information Unit of measurement associated with value An equivalent unit of measurement associated with value Container for unit conversion information Conversion unit of measurement Conversion unit multiplication factor 34

35 SHRINE Evaluation 35

36 Electronic Health Record For Clinical Research (EHR4CR) LIMICS UMRS 1142 Hierarchy of data elements 36

37 Data element collaborative editor 37

38 Meta data repository (ISO 11179) CCD data structure Data elements ISO datatypes 38

39 Histologic SYSTÈME D INFORMATION PATIENT type ( Text Data type (Enum) -> Concept Descriptor (CD) Observation = Observable entity + value <observation classcode='obs' moodcode='evn'> <templateid root=' '/> <code code=' ' displayname= Histologic type' codesystem=' ' codesystemname= SNOMED CT'/> <effectivetime value=' '/> <value xsi:type= CD' code=' displayname= Non infiltrating value Intraductal Carcinoma' set codesystem=' ' codesystemname= SNOMED CT'/> </observation> 39

40 Systolic blood pressure ( Number data type - Physical quantity) Observation = Observable entity + value <observation classcode='obs' moodcode='evn'> <templateid root=' '/> <code code '8480-6' displayname= Intravascular systolic blood pressure' codesystem=' ' codesystemname='loinc'/> <effectivetime value=' '/> <value xsi:type='pq' value= 120' unit='mmhg'/> </observation> 40

41 Conclusion ORBIS Research 1) Enables enterprise-wide repurposing of health care data for research Feasibility studies, patient recruitment 2) Provides platform for Clinical Trials in silico 3) SHALL extend EHR research so that data may be shared among sites and samples may be obtained 4) SHALL enable natural language processing 5) SHALL enable bid data processing & mining 41

42 Acknowledgments AP-HP Stéphane Bréant, Amina Chniti, Equipe PRISME, Philippe Letoumelin, Eric Lepage AGFA Healthcare INSERM - LIMICS U1142 Sajjad Hussain, David Ouagne, Eric Sadou, Jean Charlet, Marie-Christine Jaulent EHR4CR WP4 members : Special thanks to Julie James (UCL), Richard Bache (KCL), Landen Bain (CDISC), Kerstin Forsberg, Nishaban Talukdar (AZ), Thomas Ganslandt, Sebastian Mate (FAU), Marc Mc Gilchrist (UNIVDUN), Dirk Schwarz-hertzner, Pascal Van Hille, Isabelle Stevant (U936), Eric Zapletal (AP-HP), Bartholomaus Kahl Justin Doods, Inaki SotoRey (WWU), Nicolas de Saint-Jorre, Manuel Neukum (Xclinical), Luka Toldo (Merck), Ward Lemaire (Janssen), Louis Schilders (Custodix) WPG2 members 42

43 Thank you for your attention Any question? 43