ULICE WP7 Services for CPT Research. Interim report Steve Harris, University of Oxford

Transcription

1 ULICE WP7 Services for CPT Research Interim report Steve Harris, University of Oxford 1

2 Union of Light Ion Centres in Europe Start Date End Date Lead Beneficiary M1 M48 University of Oxford Effort 57 Deliverables Submitted 7.1 M3 (Grid infrastructure), 7.2 M6 (Semantics infrastructure) Milestones 7.1 M3 (Grid infrastructure), 7.2 M6 (Semantics infrastructure), WP7 meeting (CERN, May 2010) Active Delays N.A. The ULICE project is co-funded by the European Commission under FP7 Grant Agreement Number

3 Union of Light Ion Centres in Europe (Original) Gantt chart TASK STATUS WORK PERFORMED /RESULTS Task 7.1 Grid infrastructure Done >> 7.5 Infrastructure update (ongoing) Task 7.2 Semantics infrastructure Done >> 7.6 Tools update (ongoing) Task 7.3 Services for Data Acquisition and Processing Ongoing Integration with OpenClinica complete, harmonisation of example protocol and CTEP standards in progress Task 7.4 Tools to facilitate the comparison of Hadron Therapy Treatment plans Ongoing Initial development of services for comparison of treatment plans and Monte Carlo simulations, and for calculation of malignant induction probability complete The ULICE project is co-funded by the European Commission under FP7 Grant Agreement Number

4 introductory remarks 4

5 early breast cancer trialists collaborative group initiated in 1983 hundreds of institutions worldwide consensus on 30 variables, a data model and submission format now increasing to 200 variables analyse data every 5 years computable data and follow-up for 200,000 cases in the 2000 review rock-solid evidence base for the treatment of early breast cancer 5 5

6 doesn t always work (failed) systematic review of TP53 and Platinum response in ovarian cancer 75 clinical studies 8331 patients prognostic value of TP53 mutation: no conclusions could be drawn most of the study metadata was missing insufficient detail about the IHC only some exons sequenced 6 6

7 7

8 8

9 WP7 data standards CPT specific standards and assessment of existing data being developed in other work packages WP7 aims to identify and utilise best international standards for basic cancer therapy evaluation baseline variables: diagnosis and staging adverse event observations key dates: treatment, adverse events, recurrence, progression, death cause of death cost calculations meta-standard: ISO/IEC11179 ISO/IEC19763 standards: US Cancer Therapy Evaluation Program (CTEP) 9 9

10 Grid Infrastructure (7.1) 10

11 grid infrastructure delivered as specified in proposal (with CERN) established basic grid infrastructure for deployment of services provides a pan-project single sign-on and identification framework if so required installation of metadata registry software and default content additional capabilities for study and dataset registration from SAS/SPSS files added on maintenance (7.5) 11 11

12 12

13 Semantics Infrastructure (7.2) 13

14 semantics infrastructure delivered as specified, later than planned but at no cost to project existing standards for vocabulary explored definition of core variables required for therapy evaluation for augmentation throughout the project 14 14

15 Name Definition Units of Measure/ Enumerations Followup interval The time period of the follow up event 12 months 24 months 36 months 48 months 60 months Data type Format Related Data Elements String n.a. TCGA FU Form question 1 Tumour progression observed A boolean indicator to gate questions about tumour progression. When Yes implementing on forms, ensure that it is possible to distinguish between No null, yes and no. String n.a. TCGA FU Form question 2 Tumour progression year Numeric value to represent the year of tumor progression in an individual after initial treatment. n.a. String YYYY TCGA FU Form question 2.3, cadsr Tumour progression month Numeric value to represent the month of tumour progression in an individual after initial treatment. n.a. String MM TCGA FU Form question 2.1, cadsr Tumour progression day Numeric value to represent the day of tumour progression in an individual after initial treatment. n.a. String DD TCGA FU Form question 2.2, cadsr Tumour recurrence observeda boolean indicator to gate questions about tumour recurrence. When Yes implementing on forms, ensure that it is possible to distinguish between No null, yes and no. String n.a. TCGA FU Form question 3 Tumour recurrence year Numeric value to represent the year of tumor recurrence in an individual after initial treatment. n.a. String YYYY TCGA FU Form question 2.3, cadsr Tumour recurrence month Numeric value to represent the month of tumour recurrence in an individual after initial treatment. n.a. String MM TCGA FU Form question 2.1, cadsr Tumour recurrence day Numeric value to represent the day of tumour recurrence in an individual after initial treatment. n.a. String DD TCGA FU Form question 2.2, cadsr Date of last contact year Numeric value to represent the year the participant was last contacted. n.a. String YYYY TCGA FU Form question 4.3, cadsr Date of last contact month Numeric value to represent the month the participant was last contacted. n.a. String MM TCGA FU Form question 4.1, cadsr Date of last contact day Numeric value to represent the day the participant was last contacted. n.a. String DD TCGA FU Form question 4.2, cadsr

16 protocol harmonisation and automatic data collection Task

17 framing the big picture support for systematic reviews (with Mark Lodge) highest level of clinical evidence increasingly relied upon for treatment decisions increasingly important as personalised medicine becomes more common plan now!! support for cost benefit studies (with Madelon-Pijls Johannesma) difficult to get all of the parameters for the ideal models agree the models in advance then we can design trials to gather the parameters quality of life/low level adverse events (with Bleddyn Jones) expect fewer serious adverse events and a reduction in their severity difficult to gather data as not presented in the clinic plan to gather information directly from patients 17 17

18 Oxford + Lyon/CNAO develop a set of core case report form standards consistent with US CTEP supporting a case register of (international) charged particle therapy (CPT) treatments demonstrate and support automated study design, registration, system deployment and reporting for CPT studies provide standard, validated installations and tools for the creation of harmonised protocols 18 18

19 19

20 20

21 21 21

22 22 22

23 23

24 metamodels for semantics Task

25 forms and markov cost benefit studies working with PARTNER students develop metamodels to allow semantic annotation and exchange of form definitions: support reuse of forms across clinical trial management systems markov cost benefit models: properly described derivation of parameters; swap-able death tables - exchange and reuse of research for local planning 25 25

26 26

27 27

28 28

29 29

30 grid services for treatment planning (7.4) 30

31 grid services for treatment planning computing grids make an ideal vehicle for implementing calculation intensive services - particularly Monte-Carlo based simulations developing a number of services in Oxford including Monte Carlo planning from virtual phantoms malignant induction probability maps 31 31

32 MIP Calculations Heatmaps for the probability of malignant induction for different treatments (with the Mayo Clinic) Subtotally resected atypical meningioma Compare plans for different types of radiotherapy 3D Conformal RT (standard treatment) IMRT RapidArc (helical RT) Spot scanning protons Account for fractionation 32

33 33