Deliverable

ICT-2010-270253
INTEGRATE
Driving excellence in Integrative Cancer Research through Innovative Biomedical Infrastructures

STREP

Contract Nr: 270253

Deliverable: D5.1 Report on the VPH use case study

Due date of deliverable: (9-30-2011)

Actual submission date: (10-7-2011)

Start date of Project: 01 February 2011

Duration: 36 months

Responsible WP: FORTH

Revision:

Project co-funded by the European Commission within the Seventh Framework Programme (2007-2013)
Dissemination level
PU	Public	X
PP	Restricted to other programme participants (including the Commission Service
RE	Restricted to a group specified by the consortium (including the Commission Services)
CO	Confidential, only for members of the consortium (excluding the Commission Services)

1DOCUMENT INFO

1.1Author

Author	Company	E-mail
George Manikis	FORTH
Kostas Marias	FORTH
Manolis Tsiknakis	FORTH

1.2Documents history

Document version #	Date	Change
V0.1	30/6/2011	Starting version, template
V0.2		Definition of ToC
V0.3		First complete draft
V0.4	15/8/2011	Integrated version (send to WP members)
V0.5		Updated version (send PCP)
V0.6		Updated version (send to project internal reviewers)
Sign off		Signed off version (for approval to PMT members)
V1.0		Approved Version to be submitted to EU

1.3Document data

Keywords
Editor Address data	Name: George Manikis Partner: FORTH Address: N. Plastira 100, Vassilika Vouton Phone: [phone] Fax: E-mail: [e-mail]
Delivery date

1.4Distribution list

Date	Issue	E-mailer

Table of Contents

1DOCUMENT INFO 2

1.1Author 2

1.2Documents history 2

1.3Document data 2

1.4Distribution list 3

2Definitions and Abbreviations 5

3Introduction 6

3.1Breast cancer modelling and going beyond the state-of the art 7

4SUMMARY 10

5Data description 11

5.1Available data from TOP clinical trial 11

5.1.1Clinical Data 11

5.1.2Radiology Imaging Data 12

5.1.3Genomic Data 12

5.1.3.1 Gene Expression Data 12

5.1.3.2Affymetrix SNP and CNV data 12

5.1.3.3Illumina Methylation Data 12

5.2Expected data from other clinical trials 12

5.2.1Radiology Imaging Data 12

5.2.2Digital Pathology Images 13

5.2.3High-throughput Sequencing Data 13

6Clinical Scenarios 14

6.1Predictive Modelling Methodologies 14

6.1.1Feature Extraction from Images 14

6.1.2Feature Selection 15

6.1.3Integrating Heterogeneous Data 16

6.1.3.1Integration of Genomic Data 16

6.1.3.2Machine Learning Methods for Integration 16

6.1.4Kernel-Based Classification and MKL 19

6.1.5Decision Trees and Ensembles of Trees 20

6.1.6Evaluating the performance of the classifier 21

6.1.7Estimating the generalization error 23

6.1.8Feature Selection in Kernel Space 23

6.2Scenario A-Retrospective use of data 24

6.3Scenario B-Retrospective use of data 27

6.4Scenario C-Retrospective use of data 28

7Conclusion 30

8Appendix 31

8.1Scenario D-Retrospective use of clinical data 31

8.2Scenario E-Retrospective use of clinical data 33

8.3Scenario F-Retrospective use of imaging data 35

9REFERENCES 37

List of Figures

List of Tables