WG5: Informatics. Martin Dugas, Jaakko Hollmen. European Genomics and Epigenomics Study on MDS and AML

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1 WG5: Informatics Martin Dugas, Jaakko Hollmen EuGESMA European Genomics and Epigenomics Study on MDS and AML

2 Presentations from WG5 members Hans Ulrich Klein Detection of Fusion Genes by Targeted Roche 454 Sequencing Cesare Furlanello Prognostic models in MDS AML transformation Bjorn Tore Gjertsen: p53 full length, beta and gamma protein isoforms in a possible relapse mechanism Kathlenn O Hagan Identification of gene networks associated with acute myeloid dleukemia by integrated molecular methylation and expression profiling Leo Lahti Multi platform data integration for gene expression and copy number Katharina Jorgenson Hunting for biomarkers in multivariate data from offshore workers exposed to low levels of benzene Silvio Bicciato Analysis of gene expression profiling data for the classification of differentiation stages in normal and leukemic populations

3 WG5 action plan & deliverables Consensus on multi platform data analysis: Review paper pp coordinated by Leo Lahti Collection of References and Data analysis Collection of References and Data analysis recommendations, e.g. regarding Batch Effects

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6 WG5 action plan & deliverables Next Generation Sequencing (NGS) data analysis Consensus on QC Extension of NGS toolbox Meta Analysis of NGS + GEP/CN data

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9 WG5 action plan & deliverables Leukemia Gene Atlas Comprehensive database for molecular and clinical leukemia data High throughput data types: genetic and epigenetic information ChIP-chip, gene expression, SNP-chip, ChIP-Seq Online-Data analysis and Meta-Analysis Free access to published Leukemia Data Sets (cave: NIH eracommons) Collaboration partners: Carsten Müller-Tidow, Torsten Haferlach (München), Phil Koeffler (Los Angeles), Lars Bullinger (Ulm), Christian Thiede (Dresden), Wolf-Karsten Hofmann (Mannheim)

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18 WG5: Informatics Martin Dugas, Jaakko Hollmen EuGESMA European Genomics and Epigenomics Study on MDS and AML

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20 Leukemia Gene Atlas: Work packages Data management and integration of published molecular and clinical leukemia data (status: approx. 130 molecular signatures were processed; need for relevant references) Dt Data exploration procedures and tools Semi-automatic analysis of leukemia gene signatures (status: prototype available)

21 Automated analysis of gene signatures

22 WG5 key topics Leukemia Gene Atlas: Data repository & analysis tool Integrative analysis: GEP + CN Next generation sequencing analysis Network analysis Statistical ti ti methods for prognostic markers

23 Goals of WG5 Central support for data analysis, management and interpretation Research into novel methods for integration of clinical andmolecular data, initiallywithrespect to the analysis of microarray data Integrative data analysis will be performed in collaboration with expert biostatisticians ti ti i in the field Development of data management and analysis systems for various chip platforms, such as gene expression profiling (Affymetrix), SNP arrays, array CGH, ChIP on chip, microrna data, epigenetic profiling, proteomic data, high throughput sequencing Application of standard biometric procedures (e.g. survival analysis) to data from AML and MDS trials il

24 Expected outcomes of WG5 Harmonization i of data from multiple li l centres who may be using different chip array types and platforms Integration ti of molecular l dt data from mrna, mirna, epigenetic, SNP and CGH studies via an interactive and dynamic interface driven through mutation, cytogenetic and outcome parameters The identification of target genes and pathways for development of, and testing of, novel therapeutic drugs, molecules and agents The generation and frequently updating the Action specific website