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Fp7-Env-2013- 603946 FP7-ENV-2013- 603946 http://www.heals-eu.eu/ 7.2 Predictive biomarkers appropriate for environment-wide association health assessments WP 7 Novel bioinformatics for predictive biomarker discovery Version 1.0 Lead beneficiary: AUTH Date: 31/5/2017 Nature: Report Dissemination level: Public D7.2 - Predictive biomarkers appropriate for EWAS WP7: Novel bioinformatics for predictive Security: biomarker discovery FP7-ENV-2013-603946 Author(s): Denis A. Sarigiannis Version: 2/111 Document Information Grant Agreement ENV-603946 Acronym HEALS Number Health and Environment-wide Associations based on Large population Full title Surveys Project URL http://www.heals-eu.eu/ EU Project Officer Tuomo Karjalainen,- [email protected] Predictive biomarkers Deliverable Number 7.2 Title appropriate for environment-wide association health assessments Work Package Number 7 Title Novel bioinformatics for predictive biomarker discovery Delivery date Contractual M30 Actual 30/04/2017 Status Draft Final X Nature Demonstrator Report X Prototype Other Dissemination level Confidential Public X Author (Partners) Denis A. Sarigiannis, S. Karakitsios, I. Frydas, N. Papaioannou (AUTH) R. Stierum, E. van Someren (TNO) Responsible Denis A. Sarigiannis Email [email protected] Author Partner AUTH Phone +30-2310-994562 Document History Name Date Version Desciption D7.2 - Predictive biomarkers appropriate for EWAS WP7: Novel bioinformatics for predictive Security: biomarker discovery FP7-ENV-2013-603946 Author(s): Denis A. Sarigiannis Version: 3/111 TABLE OF CONTENTS 1 SUMMARY ............................................................................................................................ 7 2 INTRODUCTION - GENERAL CONSIDERATIONS ....................................................................... 8 3 PREDICTIVE BIOMARKERS FOR ENVIRONMENT-WIDE ASSOCIATION HEALTH ASSESSMENTS . 10 3.1 Allergies and asthma ................................................................................................... 10 3.1.1 Transcriptomics ................................................................................................................. 10 3.1.2 Proteomics ......................................................................................................................... 10 3.1.3 Metabolomics .................................................................................................................... 10 3.1.4 Biochemical markers ......................................................................................................... 11 3.1.5 Susceptibility markers ....................................................................................................... 13 3.2 Neurodevelopmental and neurodegenerative diseases ................................................. 14 3.2.1 Transcriptomics ................................................................................................................. 14 3.2.2 Proteomics ......................................................................................................................... 14 3.2.3 Metabolomics .................................................................................................................... 14 3.2.4 Biochemical markers ......................................................................................................... 19 3.2.5 Susceptibility markers ....................................................................................................... 19 3.3 Obesity and childhood diabetes ................................................................................... 21 3.3.1 Transcriptomics ................................................................................................................. 21 3.3.2 Proteomics ......................................................................................................................... 21 3.3.3 Metabolomics .................................................................................................................... 21 3.3.4 Biochemical markers ......................................................................................................... 23 3.3.5 Susceptibility markers ....................................................................................................... 23 4 PATHWAY ANALYSIS ........................................................................................................... 27 4.1 Transcriptomics data ................................................... Errore. Il segnalibro non è definito. 4.2 Metabolomics data ...................................................... Errore. Il segnalibro non è definito. 4.2.1 General info ................................................................. Errore. Il segnalibro non è definito. 4.2.1.1 Spectral Processing ...................................................... Errore. Il segnalibro non è definito. 4.2.1.2 Baseline Correction ..................................................... Errore. Il segnalibro non è definito. 4.2.1.2.1 Peak detection and Chromatogram Builder............. Errore. Il segnalibro non è definito. D7.2 - Predictive biomarkers appropriate for EWAS WP7: Novel bioinformatics for predictive Security: biomarker discovery FP7-ENV-2013-603946 Author(s): Denis A. Sarigiannis Version: 4/111 4.2.1.2.2 Chromatogram Deconvolution................................. Errore. Il segnalibro non è definito. 4.2.1.2.3 Peak alignment ................................ ......................... Errore. Il segnalibro non è definito. 4.2.1.2.4 Gap Filling ................................................................. Errore. Il segnalibro non è definito. 4.2.1.2.5 Identification ................................ ............................ Errore. Il segnalibro non è definito. 4.2.1.3 Preprocessing steps ..................................................... Errore. Il segnalibro non è definito. 4.2.1.3.1 Filtering .......................................................................................................................... 39 4.2.1.3.2 Normalization ........................................................... Errore. Il segnalibro non è definito. 4.2.1.3.4 Multivariate Statistical Analysis ..................................................................................... 40 4.2.1.3.5 PCA ................................................................................................................................. 40 4.2.1.3.6 Fold Change .............................................................. Errore. Il segnalibro non è definito. 4.2.1.3.7 t-test ......................................................................... Errore. Il segnalibro non è definito. 4.2.1.3.8 Clustering Analysis ................................................... Errore. Il segnalibro non è definito. 5 SYNTHESIS OF METHODS AND DATA ........................ ERRORE. IL SEGNALIBRO NON È DEFINITO. 5.1 Joint pathway analysis ................................................................................................. 41 5.2 Fusion of biomarkers ................................................... Errore. Il segnalibro non è definito. 6 PRACTICAL EXAMPLE FROM HEALS: IDENTIFICATIONS OF BIOMARKERS FOR NEURODEVELOPMENTAL DISORDERS .............................. ERRORE. IL SEGNALIBRO NON È DEFINITO. 6.1 Introduction and study design ...................................... Errore. Il segnalibro non è definito. 6.2 Metabolic pathway analysis ......................................... Errore. Il segnalibro non è definito. 6.3 Association of metabolic pathways and child neurodevelopment through EWASErrore. Il segnalibro non è definito. 6.4 Identification of metabolites aassociated with children neurodevelopmental disorders .... ................................................................................................................................... 44 7 CONCLUSIONS .................................................................................................................... 61 8 REFERENCES ....................................................................................................................... 62 D7.2 - Predictive biomarkers appropriate for EWAS WP7: Novel bioinformatics for predictive Security: biomarker discovery FP7-ENV-2013-603946 Author(s): Denis A. Sarigiannis Version: 5/111 From DOW D7.2) Report on predictive biomarkers appropriate for environment-wide association health assessments: This is a synthesis report on the most appropriate biomarkers to use with predictive power in support of environment-wide associations with health effects. [month 30] Task 7.2 Predictive data mining – data models design and analysis (AUTH, TNO, CERETOX, UPD) For predictive data mining we will develop a set of models to perform inference on the available (combination of) multidisciplinary datasets. Several techniques can be used for that purpose, ranging from typical approaches based on decision trees or k-nearest neighbors to more sophisticated ones that employ artificial neural networks (ANNs), support vector machines (SVMs) or Bayesian networks (BNs). We will implement and test all of the aforementioned approaches, since our goal is not only to perform mere classification but also to study and unravel the feature attributes concealed in the exposome data. To estimate the reliability of the proposed predictive models we will employ the k-fold cross-validation schema and measure standard performance indices like sensitivity, specificity and accuracy. ROC analysis will also be carried
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