4/23/2016 Computational Analysis Plan for CFS Study 23-Apr-16 - PDF document

4/23/2016 Computational Analysis Plan for CFS Study 23-Apr-16 Integrative Visualization System Omics Data Processing Pipelines Big Data Analytics & Knowledge Discovery Disease Driven Applications Research Plan for the Big Data Study of CFS 1 ME/CFS Severely Ill-BIG DATA Study: Research Data 23-Apr-16 RNA Gene Expression - PBMCs Autoantibody panel RNA Gene Expression - NKs T-cell Repertoire DNA Sequencing-Stanford RNA Gene Expression - Monocytes T-cell Repertoire DNA Sequencing-Sequenta RNA Gene Expression - T-Cells CyTOF Standard Panel RNA Gene Expression - B-Cells CyTOF Additional Panels RNA Gene Expression - Macrophages Pan Viral Panel RNA Gene Expression - Dendritic Cells Serum Cytokines MicroRNA in Plasma Ceres Nano Lyme Proteomics Microbiome - stool Cell-Free DNA Metabolomics - stool Whole Genome Sequencing Metabolomics - plasma Whole Exome Genome Sequencing Metabolomics - urine Mitochondrial Genome Sequencing Heavy Metals - blood Mitochondrial DNA/Nuclear DNA Radio Heavy Metals - urine HLA DNA Sequencing Mycotoxins by Magarray WBC density Research Plan for the Big Data Study of CFS 2 1

4/23/2016 ME/CFS Severely Ill-BIG DATA Study: Clinical Tests 23-Apr-16 Acylcarnitines MTHFR Mutations (Methylenetetrahydrofolate) Ammonia Natural Killer Cell (Count & Function) Bartonella extended cx Organic Acids - urine Biotin (Vitamin B7) Pyruvate CBC (Complete Blood Count) Serotonin Chemistry Comprehensive Panel Testosterone Creatine Kinase Thyroid Panel Copper Uric Acid C- Reactive Protein Vasopressin/ADH Cysteine Viral Digital PCR Folate Viral Serologies: FSH (Follicle-Stimulating Hormone) EBV EA (Epstein Barr Virus EA) LH (Luteinizing Hormone) EBV NA (Epstein Barr Virus NA) Estrogen EBV VCA (Epstein Barr Virus VCA) HbA1C (Hemoglobin A1c) CMV (Cytomegalovirus) Homocysteine HHV-6 (Human Herpesvirus 6) Parvovirus IgG Subsets HHV-7 (Human Herpes Virus 7) Lactate HSV1&2 (Herpes Simplex 1 & 2) Lyme Serology with reflex Western Blot Vitamin B12 (Cobalamin) Lymphocyte Subsets Vitamin D25 OH MMA (Methylmalonic Acid) Research Plan for the Big Data Study of CFS 3 ME/CFS Severely Ill-BIG DATA Study: Other Tests 23-Apr-16 Extended EEG Sleep monitoring Fitbit Cognitive Testing Questionnaires - SF36, PROMIS Research Plan for the Big Data Study of CFS 4 2

4/23/2016 23-Apr-16 Omics Data Analysis Pipelines Research Plan for the Big Data Study of CFS 5 23-Apr-16 Omics Data Analysis System Quick Quick To Deploy To Deploy Easy Easy To Scale To Scale Intuitive Intuitive To Use To Use Cluster Research Plan for the Big Data Study of CFS 6 3

4/23/2016 23-Apr-16 Integrative Visualization System Genome: Inherited and Somatic Variations Epigenome and Transcriptome Proteome and Metabolome Cell biology Organ/Tissue physiology Microbiome Environmentome Clinical Information Research Plan for the Big Data Study of CFS 7 23-Apr-16 Visualization Design Research Plan for the Big Data Study of CFS 8 4

4/23/2016 23-Apr-16 Visualization Design Research Plan for the Big Data Study of CFS 9 23-Apr-16 Big Data Analytics and Knowledge Discovery Research Plan for the Big Data Study of CFS 10 5

4/23/2016 23-Apr-16 Big Data Analytics and Knowledge Discovery Research Plan for the Big Data Study of CFS 11 23-Apr-16 Disease Driven Applications Research Plan for the Big Data Study of CFS 12 6