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

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Research Plan for the Big Data Study of CFS

Computational Analysis Plan for CFS Study

1 Omics Data Processing Pipelines Integrative Visualization System Disease Driven Applications Big Data Analytics & Knowledge Discovery

23-Apr-16

Research Plan for the Big Data Study of CFS

ME/CFS Severely Ill-BIG DATA Study: Research Data

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RNA Gene Expression - PBMCs RNA Gene Expression - NKs RNA Gene Expression - Monocytes RNA Gene Expression - T-Cells RNA Gene Expression - B-Cells RNA Gene Expression - Macrophages RNA Gene Expression - Dendritic Cells MicroRNA in Plasma Proteomics Cell-Free DNA Whole Genome Sequencing Whole Exome Genome Sequencing Mitochondrial Genome Sequencing Mitochondrial DNA/Nuclear DNA Radio HLA DNA Sequencing WBC density Autoantibody panel T-cell Repertoire DNA Sequencing-Stanford T-cell Repertoire DNA Sequencing-Sequenta CyTOF Standard Panel CyTOF Additional Panels Pan Viral Panel Serum Cytokines Ceres Nano Lyme Microbiome - stool Metabolomics - stool Metabolomics - plasma Metabolomics - urine Heavy Metals - blood Heavy Metals - urine Mycotoxins by Magarray

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Research Plan for the Big Data Study of CFS

ME/CFS Severely Ill-BIG DATA Study: Clinical Tests

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Acylcarnitines Ammonia Bartonella extended cx Biotin (Vitamin B7) CBC (Complete Blood Count) Chemistry Comprehensive Panel Creatine Kinase Copper C- Reactive Protein Cysteine Folate FSH (Follicle-Stimulating Hormone) LH (Luteinizing Hormone) Estrogen HbA1C (Hemoglobin A1c) Homocysteine IgG Subsets Lactate Lyme Serology with reflex Western Blot Lymphocyte Subsets MMA (Methylmalonic Acid) MTHFR Mutations (Methylenetetrahydrofolate) Natural Killer Cell (Count & Function) Organic Acids - urine Pyruvate Serotonin Testosterone Thyroid Panel Uric Acid Vasopressin/ADH Viral Digital PCR Viral Serologies: EBV EA (Epstein Barr Virus EA) EBV NA (Epstein Barr Virus NA) EBV VCA (Epstein Barr Virus VCA) CMV (Cytomegalovirus) HHV-6 (Human Herpesvirus 6) Parvovirus HHV-7 (Human Herpes Virus 7) HSV1&2 (Herpes Simplex 1 & 2) Vitamin B12 (Cobalamin) Vitamin D25 OH

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Research Plan for the Big Data Study of CFS

ME/CFS Severely Ill-BIG DATA Study: Other Tests

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Extended EEG Sleep monitoring Fitbit Cognitive Testing Questionnaires - SF36, PROMIS

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Research Plan for the Big Data Study of CFS

Omics Data Analysis Pipelines

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Research Plan for the Big Data Study of CFS

Omics Data Analysis System

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Intuitive To Use Intuitive To Use Easy To Scale Easy To Scale Quick To Deploy Quick To Deploy

Cluster

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Research Plan for the Big Data Study of CFS

Integrative Visualization System

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Organ/Tissue physiology

Epigenome and Transcriptome Proteome and Metabolome Cell biology Genome: Inherited and Somatic Variations Clinical Information Microbiome Environmentome

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Research Plan for the Big Data Study of CFS

Visualization Design

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Research Plan for the Big Data Study of CFS

Visualization Design

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Research Plan for the Big Data Study of CFS

Big Data Analytics and Knowledge Discovery

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Research Plan for the Big Data Study of CFS

Big Data Analytics and Knowledge Discovery

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Research Plan for the Big Data Study of CFS

Disease Driven Applications

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