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Undiagnosed Diseases Network Manual of Operations February 21, 2018

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Undiagnosed Diseases Network Manual of Operations February 21, 2018 Undiagnosed Diseases Network Manual of Operations February 21, 2018 1 Table of Contents Table of Acronyms ...................................................................................................................... 3 I. Network Overview and Operating Procedures ........................................................................ 5 II. [Content to be Determined] ................................................................................................. 12 III. Clinical Protocol ................................................................................................................... 13 IV. Data Standards .................................................................................................................... 30 V. Technology and Data Management ..................................................................................... 34 VI. Sequencing .......................................................................................................................... 39 VII. Data Sharing ....................................................................................................................... 55 VIII. Publications and Research ................................................................................................ 59 IX. Website and Social Media ................................................................................................... 63 X. Milestones and Metrics ........................................................................................................ 65 XI. Biospecimens ...................................................................................................................... 67 XII. Central Biorepository ......................................................................................................... 77 XIII. Metabolomics ................................................................................................................... 81 XIV. Model Organisms Screening Center .................................................................................. 93 XV. Institutional Review Board Communications ..................................................................... 99 XVI. Billing Procedures ........................................................................................................... 103 XVII. Surveys ........................................................................................................................... 105 XVIII. APPENDICES .................................................................................................................. 109 APPENDIX 1: The NIH UDP Protocol ................................................................................................ 109 APPENDIX 2: NIH UDP Participant Flow .......................................................................................... 113 APPENDIX 3: NIH-UDP Pre-CRC Admission ...................................................................................... 114 APPENDIX 4: Case Review Committee of the UDN .......................................................................... 115 APPENDIX 5: ClinicalTrials.gov Record ............................................................................................ 116 APPENDIX 6: Example Study Recommendation Letters................................................................... 121 APPENDIX 7: Suggested Triage Methods ......................................................................................... 129 APPENDIX 8: Applicant Review Form (completed by Clinical Sites) ................................................. 130 APPENDIX 9: UDN Generic Letters (for patients and health care providers) ................................... 133 APPENDIX 10: Suggested Sites for Testing....................................................................................... 150 APPENDIX 11: Wrap-up Template ................................................................................................... 151 APPENDIX 12: Participant Follow-up Surveys .................................................................................. 154 APPENDIX 13: Research Inventory Form ......................................................................................... 158 APPENDIX 14: Feature Request Form .............................................................................................. 159 APPENDIX 15: UDN Data Sharing and Use Agreement .................................................................... 160 APPENDIX 16: UDN Research Concept Sheet .................................................................................. 170 APPENDIX 17: UDN Metrics ............................................................................................................. 173 APPENDIX 18: UDN Sequencing – Medically Actionable and Carrier Status Findings ...................... 174 APPENDIX 19: UDNCB Sample Inquiry Form.................................................................................... 175 APPENDIX 20: UDN Metabolomics Core Request Form ................................................................... 176 APPENDIX 21: Annual UDN Survey Review Worksheet ................................................................... 177 APPENDIX 22: UDN Survey Documentation Form ........................................................................... 178 APPENDIX 23: UDN PEER Charter and Application .......................................................................... 181 APPENDIX 24: UDN Standard Operating Procedures for Not Accepted Applicants ......................... 186 APPENDIX 25: UDN Standard Operating Procedure for Media Inquiries ......................................... 189 2 Table of Acronyms Acronym Definition ACMG American College of Medical Genetics and Genomics BCM Baylor College of Medicine bp Base pairs BWA Burrows Wheeler Aligner CC Undiagnosed Diseases Network Coordinating Center CIRB Central Institutional Review Board CLIA Clinical Laboratory Improvement Amendments COI Conflict of Interest CPT Cell Preparation Tube CR Continuing Review CRC Clinical Research Center CS Undiagnosed Diseases Network Clinical Site CSF Cerebrospinal fluid CSL Clinical Services Laboratory dbGaP Database of Genotypes and Phenotypes DOB Date of birth EEG Electroencephalogram EMG Electromyography FFQ Food FreQuency Questionnaire FIPS Federal Information Processing Standards FISMA Federal Information Security Management Act FWA Federalwide Assurance gDNA Genomic DNA GSL Genomic Services Laboratory HA HudsonAlpha Institute for Biotechnology HIPAA Health Insurance Portability and Accountability Act HPO Human Phenotype Ontology HRPP Human Research Protections Program ICD International Classification of Diseases ICF Informed Consent and Assent Forms IRB Institutional Review Board LCF Lipidomics Core Facility LIMS Laboratory Information Management System MC Undiagnosed Diseases Network Metabolomics Core MRI Magnetic Resonance Imaging MRS Magnetic Resonance Spectroscopy NCV Nerve Conduction Velocity NHANES National Health and Nutrition Examination Survey 3 NHGRI National Human Genome Research Institute NHGRI-IRP National Human Genome Research Institute-Intramural Research Program NIH National Institutes of Health NIST National Institute of Standards and Technology NORD National Organization for Rare Disorders OMIM Online Mendelian Inheritance in Man ORDR Office of Rare Diseases Research OSC Office of Strategic Coordination PBMC Peripheral Blood Mononuclear Cell PCC Participant Care Coordinator PCR Polymerase chain reaction PE Paired-end PEER UDN Participant Engagement and Empowerment Resource PHI Personal Health Information PI Principal Investigator PII Personally Identifiable Information QC Quality Control QWES Quick Whole Exome SeQuencing SC Undiagnosed Diseases Network SeQuencing Core SNP Single Nucleotide Polymorphism SRC Scientific Review Committee SST Serum separator tube TAT Turnaround time UDN Undiagnosed Diseases Network UDNCB Undiagnosed Diseases Network Central Biorepository UDN NIH PO Undiagnosed Diseases Network National Institutes of Health Program UDP UndiagnosedOfficial Diseases Program UDPICS Undiagnosed Diseases Program Integrated Collaboration System UUID Universally UniQue Identifier WES Whole Exome SeQuencing WGS Whole Genome SeQuencing WGL Whole Genome Laboratory 4 I. Network Overview and Operating Procedures A. Network Overview The Undiagnosed Diseases Network (UDN) consists of 7 Clinical Sites (CSs), a Coordinating Center (CC), 2 DNA SeQuencing Cores (SCs), a Model Organisms Screening Center, a Metabolomics Core (MC), and a Central Biorepository. The CC is located at the following institution, with the following PIs: • Harvard Medical School, Boston, MA - Isaac Kohane, MD, PhD and Alexa McCray, PhD The CSs are located at the following institutions, with the following PIs: • Baylor College of Medicine, Houston, TX - Brendan Lee, MD, PhD • Duke University Medical Center (with Columbia University Medical Center), Durham, NC - David Goldstein, PhD and Vandana Shashi, MBBS, MD • Harvard Teaching Hospitals (including Boston Children's Hospital, Brigham and Women's Hospital, and Massachusetts General Hospital), Boston, MA - Joseph Loscalzo, MD, PhD • National Institutes of Health (NIH), Bethesda, MD – David Adams, MD, PhD; William Gahl, MD, PhD; and Cynthia Tifft, MD, PhD • Stanford Medicine, Palo Alto, CA - Euan Ashley, MD; Jonathan Bernstein, MD; and Paul Fisher, MD • University of California Los Angeles (with Children’s National Medical Center), Los
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