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Manual of Procedures, Version 12.0 Manual of Procedures for Human Microbiome Project Core Microbiome Sampling Protocol A HMP Protocol # 07-001 Version Number: 12.0 29 Jul 2010 Coordinating Authors: Pamela McInnes, DDS, MSc.(Dent.) Director, Division of Extramural Research National Institute of Dental and Craniofacial Research (NIDCR) National Institutes of Health 6701 Democracy Blvd. Room 610, Mail Stop 4878 Bethesda, MD 20892-4878 (301) 443-8618 [email protected] and Mary Cutting, NIH Contractor Manual of Procedures – Human Microbiome Project Version 12.0 Core Microbiome Sampling Protocol A 29 Jul 2010 ____________________________________________________________________________________________ TABLE OF CONTENTS page 1 INTRODUCTION ............................................................................................................... 1-1 1.1 NIH-Sponsored Studies of the Human Microbiome ............................................... 1-1 1.2 Sponsoring Institution and Study Support ............................................................. 1-1 1.3 Composition and Responsibilities of the Study Steering Committee ...................... 1-1 1.4 Responsibilities of the Clinical Principal Investigator at Each Core Clinical Site .... 1-2 1.5 Protocol Amendments and Modifications .............................................................. 1-2 1.6 Publications and Confidentiality ............................................................................ 1-2 1.7 MOP Distribution and Updates .............................................................................. 1-4 2 REGULATORY REQUIREMENTS .................................................................................... 2-1 2.1 Study Conduct ...................................................................................................... 2-1 2.2 Protection of Human Subjects ............................................................................... 2-1 2.3 IRB Submission .................................................................................................... 2-2 2.4 Informed Consent ................................................................................................. 2-2 2.5 Protocol Deviations ............................................................................................... 2-3 2.6 Study Site Regulatory Document Requirements ................................................... 2-4 2.7 Study Task Delegation and Staff Signature Lists ................................................... 2-4 2.8 Retention of Records ............................................................................................ 2-5 2.9 Site Monitoring Visit .............................................................................................. 2-5 2.9.1 Site Visit Expectations ............................................................................... 2-5 2.9.2 Site Visit Reports ...................................................................................... 2-6 3 DATA MANAGEMENT ...................................................................................................... 3-1 3.1 Source Documentation .......................................................................................... 3-1 3.2 Case Report Forms ............................................................................................... 3-1 3.3 Form Submission Schedule .................................................................................. 3-2 3.4 Data Review and Quality ....................................................................................... 3-2 3.5 Archiving of Data ................................................................................................... 3-2 3.6 Handling of Data to Ensure Confidentiality ............................................................ 3-2 4 UNANTICIPATED PROBLEMS AND SERIOUS ADVERSE EVENTS .............................. 4-1 4.1 Definition of an Unanticipated Problem ................................................................. 4-1 4.2 Reporting of Unanticipated Problems .................................................................... 4-2 4.3 Definition of a Serious Adverse Event ................................................................... 4-3 4.4 SAE Reporting Requirements ............................................................................... 4-4 5 STUDY OVERSIGHT AND SAFETY MONITORING ......................................................... 5-1 5.1 Roles and Responsibilities of the Clinical Study Oversight Committee .................. 5-1 5.2 CSOC Membership ............................................................................................... 5-2 5.2.1 Conflict of Interest ..................................................................................... 5-3 5.2.2 Selection and Invitation to Participate ....................................................... 5-3 5.3 CSOC Meetings .................................................................................................... 5-3 5.3.1 CSOC Meeting Format .............................................................................. 5-4 5.3.2 Voting ....................................................................................................... 5-4 5.4 Study Reports for CSOC Review .......................................................................... 5-5 5.5 Other Reports of Study Progress .......................................................................... 5-5 -i- Manual of Procedures – Human Microbiome Project Version 12.0 Core Microbiome Sampling Protocol A 29 Jul 2010 ____________________________________________________________________________________________ TABLE OF CONTENTS - continued page 5.6 Reports from the CSOC ........................................................................................ 5-5 5.7 Independent Safety Monitor .................................................................................. 5-6 5.7.1 ISM Roles and Responsibilities ................................................................. 5-6 5.7.2 Study Materials for ISM Review ................................................................ 5-6 5.7.3 ISM Selection and Invitation to Participate ................................................ 5-7 5.7.4 ISM Review Report ................................................................................... 5-7 5.8 Relationship between the CSOC and IRBs ........................................................... 5-7 6 SCREENING, ENROLLMENT AND STUDY ID ASSIGNMENT ........................................ 6-1 6.1 Subject Study ID ................................................................................................... 6-1 6.2 Screening and Re-screening Schedule ................................................................. 6-1 6.3 Screening Procedures ........................................................................................... 6-2 6.3.1 Screening for Pregnancy* ......................................................................... 6-2 6.3.2 Screening for Viral Markers* ..................................................................... 6-3 6.3.3 Oral Cavity Screening ............................................................................... 6-5 6.3.4 Skin Examination ...................................................................................... 6-7 6.3.5 Nasal Examination .................................................................................... 6-7 6.3.6 Gastrointestinal Examination ..................................................................... 6-8 6.3.7 Vaginal Examination and pH Determination .............................................. 6-9 6.4 Enrollment and Screening Failures ..................................................................... 6-11 6.4.1 Screening ................................................................................................ 6-11 6.4.2 Enrollment ............................................................................................... 6-11 6.4.3 Screening Failures .................................................................................. 6-11 7 BIOLOGICAL SPECIMENS ............................................................................................... 7-1 7.1 Safety Precautions ................................................................................................ 7-1 7.2 Collection of Specimens for Screening .................................................................. 7-1 7.2.1 Urine Pregnancy Test ............................................................................... 7-1 7.2.2 Viral Markers Screening ............................................................................ 7-1 7.3 Collection of Clinical Specimens ........................................................................... 7-2 7.3.1 Specimen Collection from the Oral Cavity ................................................. 7-3 7.3.2 Specimen Collection from the Skin and Nasal Cavity ................................ 7-8 7.3.3 Specimen Collection from the Gastrointestinal Tract ............................... 7-11 7.3.4 Specimen Collection from the Vagina ..................................................... 7-18 7.3.5 Collection of Blood Specimens (Baseline collection only) ........................ 7-20 7.4 Bar-code labeling of Clinical Specimens ............................................................. 7-21 7.5 Entering the Barcoded Specimens into the GTS Inventory .................................. 7-22 7.6 Specimen Transport
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