Section outline

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    • Designing Clinical Research (Two Month)

      EPI 202 Summer 2017 (2 units).
      Course Director: Mark Pletcher, MD, MPH.
      Professor, Department of Epidemiology & Biostatistics

    • News forum
    • Elena Flowers Forum
      Not available unless: You belong to a group in Flowers Section
    • Richard Grant Forum
    • Laura Jelliffe Forum
      Not available unless: You belong to a group in Jelliffe/Paynter Section
    • Lori Sakoda Forum
      Not available unless: You belong to a group in Sakoda Section
    • Victoria Tang Forum
    • Jacqueline Torres Forum

  • Tuesday, July 25, 2017; 9:00 AM - 10:00 AM

    Lecture: Introduction to the Course, Clinical Research, and Research Questions

    Introduction to the course; anatomy and physiology of research; components of a research protocol, and how measurements in a sample are used to draw inferences about a population; real-world tradeoffs between importance and feasibility

    Faculty:  Mark Pletcher
     
    Location:      MB-Genentech Hall 106, Byers Auditorium

  • Tuesday, July 25, 2017; 10:00 AM - 12:00 PM (Times and dates for online sessions may differ)

    Small Group Discussion Section

    Faculty: Elena Flowers, Richard Grant, Michael Cabana, Stephen Francis, Joel Simon, Megie Okumura, Victoria Tang, Lori Sakoda, Helen Kim, Jennifer Smith, Laura Jelliffe/Randi Paynter, Jacqueline Torres, Ben Chaffee
     
    Location: Flowers MH-1105, Grant MH-1106, Cabana MH-1107, Francis Online, Simon MH-1108, Okumura MH-1109, Tang MH-2105, Sakoda MH-1405, Kim MH-2106, Smith MH-2107, Jelliffe/Paynter MH-2110, Torres MH-2109, Chaffee S-609

  • Tuesday, August 1, 2017; 9:00 AM - 10:00 AM

    Full-Class Online Conversation with Deborah Grady

    Recorded lecture segments by Tom Newman on Subjects and Variables:  Defining target and accessible populations; inclusion and exclusion criteria; balancing feasibility and generalizability; sampling; types of variables and measurements; maximizing precision and accuracy; example from Tom's research on hyperbilirubinemia in neonates.

    Full-class online conversation with Deborah Grady:  Join an online discussion with Dr. Grady about the week's lecture material, brief comments about clinical trials (upcoming week's lecture topic), her career in clinical research and advice for early career investigators, and Q&A with students about topics, concepts and specific projects, with facilitation by Dr. Pletcher.  We will use Zoom video conference technology, online polling, a brief online breakout discussion session.

    Location:  Online video conference, click here to join from PC, Mac, Linus iOS or Android, or telephone only at +1 646 558 8656 (US Toll) or +1 408 638 0968 (US Toll), Meeting ID: 831 131 839.  International numbers available, click here for information.


    • Session Slides:

    • Lecture 2 - Tom Newman - Subjects and Variables File

    • Session Audio/Video Recording (Access restricted to registered students):

    • Watch URL
      Not available unless: You belong to Registered Students Only
    • Tom Newman - Lecture 2, Part 1 Media Resource
      Not available unless: You belong to a group in Registered Students Only
    • Tom Newman - Lecture 2, Part 2 Media Resource
      Not available unless: You belong to a group in Registered Students Only
    • Tom Newman - Lecture 2, Part 3 Media Resource
      Not available unless: You belong to a group in Registered Students Only

    • Assignment 2:

      • Read Chapters 3 and 4 of DCR-4
      • Watch Tom Newman’s recorded lecture segments on “Subjects and Variables” (see Materials)
      • Watch Mark Pletcher's recorded mini-lecture on "Study Design Basics" (See Materials)
      • Make an appointment to meet with your mentor sometime in the next 2 weeks
      • Write 1-page protocol outline for your study
      • Write <1 page "Study Subjects" section
      • Bring paper copy of writing to Small Group on Tuesday, and turn in revised version by Wednesday at Midnight
      • Do Exercise 3 (Chapter 3) and Exercise 3 (Chapter 4) of DCR-4 (Optional)
    • Assignment 2 Details File
    • Assignment 2 Example File

    • Materials:

    • Mark Pletcher - Mini-lecture - Study Design Basics Media Resource
      Not available unless: You belong to Registered Students Only

    • Optional reading from Tom Newman relevant to his Subjects and Variables lecture:

    • Newman 2006 NEJM Outcomes of TB 25 or more File
    • Newman 1991 AJDC Direct Bilirubin Measurements in Jaundiced Term Newborns File
    • Newman 2003 Stories Statistics BMJ File

  • Tuesday, August 1, 2017; 10:00 AM - 12:00 PM (Times and dates for online sessions may differ)

    Small Group Discussion Section

    Faculty: Elena Flowers, Richard Grant, Michael Cabana, Stephen Francis, Joel Simon, Megie Okumura, Victoria Tang, Lori Sakoda, Helen Kim, Jennifer Smith, Laura Jelliffe/Randi Paynter, Jacqueline Torres, Ben Chaffee
     
    Location: Flowers MH-1105, Grant MH-1106, Cabana MH-1107, Francis Online, Simon MH-1108, Okumura MH-1109, Tang MH-2105, Sakoda MH-1405, Kim MH-2106, Smith MH-2107, Jelliffe/Paynter MH-2110, Torres MH-2109, Chaffee S-609

  • Tuesday, August 8, 2017; 9:00 AM - 10:00 AM

    Full-Class Conversation with Steve Cummings: Sample Size, P-Values and Confidence Intervals

    Recorded lecture segments by Steve Cummings: An introduction to the concepts and information needed to estimate sample sizes for various types of studies. It includes suggestions for making more affordably sized studies.

    Full-class online conversation with Steve Cummings:  Join an in-person discussion with Dr. Cummings about the week's lecture material, his career in clinical research and advice for early career investigators, and Q&A with students about topics, concepts and specific projects, with facilitation by Dr. Pletcher.

    Faculty: Steve R. Cummings, MD

    Steve is a UCSF-trained general internist who led the UCSF Division of General Internal Medicine for a decade. He has spent almost 40 years designing, conducting, and teaching about clinical research.  He founded and directs the S.F. Coordinating Center that has designed, led, and conducted many large multicenter clinical trials and cohort studies.  He co-founded the Clinical Research Training program and co-authors Designing Clinical Research.  He is an Professor of Medicine, Epidemiology and Biostatistics at UCSF and also Senior Scientist at the CPMC Research Institute.  Steve’s own research has focused mainly on predicting and preventing fractures and understanding the biological basis of aging.  He has published over 500 peer-reviewed papers and has received numerous awards for his research in osteoporosis and women’s health, and was elected to the Institute of Medicine (now the National Academy of Medicine) for his work in clinical research in general and women’s health in particular.

    Location:  MB-Genentech Hall 106, Byers Auditorium


    • Session Slides:

    • Lecture 3 - Steve Cummings - Sample Size File

    • Session Audio/Video Recording (Access restricted to registered students):

    • Steve Cummings - Lecture 3, Part 1 Media Resource
      Not available unless: You belong to a group in Registered Students Only
    • Steve Cummings - Lecture 3, Part 2 Media Resource
      Not available unless: You belong to a group in Registered Students Only
    • Steve Cummings - Lecture 3, Part 3 Media Resource
      Not available unless: You belong to a group in Registered Students Only

    • Assignment 3:

      • Read Chapters 5 and 6 in DCR-4
      • Read Bacchetti 2010 on Sample Size Reasoning (see Materials)
      • Optional: Read Chapter from Goldman Textbook written by Tom and Chuck (see Materials)
      • Watch Steve Cummings’s recorded lecture segments on “Sample Size, P-Values and Confidence Intervals” (See Materials)
      • Write a 1/2-page Sample Size Justification (see Assignment Details)
      • Bring paper copy of writing to Small Group on Tuesday, and turn in revised version by Wednesday at Midnight
    • Assignment 3 Details File
    • Assignment 3 Example File

    • Materials:

    • Bacchetti 2010: Current sample size conventions: Flaws, harms and alternatives File
      Not available unless: Your ID number contains 02
    • Statistical Interpretation of Data (Chapter from Goldman Textbook of Medicine, 24th ed, by Tom and Chuck). Note material in green is included only in the online text, hence it is not what is most important. File
      Not available unless: Your ID number contains 02
    • Sample size calculator (CTSI) URL
    • Sample size calculator (Quesgen) URL
    • Downloadable sample size program URL

  • Tuesday, August 8, 2017; 10:00 AM - 12:00 PM (Times and dates for online sessions may differ)

    Small Group Discussion Section

    Faculty: Elena Flowers, Richard Grant, Michael Cabana, Stephen Francis, Joel Simon, Megie Okumura, Victoria Tang, Lori Sakoda, Helen Kim, Jennifer Smith, Laura Jelliffe/Randi Paynter, Jacqueline Torres, Ben Chaffee
     
    Location: Flowers MH-1105, Grant MH-1106, Cabana MH-1107, Francis Online, Simon MH-1108, Okumura MH-1109, Tang MH-2105, Sakoda MH-1405, Kim MH-2106, Smith MH-2107, Jelliffe/Paynter MH-2110, Torres MH-2109, Chaffee S-609

  • Tuesday, August 15, 2017; 9:00 AM - 10:00 AM

    Full-Class Conversation with Tom Newman

    Recorded lecture from last year by Warren Browner: Review common study designs, discuss how to choose what's right for your research question; also describe studies of diagnostic tests.

    Full-class online conversation with Tom Newman:  Join an in-person discussion with Dr. Newman about the week's lecture material, his career in clinical research and advice for early career investigators, and Q&A with students about topics, concepts and specific projects, with facilitation by Dr. Pletcher.

    Faculty: Tom Newman, MD MPH

    Dr. Tom Newman is Professor of Epidemiology & Biostatistics and Pediatrics and Chief of the Division of Clinical Epidemiology at the University of California, San Francisco School of Medicine.   He received his undergraduate degree from UC Santa Cruz, MD from UC San Diego, Residency Training in Pediatrics at UCSF and MPH in Epidemiology from UC Berkeley.  Tom attends in the newborn nursery at the UCSF Children's Medical Center and in the pediatric urgent care clinic at Zuckerberg San Francisco General Hospital.  Most of his research has used existing data to answer clinically relevant research questions.  He has a major role in UCSF's Training in Clinical Research (TICR) Program, and is a coauthor of two of the textbooks used in that training program: Designing Clinical Research and Evidence-Based Diagnosis.  He is on the Steering Committee of the Greater SF Bay Area Chapter of Physicians for Social Responsibility (PSR), chairs its Environmental Health Committee and recently completed 9 years on PSR's national Board of Directors.  He received the Academic Pediatric Association's Research Award in 2004, the American Academy of Pediatrics' Elizabeth Leistikow Award for Promotion of Evidence-based Pediatrics and the Stephen B. Hulley Award for Excellence in the Teaching of Clinical Research in 2010, the first UCSF Faculty Sustainability Award in 2011, and the Academic Pediatric Association's Miller-Sarkin mentoring award in 2017. 

    Location:  MB-Genentech Hall 106, Byers Auditorium


    • Session Slides:

    • Lecture 4 - Warren Browner - Observational Studies File

    • Session Audio/Video Recording (Access restricted to registered students):

    • Lecture 4 - Warren Browner - Recorded from 2016 (start at minute 4:00) URL
      Not available unless: You belong to Registered Students Only

    • Assignment 4:

      • Read Chapters 7, 8, and either 12, 13 or 18 DCR-4
      • Watch Tom Newman’s lecture on “How do we know what we know?”
      • Watch Warren Browner’s recorded lecture on “Observational Studies"
      • Write a short paragraph for Overview of Study Design (See Assignment Details)
      • Write a ½ - ¾-page Measurements Section (see Assignment Details)
      • Write a 1-page outline for a different study (see Assignment Details)
      • Bring paper copy of writing to Small Group on Tuesday, and turn in revised version by Wednesday at Midnight
      • Optional: Do DCR-4 Exercises 7.2 and 8.2
    • Assignment 4 Details File
    • Assignment 4 Example File

    • Materials:

    • Tom Newman: How do we know what we know? URL

    • Optional reading from Warren Browner:

    • Newman & Browner 1988 AJPH Epidemiology of Life and Death File

    • Optional reading on study design:

    • Page proofs, Evidence-Based Diagnosis (EBD) Chapter 10 File
      Not available unless: Your ID number contains 02
    • Example of a nested case-control study (Vit D and Colorectal cancer). Wu JNCI 2007;99:-1120-9 File

    • Optional reading on chart review methods (example of Measurements methods):

    • Gilbert 1996 AnnEmergMed Chart review methods File

    • Optional reading on case-control studies:

    • Vandenbroucke Int J Epidemiol 2012 File
    • Wacholder AJE 1992 File

  • Tuesday, August 15, 2017; 10:00 AM - 12:00 PM (Times and dates for online sessions may differ)

    Small Group Discussion Section

    Faculty: Elena Flowers, Richard Grant, Michael Cabana, Stephen Francis, Joel Simon, Megie Okumura, Victoria Tang, Lori Sakoda, Helen Kim, Jennifer Smith, Laura Jelliffe/Randi Paynter, Jacqueline Torres, Ben Chaffee
     
    Location: Flowers MH-1105, Grant MH-1106, Cabana MH-1107, Francis Online, Simon MH-1108, Okumura MH-1109, Tang MH-2105, Sakoda MH-1405, Kim MH-2106, Smith MH-2107, Jelliffe/Paynter MH-2110, Torres MH-2109, Chaffee S-609

  • Tuesday, August 22, 2017; 9:00 AM - 10:00 AM

    Full-Class Conversation with Warren Browner

    Recorded lecture by Deborah Grady: Causal Inference and Clinical Trials

    In-class conversation with Warren Browner: Join an in-person discussion with Dr. Browner about the week's lecture material, his career in clinical research and advice for early career investigators, and Q&A with students about topics, concepts and specific projects, with facilitation by Dr. Pletcher.

    Faculty:  Warren Browner, MD MPH

    Dr. Warren Browner is CEO  of California Pacific Medical Center (CPMC), a Senior Scientist in the CPMC Research Institute, and Professor (adjunct) of Epidemiology & Biostatistics at UCSF.  He previously was Professor of Medicine and of Epidemiology & Biostatistics at UCSF; Chief of General Internal Medicine and Acting Chief of the Medical Service at the San Francisco VA, and Vice President, Academic Affairs at CPMC.  He received an A.B. from Harvard, an M.D. from UCSF, and an M.P.H. in Epidemiology from Berkeley; he completed a residency in internal medicine and a fellowship in clinical epidemiology at UCSF. He has been a member of panels for the National Institutes of Health, the Department of Veterans Affairs, the Agency for Health Care Policy and Research, the Food and Drug Administration, and the California Hospital Association’s Hospital Quality Institute. He is the author of Publishing and Presenting Clinical Research, a co-author of Designing Clinical Research, and was the Executive Editor of the American Journal of Medicine.  He received a Distinguished Teaching Award from the UCSF Academic Senate in 1988; was one of UCSF’s 125 Distinguished Employees in 1989; and one of 150 Distinguished Alumni of UCSF in 2015. He serves on the Board of the San Francisco Chamber of Commerce and is the Immediate Past-Chair of the Board of the Jewish Community Center of San Francisco. He has lived in San Francisco since 1975, when he moved here to attend medical school.

    Location:  MB-Genentech Hall 106, Byers Auditorium

    • Session Slides:

    • Lecture 5 - Deborah Grady - Causal Inference File

    • Session Audio/Video Recording (Access restricted to registered students):

    • Deborah Grady’s lecture on Causal Inference URL
      Not available unless: You belong to a group in Registered Students Only
    • Watch Warren Browner discussion File
      Not available unless: You belong to a group in Registered Students Only

    • Assignment 5:

      • Read Chapters 9, 10, and 11 of DCR-4
      • Watch Deborah Grady's recorded lecture on "Causal Inference"
      • Write <1 page on enhancing inference in your study (See Assignment Details):
      • Bring paper copy of writing to Small Group on Tuesday, and turn in revised version by Wednesday at Midnight
      • Optional: Do DCR-4 All Exercises in Chapter 9 (if you’re doing an observational study) or Chapters 10 and 11 (if you’re doing a trial)
    • Assignment 5 Details File
    • Assignment 5 Example File

    • Materials:

    • SPI Study - Warren Browner, NEJM 1990 File
      Not available unless: Your ID number contains 02

    • Optional reading, especially for students designing studies of diagnostic tests:

    • Page proofs, Evidence-Based Diagnosis, Chapter 7 File
      Not available unless: Your ID number contains 02
    • Page proofs, Evidence-Based Diagnosis, Chapter 8 File
      Not available unless: Your ID number contains 02

  • Tuesday, August 22, 2017; 10:00 AM - 12:00 PM (Times and dates for online sessions may differ)

    Small Group Discussion Section

    Faculty: Elena Flowers, Richard Grant, Michael Cabana, Stephen Francis, Joel Simon, Megie Okumura, Victoria Tang, Lori Sakoda, Helen Kim, Jennifer Smith, Laura Jelliffe/Randi Paynter, Jacqueline Torres, Ben Chaffee
     
    Location: Flowers MH-1105, Grant MH-1106, Cabana MH-1107, Francis Online, Simon MH-1108, Okumura MH-1109, Tang MH-2105, Sakoda MH-1405, Kim MH-2106, Smith MH-2107, Jelliffe/Paynter MH-2110, Torres MH-2109, Chaffee S-609

  • Monday, August 28, 2017; 4:00 PM - 5:00 PM

    Make-Up Online Session with Warren Browner

    Full-class online conversation with Warren Browner: Join an online discussion with Dr. Browner about Causal Inference and Clinical Trials with Q&A from students, to make up for the in-class session we missed on Tuesday Aug 22.  We will discuss the SPI Study (see Materials under Aug 22 session above).  Note: the session will be recorded for those who can’t join live.

    Faculty:  Warren Browner, MD MPH (bio above)

    Location:  online Zoom Conference, information below:

     Join from a PC, Mac, Linux, iOS or Android device:

    https://ucsf.zoom.us/j/330652392

    Telephone:

    Dial: 1-408-638-0968

    International Dial-in Options: https://zoom.us/zoomconference

    Meeting ID: 330 652 392

     

  • Tuesday, August 29, 2017; 9:00 AM - 10:00 AM

    Lecture: Questionnaires, Data Collection Forms and Data Management

    Standard In-Class Lecture: Development of paper and online questionnaires and data collection forms. The limitations of spreadsheet programs (e.g. Excel) for database management. Alternative software platforms for data collection and management.

    Faculty:  Michael Kohn
     
    Location:      MB-Genentech Hall 106, Byers Auditorium


    • Session Slides:

    • Lecture 6 - Michael Kohn - Data Collection File

    • Session Audio/Video Recording (Access restricted to registered students):

    • Assignment 6 Details File
    • Assignment 6 Example File

    • Assignment 6:

      • Read Chapters 12, 13, 15, and 16 of DCR-4
      • Bring 1 page of a data collection form (See Assignment Details)
      • Create a corresponding data dictionary (See Assignment Details)
      • Write ½ - ¾ page data management plan for your study (See Assignment Details)
      • Bring paper copy of writing to Small Group on Tuesday, and turn in revised version by Wednesday at Midnight
      • Optional: Do DCR-4 exercises 12.2 and 12.3 (if you’re doing a diagnostic test study) and Chapter 16 exercises (if you’re not taking Epi 218 on Database Management Systems)

    • Materials:

    • NHAMCS Files (for Lecture 6 demonstrations) Folder
    • HOW TO GET A REDCap ACCOUNT 2015-0824 File

  • Tuesday, August 29, 2017; 10:00 AM - 12:00 PM (Times and dates for online sessions may differ)

    Small Group Discussion Section

    Faculty: Elena Flowers, Richard Grant, Michael Cabana, Stephen Francis, Joel Simon, Megie Okumura, Victoria Tang, Lori Sakoda, Helen Kim, Jennifer Smith, Laura Jelliffe/Randi Paynter, Jacqueline Torres, Ben Chaffee
     
    Location: Flowers MH-1105, Grant MH-1106, Cabana MH-1107, Francis Online, Simon MH-1108, Okumura MH-1109, Tang MH-2105, Sakoda MH-1405, Kim MH-2106, Smith MH-2107, Jelliffe/Paynter MH-2110, Torres MH-2109, Chaffee S-609

  • Tuesday, September 5, 2017; 9:00 AM - 10:00 AM

    Lecture: Using Electronic Health Records for Research

    Standard In-Class Lecture: Opportunities and challenges of using electronic health records for research, demonstration of use for Statin Duration Study

    Faculty:  Mark Pletcher
     
    Location:      MB-Genentech Hall 106, Byers Auditorium

    • Session Slides:

    • Lecture 7 - Mark Pletcher - Using EHR Data for Research File

    • Session Audio/Video Recording (Access restricted to registered students):

    • Assignment 7:

      • Read Chapters 17 and 19 of DCR-4
      • Obtain and read a real grant application from your mentor
      • Assemble a complete draft of your 5-page protocol
      • Bring <1 page pretesting plan (See Assignment Details)
      • Bring <1 page unsettled issue discussion – your choice! (See Assignment Details)
      • Bring paper copy of writing to Small Group on Tuesday.  These assignments do not need to be turned in.
    • Assignment 7 Details File

    • Materials:

    • Stata .do files from lecture demonstration Folder
    • Stata "How to" handouts relevant to EHR data analysis Folder

  • Tuesday, September 5, 2017; 10:00 AM - 12:00 PM (Times and dates for online sessions may differ)

    Small Group Discussion Section

    Faculty: Elena Flowers, Richard Grant, Michael Cabana, Stephen Francis, Joel Simon, Megie Okumura, Victoria Tang, Lori Sakoda, Helen Kim, Jennifer Smith, Laura Jelliffe/Randi Paynter, Jacqueline Torres, Ben Chaffee
     
    Location: Flowers MH-1105, Grant MH-1106, Cabana MH-1107, Francis Online, Simon MH-1108, Okumura MH-1109, Tang MH-2105, Sakoda MH-1405, Kim MH-2106, Smith MH-2107, Jelliffe/Paynter MH-2110, Torres MH-2109, Chaffee S-609

  • Monday, September 11, 2017

    Protocols DUE 5:00 PM