Section outline

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    • Designing Clinical Research (Two Month)  

      (Click for Course Description)

      EPI 202 Summer 2021 (1 unit) .

      Course Director: Mark Pletcher, MD, MPH
      Professor, Department of Epidemiology and Biostatistics.

    • News forum
    • Joel Simon Forum
      Not available unless: You belong to Simon Section
    • Catie Oldenburg Forum
      Not available unless: You belong to Oldenburg Section
    • Ali Mirzazadeh Forum
      Not available unless: You belong to Mirzazadeh Section
    • Alan Go Forum
      Not available unless: You belong to Go Section
    • Megie Okumura Forum
      Not available unless: You belong to Okumura Section
    • Pam Murnane Forum
      Not available unless: You belong to Murnane Section
    • Young Shin Kim Forum
      Not available unless: You belong to Kim Section
    • Janet Wojcicki Forum
      Not available unless: You belong to Wojcicki Section
    • Rakesh Ghosh Forum
      Not available unless: You belong to Ghosh Section
    • Jennifer Smith Forum
      Not available unless: You belong to Smith Section
    • Byakwaga Forum
      Not available unless: You belong to Byakwaga Section

  • Tuesday, July 20, 2021; 9:00 AM - 9:45 AM

    Introduction to the Course, Clinical Research, and Research Questions

         Course history and objectives; course schedule and logistics; 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; systematic reviews.

    Faculty: Mark Pletcher

  • Tuesday, July 20, 2021; 10:00 AM - 12:00 PM (Additional sessions: Tuesday 6 - 8 PM; and Wednes. 8 to 10 AM)

    Small Group Discussion Section (see Roster for your section assignment)

    Review of prior lecture and problem set

    Faculty: Joel Simon, Catie Oldenburg, Ali Mirzazadeh, Alan Go, Megie Okumura, Pam Murnane, Young Shin Kim, Janet Wojcicki, Rakesh Ghosh, Jennifer Smith, Hal Barron
     
    Location: Mission Hall and Zoom

    • DCR Roster 2021 and Small Group Assignments URL
      Not available unless: You belong to a group in Registered Students Only

  • Friday, July 23, 2021; 10:10 AM - 11:00 AM

    Drop-in Help

    Course faculty are available for interactive discussion and to address questions.  

    Location (Access restricted to registered students): Zoom URL

  • Tuesday, July 27, 2021; 9:00 AM - 9:45 AM

    Subjects and Variables

    Faculty: Tom Newman

    Faculty Bio: Tom is Professor Emeritus of Epidemiology & Biostatistics and Pediatrics at UCSF. 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. He was chief of the Division of Clinical Epidemiology from 2001-2016. Though semi-retired, Tom still attends in the newborn nursery at the UCSF Children's Medical Center. Most of his research has focused on avoiding overuse and improving healthcare value. He is a coauthor of the Designing Clinical Research textbook, as well as Evidence-Based Diagnosis (used for Epi 204; 2nd edition due out this Fall). He is on the Board of Directors 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 has received the Academic Pediatric Association's Research Award, the American Academy of Pediatrics' Elizabeth Leistikow Award for Promotion of Evidence-based Pediatrics, the Stephen B. Hulley Award for Excellence in the Teaching of Clinical Research, the UCSF Faculty Sustainability Award, and the Academic Pediatric Association's Miller-Sarkin mentoring award.

    • Lecture Slides:

    • Newman Lecture 2 Subjects and Variables 2019-0805 to post File

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

    • Lecture 2, Part 1 (Tom Newman) Media Resource
      Not available unless: You belong to a group in Registered Students Only
    • Lecture 2, Part 2 (Tom Newman) Media Resource
      Not available unless: You belong to a group in Registered Students Only
    • Lecture 2, Part 3 (Tom Newman) Media Resource
      Not available unless: You belong to a group in Registered Students Only
    • Study Design Basics (Mark Pletcher) Media Resource
      Not available unless: You belong to Registered Students Only

    • Large Group Discussion (Access restricted to registered students): Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.

    • Lecture 2 Discussion Recording Media Resource
      Not available unless: You belong to a group in Registered Students Only

    • Assignment 2:

    • Assignment 2 File
    • Assignment 2 Example File

    • Materials:

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

    • Newman et al 2006 NEJM Outcomes of TB 25 or more File
    • Newman et al 1991 AJDC Direct Bilirubin Measurements in Jaundiced Term Newborns File
    • Newman 2003 BMJ The Power of Stories over Statistics File
    • Marmor & Newman 2011 Otitis media evidence File
    • Schroeder et al 2011 Pediatrics Safely doing less File

  • Tuesday, July 27, 2021; 10:00 AM - 12:00 PM (Additional sessions: Tuesday 6 - 8 PM; and Wednes. 8 to 10 AM)

    Small Group Discussion Section

    Review of prior lecture and problem set

    Faculty: Joel Simon, Catie Oldenburg, Ali Mirzazadeh, Alan Go, Megie Okumura, Pam Murnane, Young Shin Kim, Janet Wojcicki, Rakesh Ghosh, Jennifer Smith, Hal Barron

    Location: Mission Hall and Zoom

  • Monday Aug 2, 2021; 3:30 PM - 4:30 PM

    Drop-in Help

    Course faculty are available for interactive discussion and to address questions.  

    Location (Access restricted to registered students): Zoom URL

  • Tuesday, August 3, 2021; 9:00 AM - 9:45 AM

    Sample Size, P-Values and Confidence Intervals

    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.

    Faculty: Steve Cummings

    Faculty Bio: 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.

    • Lecture Slides:

    • Lecture 3 Slides File

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

    • Lecture 3, Part 1 (Steve Cummings) Media Resource
      Not available unless: You belong to a group in Registered Students Only
    • Lecture 3, Part 2 (Steve Cummings) Media Resource
      Not available unless: You belong to a group in Registered Students Only
    • Lecture 3, Part 3 (Steve Cummings) Media Resource
      Not available unless: You belong to a group in Registered Students Only
    • How do we know what we know? (Tom Newman) Media Resource
      Not available unless: You belong to a group in Registered Students Only

    • Large Group Discussion (Access restricted to registered students): Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.

    • Lecture 3 Discussion Recording Media Resource
      Not available unless: You belong to a group in Registered Students Only

    • Assignment 3:

    • Assignment 3 File
    • Assignment 3 Example File

    • Materials:

    • SD for analyzing change in a continuous variable File
    • 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.net (from UCSF's CTSI) URL

  • Tuesday, August 3, 2021; 10:00 AM - 12:00 PM (Additional sessions: Tuesday 6 - 8 PM; and Wednes. 8 to 10 AM)

    Small Group Discussion Section

    Review of prior lecture and problem set

    Faculty: Joel Simon, Catie Oldenburg, Ali Mirzazadeh, Alan Go, Megie Okumura, Pam Murnane, Young Shin Kim, Janet Wojcicki, Rakesh Ghosh, Jennifer Smith, Hal Barron

    Location: Mission Hall and Zoom

  • Friday, August 6, 2021; 10:10 AM - 11:00 AM

    Drop-in Help

    Course faculty are available for interactive discussion and to address questions.  

    Location (Access restricted to registered students): Zoom URL

  • Tuesday, August 10, 2021; 9:00 AM - 9:45 AM

    Observational Designs and Studies of Diagnostic Tests

    Review common study designs, discuss how to choose what's right for your research question; also describe studies of diagnostic tests.

    Faculty: Kirsten Bibbins-Domingo

    Faculty Bio: Kirsten Bibbins-Domingo, PhD, MD, MAS is the Lee Goldman, MD Endowed Chair in Medicine, Professor and Chair of the Department of Epidemiology and Biostatistics, and Professor of Medicine. She is the inaugural Vice Dean for Population Health and Health Equity in the UCSF School of Medicine. Dr. Bibbins-Domingo co-founded the UCSF Center for Vulnerable Populations at Zuckerberg San Francisco General Hospital, a research center focused on discovery, implementation, policy, advocacy, and community engagement for communities at risk for poor health and inadequate healthcare. She is one of the PIs of the UCSF Clinical and Translational Science Institute.


    Faculty: Warren Browner

    Faculty Bio:  Dr. Warren Browner is CEO of California Pacific Medical Center (CPMC), a Senior Scientist in the CPMC Research Institute, and Professor of Epidemiology & Biostatistics at UCSF.  He previously was 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.

    • Lecture Slides:

    • Lecture 4 (Warren Browner) Slides File
    • Lecture 4 (Kirsten Bibbins-Domingo) Slides File

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

    • Lecture 4 (Warren Browner) - Observational Study Designs and Studies of Diagnostic Tests URL
      Not available unless: You belong to Registered Students Only

    • Large Group Discussion (Access restricted to registered students): Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.

    • Lecture 4 Discussion Recording Media Resource
      Not available unless: You belong to a group in Registered Students Only

    • Assignment 4:

    • Assignment 4 File
    • Assignment 4 Example File

    • Materials:

    • 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 10, 2021; 10:00 AM - 12:00 PM (Additional sessions: Tuesday 6 - 8 PM; and Wednes. 8 to 10 AM)

    Small Group Discussion Section

    Review of prior lecture and problem set

    Faculty: Joel Simon, Catie Oldenburg, Ali Mirzazadeh, Alan Go, Megie Okumura, Pam Murnane, Young Shin Kim, Janet Wojcicki, Rakesh Ghosh, Jennifer Smith, Hal Barron

    Location: Mission Hall and Zoom

  • Monday, August 16, 2021; 2:10 PM - 3:00 PM

    Drop-in Help

    Course faculty are available for interactive discussion and to address questions.  

    Location (Access restricted to registered students): Zoom URL

  • Tuesday, August 17, 2021; 9:00 AM - 9:45 AM

    Causal Inference and Randomized Trials

    Confounding, other problems with inferring causality; benefits, design, and pitfalls of randomized trials.

    Faculty: Mark Pletcher


    • Lecture Slides:

    • Lecture 5 (Deborah Grady) Slides File
    • Lecture 5 (Mark Pletcher) Slides File

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

    • Lecture 5 (Deborah Grady) URL
      Not available unless: You belong to a group in Registered Students Only
    • Lecture 5 (Mark Pletcher) URL
      Not available unless: You belong to Registered Students Only

    • Large Group Discussion (Access restricted to registered students): Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.

    • Lecture 5 Discussion Recording Media Resource
      Not available unless: You belong to a group in Registered Students Only

    • Assignment 5:

    • Assignment 5 File
    • Assignment 5 Example File

    • Materials:

    • 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 17, 2021; 10:00 AM - 12:00 PM (Additional sessions: Tuesday 6 - 8 PM; and Wednes. 8 to 10 AM)

    Small Group Discussion Section

    Review of prior lecture and problem set

    Faculty: Joel Simon, Catie Oldenburg, Ali Mirzazadeh, Alan Go, Megie Okumura, Pam Murnane, Young Shin Kim, Janet Wojcicki, Rakesh Ghosh, Jennifer Smith, Hal Barron

    Location: Mission Hall and Zoom

  • Friday, August 20, 2021; 10:10 AM - 11:00 AM

    Drop-in Help

    Course faculty are available for interactive discussion and to address questions.  

    Location (Access restricted to registered students): Zoom URL

  • Tuesday, August 24, 2021; 9:00 AM - 9:45 AM

    Questionnaires, Data Collection Forms and Data Management

    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

    Faculty Bio:  Dr. Michael Kohn is an attending emergency physician at Mills-Peninsula in Burlingame and a professor in UCSF’s Department of Epidemiology and Biostatistics, where he has taught research methods, clinical epidemiology, and database management for the past 17 years.  He also provides consultations to clinical investigators who need help with study design, sample size calculations, data management, and statistical analysis.  His primary research interest is diagnostic testing in the ED.  He co-authored (with Thomas Newman) the clinical epidemiology textbook “Evidence-Based Diagnosis,” is a contributing author to Hulley et al, “Designing Clinical Research,” and created the UCSF CTSI’s online sample size calculators (www.sample-size.net).

    Faculty: Alison Huang

    Faculty Bio:  Dr. Alison Huang is general internal medicine physician and a professor in the UCSF Departments of Medicine, Urology, and Epidemiology & Biostatistics, where she conducts patient-reported outcomes research related to women's health, genitourinary health, and aging.  She directs several UCSF research training programs directed at UCSF residents, postdoctoral fellows, and junior faculty, and she also teaches clinical research methods in other UCSF courses such as the Clinical Trials course (Epidemiology 205).

    • Lecture Slides:

    • Lecture 6 (Michael Kohn) Slides File
    • Lecture 6 (Alison Huang) Slides File

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

    • Lecture 6 (Michael Kohn): Data Collection Forms Media Resource
      Not available unless: You belong to a group in Registered Students Only
    • Lecture 6 (Alison Huang): Questionnaires - selecting and evaluating self-reported measures Media Resource
      Not available unless: You belong to Registered Students Only

    • Large Group Discussion (Access restricted to registered students): Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.

    • Lecture 6 Discussion Recording Media Resource
      Not available unless: You belong to a group in Registered Students Only

    • Assignment 6:

    • Assignment 6 File
    • Assignment 6 Example File

    • Materials:

    • NHAMCS Files (for Lecture 6 demonstrations) Folder
    • HOW TO GET A REDCap ACCOUNT 2015-0824 File
    • Field Name and Response Code Conventions File

  • Tuesday, August 24, 2021; 10:00 AM - 12:00 PM (Additional sessions: Tuesday 6 - 8 PM; and Wednes. 8 to 10 AM)

    Small Group Discussion Section

    Review of prior lecture and problem set

    Faculty: Joel Simon, Catie Oldenburg, Ali Mirzazadeh, Alan Go, Megie Okumura, Pam Murnane, Young Shin Kim, Janet Wojcicki, Rakesh Ghosh, Jennifer Smith, Hal Barron

    Location: Mission Hall and Zoom

  • Friday, August 27, 2021; 10:10 AM - 11:00 AM

    Drop-in Help

    Course faculty are available for interactive discussion and to address questions.  

    Location (Access restricted to registered students): Zoom URL

  • Tuesday, August 31, 2021; 9:00 AM - 9:45 AM

    Special Topics: Use Electronic Health Records for Research, Learning Health System Research

    Faculty: Mark Pletcher

    • Lecture Slides:

    • Lecture 7 Slides (Mark Pletcher) - Using EHR Data for Research File
    • Mark Pletcher - Learning Health System Research Projects File

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

    • Lecture 7 (Mark Pletcher) - Using EHR Data for Research (recorded live lecture) URL
      Not available unless: You belong to Registered Students Only
    • Mark Pletcher - Learning Healthcare System Research Projects (recorded live lecture) URL
      Not available unless: You belong to Registered Students Only

    • Large Group Discussion (Access restricted to registered students): Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.

    • Lecture 7 Discussion Recording Media Resource
      Not available unless: You belong to a group in Registered Students Only

    • Assignment 7:

    • Assignment 7 File

    • Materials:

    • Stata .do files from lecture demonstration Folder
    • Stata "How to" handouts relevant to EHR data analysis Folder
    • Advanced copy of DCR-5 chapter on Existing Data File

  • Tuesday, August 31, 2021; 10:00 AM - 12:00 PM (Additional sessions: Tuesday 6 - 8 PM; and Wednes. 8 to 10 AM)

    Small Group Discussion Section

    Review of prior lecture and problem set

    Faculty: Joel Simon, Catie Oldenburg, Ali Mirzazadeh, Alan Go, Megie Okumura, Pam Murnane, Young Shin Kim, Janet Wojcicki, Rakesh Ghosh, Jennifer Smith, Hal Barron

    Location: Mission Hall and Zoom

  • Monday, September 6, 2021

    Protocol Due: 5:00 PM