Section outline

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  • Tuesday, July 28, 2015; 9:00 AM - 10:00 AM

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

    Introduction to the course; components ("anatomy") of a research protocol, how measurements of variables on a sample are used to draw inferences about phenomena in populations ("physiology" of research); examples from Tom's research on jaundice in newborns

    Faculty:  Tom Newman

    Location:      MB-Genentech Hall 106, Byers Auditorium

    • Prospectus:

    • 15-Section 1 Letter to students and assignment for Chapters 1 and 2 2015-0627 File

    • Session Slides:

    • 15- Newman Lecture 1 Intro and Research Questions 2015-0727 File

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

    • Required Reading:

      DCR-4: Chapter 1: The Anatomy and Physiology of Clinical Research

      DCR-4: Chapter 2: Conceiving the Research Question

    • Saha et al. Survival guide for generalist physicians in academic fellowships File
      Not available unless: Your ID number contains 02

    • Optional Reading:

    • Flaherman et al 2013: ELF Study outlined in Appendix 1. File
      Not available unless: Your ID number contains 02
    • Newman 2003 Stories Statistics BMJ File

    • Resources:

    • HUlley DCR-4 Exercises page proofs File
      Not available unless: Your ID number contains 02
    • Hulley DCR-4 Answers page proofs File
      Not available unless: Your ID number contains 02
    • Errata for DCR-4 as of 2015-0831 File
    • Errata for DCR-3 as of July 18, 2012 File

    • Assignment:  Assignments are posted under small group sections.

       

  • Tuesday, July 28, 2015; 10:00 AM - 12:00 PM (Times and dates for online sessions may differ)

    Small Group Discussion Section: Research questions

    Faculty:  Warren Browner, Stephanie Christenson, Matthew Cooperberg, Jeffrey Gelfand, Maria Glymour, Raymond Hsu, Megie Okumura, Meyeon Park, Emily Perito, David Schopfer, Joel Simon, Anne Suskind
     
    Location:      Browner MH-1105, Christenson MH-1106, Cooperberg MH-1107, Gelfand MH-1108, Hsu MH-2105, Okumura MH-2106, Park MH-1109, Perito MH-2107, Schopfer MH-2109, Simon MH-2108,  Suskind MH-2110, Glymour Online

    • Assignment:

      See full assignment in letter below. Summary:

        1. Read Chapters 1 & 2 of DCR-4
        2. Write down answers to Chapter 1, Exercises 1 & 2, then check against answers in the book.
        3. Read mentoring section of the Survival Guide for Generalist Physicians in Academic Fellowships.
        4. Choose a research question.
        5. Identify and meet with your mentor
        6. Bring a hard copy of a 1-sentence version of your Research Question and a 1/2 to 3/4 page Significance section to class.
        7. Use a citation management program for the references. Take a class if needed.
    • 15- DCR Homework Assignment Guidelines 0706 File

    • Assignment Due Date: First assignment, to be completed before July 28

  • Tuesday, August 4, 2015; 9:00 AM - 10:00 AM

    Lecture: Subjects and variables

    Introduction to the Kaiser Permanente Division of Research; target and accessibile populations; inclusion and exclusion criteria; balancing feasibility and generalizability; sampling; types of variables and measurements; maximizing precision and accuracy; example from Alan's research on atrial fibrillation.

    Faculty:  Alan Go

    Location:      MB-Genentech Hall 106, Byers Auditorium

  • Tuesday, August 4, 2015; 10:00 AM - 12:00 PM (Times and dates for online sessions may differ)

    Small Group Discussion Section: Study Subjects

    Faculty:  Warren Browner, Stephanie Christenson, Matthew Cooperberg, Jeffrey Gelfand, Maria Glymour, Raymond Hsu, Megie Okumura, Meyeon Park, Emily Perito, David Schopfer, Joel Simon, Anne Suskind
     
    Location:      Browner MH-1105, Christenson MH-1106, Cooperberg MH-1107, Gelfand MH-1108, Hsu MH-2105, Okumura MH-2106, Park MH-1109, Perito MH-2107, Schopfer MH-2109, Simon MH-2108,  Suskind MH-2110, Glymour Online

    • Assignment:

      Download and review full assignment below. Most important:

        1. Read chapters 3 and 4 of DCR-4.
        2. Complete Chapter 3, exercise 3 and Chapter 4, exercise 3.
        3. Bring a 1-page outline of your study
        4. Bring a <1 page more detailed "Study Subjects" section
        5. Make an appointment to meet with your mentor
        6. Watch TN's presentation "How do we know what we know?"
    • 15-section 2 assignment for chapters 3 and 4 Rev 2015-0701 File
    • Assignment #2

      Upload Assignment #2 here

  • Tuesday, August 11, 2015; 9:00 AM - 10:00 AM

    Lecture: 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

    Location:      MB-Genentech Hall 106, Byers Auditorium

    • Session Slides:

    • Cummings Sample Size for DCR 2015 File

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

    • Required Reading:

      DCR-4 Chpater 5: Getting Ready to Estimate Sample Size

      DCR-4 Chapter 6: Estimating Sample Size and Power

    • Bacchetti 2010: Current sample size conventions: Flaws, harms and alternatives File
      Not available unless: Your ID number contains 02

    • Optional Reading:

    • 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

  • Tuesday, August 11, 2015; 10:00 AM - 12:00 PM (Times and dates for online sessions may differ)

    Small Group Discussion Section: Sample size

    Faculty:  Warren Browner, Stephanie Christenson, Matthew Cooperberg, Jeffrey Gelfand, Maria Glymour, Raymond Hsu, Megie Okumura, Meyeon Park, Emily Perito, David Schopfer, Joel Simon, Anne Suskind
     
    Location:      Browner MH-1105, Christenson MH-1106, Cooperberg MH-1107, Gelfand MH-1108, Hsu MH-2105, Okumura MH-2106, Park MH-1109, Perito MH-2107, Schopfer MH-2109, Simon MH-2108,  Suskind MH-2110, Glymour Online

  • Tuesday, August 18, 2015; 9:00 AM - 10:00 AM

    Lecture: Observational designs and studies of diagnostic tests

    Faculty:  Warren Browner

    Location:      MB-Genentech Hall 106, Byers Auditorium

    • Session Slides:

    • Browner Observational studies and Dx Tests Aug15 File

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

    • Required Reading:

      DCR-4 Chapter 7: Designing a Cohort Study

      DCR-4 Chapter 8: Designing Cross-Sectional and Case Control Studies

      DCR-4 Chapter 12: Designing Studies of medical Tests OR Chapter 13: Utilizing Existing Databases

    • Optional Reading:

    • Page proofs, Evidence-Based Diagnosis, Chapter 7. Read "Quantifying new information" page 148 and Box 7.3 File
      Not available unless: Your ID number contains 02
    • Page proofs, Evidence-Based Diagnosis, Chapter 8. It will be hard but relevant if you are studying a diagnostic test; read as much as you can File
      Not available unless: Your ID number contains 02
    • 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
    • Gilbert 1996 AnnEmergMed Chart review methods File
    • Newman & Browner 1988 AJPH Epidemiology of Life and Death. (This is the article Warren mentioned in his lecture. Enjoy!) File

  • Tuesday, August 18, 2015; 10:00 AM - 12:00 PM (Times and dates for online sessions may differ)

    Small Group Discussion Section: Observational studies and alternative design

    Faculty:  Warren Browner, Stephanie Christenson, Matthew Cooperberg, Jeffrey Gelfand, Maria Glymour, Raymond Hsu, Megie Okumura, Meyeon Park, Emily Perito, David Schopfer, Joel Simon, Anne Suskind

    Location:  Browner MH-1105, Christenson MH-1106, Cooperberg MH-1107, Gelfand MH-1108, Hsu MH-2105, Okumura MH-2106, Park MH-1109, Perito MH-2107, Schopfer MH-2109, Simon MH-2108,  Suskind MH-2110, Glymour Online

    • Assignment:

      Bring to section

        • a one-page "Study Design and Measurements" section for your protocol
        • a brief outline for a second study that either 1) answers your research question using a different study design, or 2) answers a different research question.
        • Read chapters 7, 8 and either 12, 13 or 18.
        • For details, see the Session 4 assignment file.
    • 15-Section 4 assignment for Chapters 7 8 12 13 Rev 0701 JAS File
    • Assignment #4

      Upload Assignment #4 here

  • Tuesday, August 25, 2015; 9:00 AM - 10:00 AM

    Lecture: Causal inference and randomized trials

    Faculty:  Deborah Grady

    Location:      MB-Genentech Hall 106, Byers Auditorium

    • Session Slides:

    • Grady Lecture 5 Causal Inference 2015-0825 File

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

    • Required Reading:

      DCR-4 Chapter 9: Enhancing Causal Infernence in Observational Studies

      DCR-4 Chapter 10: Designing a Randomized Blinded Trial

      DCR-4 Chapter 11: Alternative Trial Designs and Implementation Issues

    • Optional Reading:

      If you are doing a study of a diagnostic test, Chapters 1 and 5 of Evidence-Based Diagnosis (EBD) should also be helpful.

  • Tuesday, August 25, 2015; 10:00 AM - 12:00 PM (Times and dates for online sessions may differ)

    Small Group Discussion Section: Causal inference and randomized trials

    Faculty:  Warren Browner, Stephanie Christenson, Matthew Cooperberg, Jeffrey Gelfand, Maria Glymour, Raymond Hsu, Megie Okumura, Meyeon Park, Emily Perito, David Schopfer, Joel Simon, Anne Suskind
     
    Location:      Browner MH-1105, Christenson MH-1106, Cooperberg MH-1107, Gelfand MH-1108, Hsu MH-2105, Okumura MH-2106, Park MH-1109, Perito MH-2107, Schopfer MH-2109, Simon MH-2108,  Suskind MH-2110, Glymour Online

    • Assignment:

      Read Chapters 9, 10, & 11 of DCR-4

      If you are doing an observational study, discuss potential confounders and how you will deal with them.

      If you are doing an experiment, describe the details of your randomization and blinding procedures.

      If you are doing a study of diagnostic test accuracy, review how you will select the subjects and measure the variables. Then list other variables that provide information about the outcome and describe whether/how you will decide if your test provides new information. It will help to read Chapters 7 and 8 of Evidence-Based Diagnosis for this -- see optional reading from August 18 lecture for proofs.

      For details, see the Session 5 assignment file.

    • 15-Section 5 assignment for Chapters 9-11 rev 0706 File
    • Assignment #5

      Upload Assignment #5 here

  • Tuesday, September 1, 2015; 9:00 AM - 10:00 AM

    Lecture: 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:  Steve Cummings and Tom Newman

    Location:      MB-Genentech Hall 106, Byers Auditorium

    • Session Slides:

    • Cummings Lecture 6a Questionnaires 2015 slides File
    • Newman Lecture 6b Data Collection forms and data management 2015-0901 File

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

    • Required Reading:

      DCR-4 Chapter 12: Designing Studies of Medical Tests OR Chapter 13: Utilizing Existing Databases

      DCR-4 Chapter 15: Designing Questionnaires and Interviews

      DCR-4 Chapter 16: Data Management

    • Optional Reading:

    • Resources:

    • HOW TO GET A REDCap ACCOUNT 2015-0824 File
    • Productivity Files 2015-0831 Folder

    • Assignment:

      If you are not taking Epi 218 (Database Management for Clinical Research), take a look at the Chapter 16 ("Data Management") Exercises starting on page 301 of Designing Clinical Research (Hulley et al), 4th Edition.


      These are not to turn in (especially since the answers are in the book).  Note the layout of the PHTSE forms on pages 302-3 is not quite right: the field next to "Study Drug Administration" is the Subject ID, and the form for subject 189 has an inconsistency.

  • Tuesday, September 1, 2015; 10:00 AM - 12:00 PM (Times and dates for online sessions may differ)

    Small Group Discussion Section: Questionnaires and data collection forms 

    Faculty:  Warren Browner, Stephanie Christenson, Matthew Cooperberg, Jeffrey Gelfand, Maria Glymour, Raymond Hsu, Megie Okumura, Meyeon Park, Emily Perito, David Schopfer, Joel Simon, Anne Suskind
     
    Location:      Browner MH-1105, Christenson MH-1106, Cooperberg MH-1107, Gelfand MH-1108, Hsu MH-2105, Okumura MH-2106, Park MH-1109, Perito MH-2107, Schopfer MH-2109, Simon MH-2108,  Suskind MH-2110, Glymour Online

    • Assignment:

      Bring to section today
      -- a marked up data collection form from a previous study
      -- a page of your data collection form
      -- a one-page summary of your data collection and management plan
      For details, see the Session 6 assignment file.

    • 15-Section 6 assignment for Chapters 12 13 15 16 Rev 0701 File
    • Assignment #6

      Upload Assignment #6 here

  • Tuesday, September 8, 2015; 9:00 AM - 10:00 AM

    Lecture: Making a difference with research

    Tips on how to design a study, implement and disseminate the results to make a difference in people's health

    Faculty:  Kevin Grumbach

    Location:      MB-Genentech Hall 106, Byers Auditorium

    • Session Slides:

    • Grumbach Lecture 7 Making a difference with research File

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

    • Required Reading:

      DCR-4 Chapter 17: Implementing the Study and Quality Control

      DCR-4 Chapter 19: Writing and Funding a Research Proposal

  • Tuesday, September 8, 2015; 10:00 AM - 12:00 PM (Times and dates for online sessions may differ)

    Small Group Discussion Section: Making a difference with research

    Faculty:  Warren Browner, Stephanie Christenson, Matthew Cooperberg, Jeffrey Gelfand, Maria Glymour, Raymond Hsu, Megie Okumura, Meyeon Park, Emily Perito, David Schopfer, Joel Simon, Anne Suskind
     
    Location:      Browner MH-1105, Christenson MH-1106, Cooperberg MH-1107, Gelfand MH-1108, Hsu MH-2105, Okumura MH-2106, Park MH-1109, Perito MH-2107, Schopfer MH-2109, Simon MH-2108,  Suskind MH-2110, Glymour Online

    • Assignment:

      Bring (1 page or less) either a pretest plan or an issue about your protocol with which you would like some help.

      For details, see the Session 7 assignment file.

    • 15-Section 7 assignment Ch 17 19 or new protocol question 2015-0705 File
    • Assignment #7

      Upload Assignment #7 here

  • Tuesday, September 15, 2015

    Protocols Due at 5 PM