Course: EPI 214: Systematic Reviews (Spring 2022)

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Systematic Reviews

EPI 214 Spring 2022 (1 unit)

Thursdays, 8:30 AM to 10:00 AM PST

Course Director: Mohsen Malekinejad, MD, DrPH

Course Assistant: Mazie Tsang, MD

Location: Zoom

Select activity EPI 214 System Reviews Syllabus Spring 2022 v9

EPI 214 System Reviews Syllabus Spring 2022 v9 File
Select activity Discussion Board

Discussion Board Forum
Select activity General Course Resources

General Course Resources Folder
Select activity Assignments

Assignments Folder

Select section Thursday, March 31, 2022; 8:30 -10:00 am

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Thursday, March 31, 2022; 8:30 -10:00 am
MODULE 1: Designing A Systematic Review Protocol

A - Introduction
B - Choosing a topic for the review
C- Protocol development & review question & defining PICO

Faculty: Mohsen Malekinejad
- Select activity Session Slides: (copy)
  
  Session Slides:
- Select activity Module 1-A: Introduction
  
  Module 1-A: Introduction File
- Select activity Module 1-B: Choosing Topic
  
  Module 1-B: Choosing Topic File
- Select activity Module 1-C: PICO Protocol
  
  Module 1-C: PICO Protocol File
- Select activity Session Audio/Video Recording (Access restricted t...
  
  Session Audio/Video Recording (Access restricted to registered students):
- Select activity Lecture 1 03.31.2022
  
  Lecture 1 03.31.2022 Media Resource
  
  Not available unless: You belong to Registered Students Only
- Select activity Lecture 1 03.31.2022 with caption
  
  Lecture 1 03.31.2022 with caption URL
  
  Not available unless: You belong to Registered Students Only
- Select activity Recommended Cochrane Handbook sections: Part 1 ...
  
  Recommended Cochrane Handbook sections:
  
  Part 1 - Chapter 1: Introduction
  
  Part 2 - Chapter 1: Starting a Review
  
  Part 1 - Chapter 2: Planning a Cochrane review (sections: 2.1.1-2.1.2)
  
  Part 2 - Chapter 2: Determining the scope of the review and the questions it will address
  
  Part 2 - Chapter 3: Defining the criteria for including studies and how they will be grouped for the synthesis
- Select activity Optional Reading: Grant MJ, Booth A. A typology...
  
  Optional Reading:
  
  Grant MJ, Booth A. A typology of reviews: an analysis of 14 review types and associated methodologies. Health Info Libr J. 2009. Jun;26(2):91-108.
  
  Cooke A, Smith D, Booth A. Beyond PICO: the SPIDER tool for qualitative evidence synthesis. Qual Health Res. 2012;22(10):1435-43.
  
  loannidis JP. The Mass Production of Redundant, Misleading, and Conflicted Systematic Reviews and Meta-anlaysis. Milbank Q. 2016 Sep;94(3):485-514.
  
  Gough D, Thomas J, Oliver S. Clarifying differences between review designs and methods. Syst Rev. 2012 Jun 9;1:28. doi: 10.1186/2046-4053-1-28. PMID: 22681772; PMCID: PMC3533815.
- Select activity Additional resources: History of Evidence-based...
  
  Additional resources:
  
  History of Evidence-based medicine: https://files.jamanetwork.com/sdebm/
  
  PICO Work Sheet.
  
  Tambe 2015 - Antiretroviral resistance testing in treatment-naïve people living with HIV (Protocol)
  
  Sample Protocols can be found in “General Resources” folder
- Select activity Assignment: No assignment
  
  Assignment: No assignment
Select section Thursday, April 7, 2022; 8:30 -10:00 am

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Thursday, April 7, 2022; 8:30 -10:00 am
MODULE 2: Data Collection Methods

A - Developing and applying comprehensive search strategies
B - Citation management & study screening
C- Data extraction & standardization

Faculty: Mohsen Malekinejad
- Select activity Session Slides:
  
  Session Slides:
- Select activity Module 2A: Develop Search Strategies
  
  Module 2A: Develop Search Strategies File
- Select activity Module 2B: Citation Management Screening
  
  Module 2B: Citation Management Screening File
- Select activity Module 2C: Data Extraction Standardization
  
  Module 2C: Data Extraction Standardization File
- Select activity Session Audio/Video Recording (Access restricted t... (copy) (copy)
  
  Session Audio/Video Recording (Access restricted to registered students):
- Select activity Lecture 2 04.07.2022
  
  Lecture 2 04.07.2022 Media Resource
  
  Not available unless: You belong to Registered Students Only
- Select activity Lecture 2 04.07.2022 with caption
  
  Lecture 2 04.07.2022 with caption URL
  
  Not available unless: You belong to Registered Students Only
- Select activity Data Standardization recording from previous years
  
  Data Standardization recording from previous years Media Resource
  
  Not available unless: You belong to Registered Students Only
- Select activity Recommended Cochrane Handbook sections: Part 2 ...
  
  Recommended Cochrane Handbook sections:
  
  Part 2 - Chapter 4: Searching for and selecting studies (sections 4.1 to 4.5)
  
  Part 2 - Chapter 4: Searching for and selecting studies (section 4.6)
  
  Part 2 - Chapter 5: Collecting data
  
  Part 2 - Chapter 6: Choosing effect measures and computing estimates of effect - you can skip following sections of chapter 6: 6.2.6 - 6.2.8, 6.5.1.3 – 6.5.1.5, 6.5.2.2 – 6.5.2.9, 6.6- 6.9
- Select activity Optional Reading: Li T, Vedula SS, Hadar N, Par...
  
  Optional Reading:
  
  Li T, Vedula SS, Hadar N, Parkin C, Lau J, Dickersin K. Innovations in data collection, management, and archiving for systematic reviews. Ann Intern Med. 2015 Feb 17;162(4):287-94.
  
  McGowan J, Sampson M, Salzwedel DM, Cogo E, Foerster V, Lefebvre C. PRESS Peer Review of Electronic Search Strategies: 2015 Guideline Statement. J Clin Epidemiol. 2016 Jul;75:40-6. doi: 10.1016/j.jclinepi.2016.01.021. Epub 2016 Mar 19. PMID: 27005575.
- Select activity Additional resources: Cochrane Group on Effecti...
  
  Additional resources:
  
  Cochrane Group on Effective Practice and Organization of Care (EPOC) – How to develop a search strategy
  
  Cochrane EPOC Group’s collection of databases, websites and journals relevant to health research in low- and middle-income countries
  
  Health Librarian Wiki (HLWIKI) - Search Engines
  
  Cochrane data collection form - Intervention review – RCTs and non-RCTs
  
  Sample data extraction codebook
- Select activity Assignment #1 (35% of grade): Develop a ...
  
  Assignment #1 (35% of grade): Develop a brief systematic review protocol. time needed to complete: 10-15 hours.
  
  Due: April 14, 2022
  
  Please click on "Assignment 1" to download the Word document for detailed instructions on this assignment.
  A brief synopsis of the assignment: Draft a brief systematic review protocol with the aim of assessing the effectiveness of a medical or public health intervention. The protocol should include a clear definition of the research question(s) and related PICO(s). Instructors will provide a template and further instruction. Your protocol will be approximately 4-5 page double-spaced document (font: Calibri/Arial 11), with 5-7 citations. Consider starting on this assignment as soon as possible. Assignment should be summitted to the CLE.
- Select activity Assignment #1
  
  Assignment #1
  
  Opened: Thursday, April 7, 2022, 12:00 AM
  
  Due: Thursday, April 14, 2022, 8:00 AM
Select section Thursday, April 14, 2022; 8:30 -10:00 am

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Thursday, April 14, 2022; 8:30 -10:00 am
MODULE 3: Data Synthesis Methods - Part 1

A - Data synthesis approaches
B - Introduction to meta-analysis
C- Assessment of heterogeneity

Faculty: Mohsen Malekinejad
- Select activity Session Slides: (copy)
  
  Session Slides:
- Select activity Module 3-A: Data Synthesis
  
  Module 3-A: Data Synthesis File
- Select activity Module 3-B: Introduction to Meta-Analysis
  
  Module 3-B: Introduction to Meta-Analysis File
- Select activity Module 3-C: Assessment of Heterogeneity
  
  Module 3-C: Assessment of Heterogeneity File
- Select activity Session Audio/Video Recording (Access restricted t... (copy)
  
  Session Audio/Video Recording (Access restricted to registered students):
- Select activity Lecture 3 04.14.2022
  
  Lecture 3 04.14.2022 Media Resource
  
  Not available unless: You belong to Registered Students Only
- Select activity Lecture 3 04.14.2022 with caption
  
  Lecture 3 04.14.2022 with caption URL
  
  Not available unless: You belong to Registered Students Only
- Select activity Recommended Cochrane Handbook sections: Part 2 ...
  
  Recommended Cochrane Handbook sections:
  
  Part 2 - Chapter 9: Summarizing study characteristics and preparing for synthesis
  
  Part 2 - Chapter 10: Analyzing data and undertaking meta-analyses (sections: 10.1 – 10.5.1).
- Select activity Optional Reading: Smith 2011 – Methodology in c...
  
  Optional Reading:
  
  Smith 2011 – Methodology in conducting a systematic review of systematic reviews of healthcare interventions.
  
  Malekinejad 2008. Using Respondent-Driven Sampling Methodology for HIV Biological and Behavioral Surveillance in International Settings: A Systematic Review
  
  Rahimi-Movaghar 2015. Transition to injecting drug use in Iran: A systematic review of qualitative and quantitative evidence
  
  Malekinejad 2015. High hepatitis C virus prevalence among drug users in Iran: systematic review and meta-analysis of epidemiological evidence (2001–2012)
  
  Malekinejad 2017. Yield of community-based tuberculosis targeted testing and treatment in foreign born populations in the United States: A systematic review
  
  Malekinejad M, Barker EK, Merai R, et al. Risk of HIV Acquisition Among Men Who Have Sex With Men Infected With Bacterial Sexually Transmitted Infections: A Systematic Review and Meta-Analysis. Sex Transm Dis. 2021;48(10):e138-e148. doi:10.1097/OLQ.0000000000001403
  
  Malekinejad M, Parriott A, Blodgett JC, et al. Effectiveness of community-based condom distribution interventions to prevent HIV in the United States: A systematic review and meta-analysis. PLoS One. 2017;12(8):e0180718. Published 2017 Aug 3. doi:10.1371/journal.pone.0180718
- Select activity Additional resources:
  
  Additional resources:
- Select activity Assignment #2 (10% of grade): Review and prov...
  
  Assignment #2 (10% of grade): Review and provide feedback on another student’s protocol. Time to complete: 1-2 hours.
  
  Due: April 23, 2022
  
  Please click on "Assignment 2" to download the detailed instructions. Please do the following steps AND the instructions in the Assignment 2 Word document:
  Each student will be paired with another student in the course. Each student pair is required to meet at least once during the course, read each other’s protocol, and discuss the importance/justification for a systematic review on their respective topics.
  When submitting your brief protocol (as part of assignment #1), you should also send a copy of that to your peer-reviewer (and cc Mazie Tsang mazie.tsang@ucsf.edu) on the same day that you are submitting your Assignment 1.
  For Assignment 2, you will then provide a written feedback on your peer’s protocol, highlighting at least three methodological areas that can be improved and two areas of strength. Final Assignment 2 should include a narrative section comprising 1-2 short paragraphs about critical comments (~ 200 words) + using marginal comments to provide comment on specific section of the protocol.
- Select activity Assignment #2
  
  Assignment #2
  
  Opened: Thursday, April 14, 2022, 12:00 AM
  
  Due: Saturday, April 23, 2022, 8:00 AM
Select section Thursday, April 21, 2022; 8:30 -10:00 am

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Thursday, April 21, 2022; 8:30 -10:00 am
MODULE 4: Data Synthesis Methods - Part 2

A - Meta-analysis - other topics
B - Meta-analysis Demo* - Conducting meta-analysis using RevMan and Stata

*Requirement: Need your computer with RevMan and Stata already installed.

Faculty: Mohsen Malekinejad
- Select activity Session Slides: (copy) (copy)
  
  Session Slides:
- Select activity Module 4-A: Meta-Analysis Subtopics
  
  Module 4-A: Meta-Analysis Subtopics File
- Select activity Module 4-B: Meta-Analysis Demo Final
  
  Module 4-B: Meta-Analysis Demo Final File
- Select activity RevMan Practice Set
  
  RevMan Practice Set Folder
- Select activity Stata Practice Set
  
  Stata Practice Set Folder
- Select activity Studies used for meta-analysis practice
  
  Studies used for meta-analysis practice Folder
- Select activity Session Audio/Video Recording (Access restricted t... (copy) (copy)
  
  Session Audio/Video Recording (Access restricted to registered students):
- Select activity Lecture 4 04.21.2022
  
  Lecture 4 04.21.2022 Media Resource
  
  Not available unless: You belong to Registered Students Only
- Select activity Lecture 4 04.21.2022 with caption
  
  Lecture 4 04.21.2022 with caption URL
  
  Not available unless: You belong to Registered Students Only
- Select activity Recommended Cochrane Handbook sections: Part 2 ...
  
  Recommended Cochrane Handbook sections:
  
  Part 2 - Chapter 10: Analyzing data and undertaking meta-analyses (sections:10.10, 10.11.1-10.11.3)
  
  Other optional chapter 10 sections: 10.5.2-10.9, 10.11.4 - 10.11.8, 10.13.
  
  Part 2 - Chapter 10: (sections: 10.11.2 - 10.11.6, 10.12, 10.14)
- Select activity Optional Reading:
  
  Optional Reading:
- Select activity Additional resources: RevMan 5.4.1:https://trai...
  
  Additional resources:
  
  RevMan 5.4.1:https://training.cochrane.org/online-learning/core-software-cochrane-reviews/revman
  
  Meta-analysis in RevMan Guide
- Select activity Assignment #3 (15% of grade): Participate and...
  
  Assignment #3 (15% of grade): Participate and present (~ 10 min) on a systematic review in a small group (in person or via Zoom). Time needed to complete: 2 – 3 hours.
  
  Due: April 30, 2022
  
  Please click on "Assignment 3" to find detailed instructions. This can also be found in the Assignments folder.
  While the following paragraph is a brief overview of the assignment, you will need to download the Assignment 3 Word document for detailed instructions.
  Students will be placed in group of 6 based on their topic of interest, and will be paired with another student in the group. You should find list of topics here and add your name under each. Each student pair will find a recent (ideally not older than 3-4 years) systematic related to the group topic, discuss strength and weakness of the systematic review (journal club format), and be prepared to answer 1-2 questions from the group. Students will be responsible to organize the meeting among themselves (find time that works, location, etc.). We will ask two group members to act as the group lead/ facilitator, Time, location, and completion of the assignment should be communicated to TA by the due date.
- Select activity Assignment #3
  
  Assignment #3
  
  Opened: Thursday, April 21, 2022, 12:00 AM
  
  Due: Saturday, April 30, 2022, 8:00 AM
Select section Thursday, April 28, 2022; 8:30 -10:00 am

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Thursday, April 28, 2022; 8:30 -10:00 am
MODULE 5: Assessment of evidence quality

A - Assessment of risk of bias (focus on interventional studies)
B - Interpretation of systematic review finding

Faculty: Mohsen Malekinejad
- Select activity Session Slides: (copy) (copy) (copy)
  
  Session Slides:
- Select activity Module 5-A: Risk of Bias
  
  Module 5-A: Risk of Bias File
- Select activity Module 5-B Systematic Review Reporting
  
  Module 5-B Systematic Review Reporting File
- Select activity Session Audio/Video Recording (Access restricted t... (copy) (copy) (copy)
  
  Session Audio/Video Recording (Access restricted to registered students):
- Select activity Lecture 5 04.28.2022
  
  Lecture 5 04.28.2022 Media Resource
  
  Not available unless: You belong to Registered Students Only
- Select activity Lecture 5 04.28.2022 with caption
  
  Lecture 5 04.28.2022 with caption URL
  
  Not available unless: You belong to Registered Students Only
- Select activity Recommended Cochrane Handbook sections: Part 2 ...
  
  Recommended Cochrane Handbook sections:
  
  Part 2 - Chapter 7: Considering bias and conflicts of interest among the included studies
  
  Part 2 - Chapter 8: Assessing risk of bias in a randomized trial
  
  Part 4 - Chapter 25: Assessing risk of bias in a non-randomized study
  
  Part 2 – Chapter 15: Interpreting results and drawing conclusions (You can skip following sections: 15.4.4, 15.5.3.1 – 15.5.3.5)
- Select activity Optional Reading: Juni et al. Hazards of scorin...
  
  Optional Reading:
  
  Juni et al. Hazards of scoring the quality of clinical trials for meta-analysis. JAMA. 1999;1054-60.
  
  Hoy D, Brooks P, Woolf A, Blyth F, March L, Bain C, Baker P, Smith E, Buchbinder R. Assessing risk of bias in prevalence studies: modification of an existing tool and evidence of interrater agreement. J Clin Epidemiol. 2012 Sep;65(9):934-9. doi: 10.1016/j.jclinepi.2011.11.014. Epub 2012 Jun 27. PMID: 22742910.
  
  Sterne JA, Hernán MA, Reeves BC, Savović J, Berkman ND, Viswanathan M, Henry D, Altman DG, Ansari MT, Boutron I, Carpenter JR, Chan AW, Churchill R, Deeks JJ, Hróbjartsson A, Kirkham J, Jüni P, Loke YK, Pigott TD, Ramsay CR, Regidor D, Rothstein HR, Sandhu L, Santaguida PL, Schünemann HJ, Shea B, Shrier I, Tugwell P, Turner L, Valentine JC, Waddington H, Waters E, Wells GA, Whiting PF, Higgins JP. ROBINS-I: a tool for assessing risk of bias in non-randomised studies of interventions. BMJ. 2016 Oct 12;355:i4919. doi: 10.1136/bmj.i4919. PMID: 27733354; PMCID: PMC5062054.
- Select activity Additional resources: https://www.riskofbias.in...
  
  Additional resources:
  
  https://www.riskofbias.info/
- Select activity Assignment #4 (40% of grade): Conduct meta-analysi...
  
  Assignment #4 (40% of grade): Conduct meta-analysis, generate forest plot (s), and provide brief answers to questions about your analysis outputs.
  
  Due: May 7, 2022
  
  Download the Assignment 4 Word document for instructions.
  
  A brief overview of the assignment: Students will receive a small dataset from the instructors. You are responsible to conduct meta-analysis to pool data for those studies, perform sub-group analysis and sensitivity analysis, and answer questions about the outputs of your analyses. Instructions for how to perform meta-analysis and those steps are provided as a part of Module 4 practice (40%). Detailed instructions with be provided. This assignment should not take more than 3-4 hours.
- Select activity Assignment #4
  
  Assignment #4
  
  Opened: Thursday, April 28, 2022, 12:00 AM
  
  Due: Saturday, May 7, 2022, 8:00 AM
Select section Thursday, May 5, 2022; 8:30 -10:00 am

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Thursday, May 5, 2022; 8:30 -10:00 am
MODULE 6: Systematic review reporting and critical appraisal

A - Risk of reporting bias (non-reporting bias)
B - Assessment of quality of body of evidence
C - Critical appraisal of systematic reviews

Faculty: Mohsen Malekinejad
- Select activity Session Slides: (copy) (copy) (copy) (copy)
  
  Session Slides:
- Select activity Module 6-A: GRADE
  
  Module 6-A: GRADE File
- Select activity Module 6-B: Assessment of Non-Reporting Bias
  
  Module 6-B: Assessment of Non-Reporting Bias File
- Select activity Module 6-C: Critical Appraisal
  
  Module 6-C: Critical Appraisal File
- Select activity Session Audio/Video Recording (Access restricted t... (copy) (copy) (copy) (copy)
  
  Session Audio/Video Recording (Access restricted to registered students):
- Select activity Lecture 6 05.05.2022
  
  Lecture 6 05.05.2022 Media Resource
  
  Not available unless: You belong to Registered Students Only
- Select activity Lecture 6 05.05.2022 with caption
  
  Lecture 6 05.05.2022 with caption URL
  
  Not available unless: You belong to Registered Students Only
- Select activity Recommended Cochrane Handbook sections: Part 2 ...
  
  Recommended Cochrane Handbook sections:
  
  Part 2 - Chapter 13: Assessing risk of bias due to missing results in a synthesis
  
  Part 2 - Chapter 14: Completing ‘Summary of findings’ tables and grading the certainty of the evidence (Sections 14.2 & 14.3)
- Select activity Optional Reading: Guyatt G, Oxman AD, Akl EA, K...
  
  Optional Reading:
  
  Guyatt G, Oxman AD, Akl EA, Kunz R, Vist G, Brozek J, Norris S, Falck-Ytter Y, Glasziou P, DeBeer H, Jaeschke R, Rind D, Meerpohl J, Dahm P, Schünemann HJ. GRADE guidelines: 1. Introduction-GRADE evidence profiles and summary of findings tables. J Clin Epidemiol. 2011 Apr;64(4):383-94. doi: 10.1016/j.jclinepi.2010.04.026. Epub 2010 Dec 31. PMID: 21195583.
  
  Shea 2017: AMSTAR 2: a critical appraisal tool for systematic reviews that include randomised or non-randomised studies of healthcare interventions, or both
  
  Page MJ, Moher D, Bossuyt PM, Boutron I, Hoffmann TC, Mulrow CD, et al. PRISMA 2020 explanation and elaboration: updated guidance and exemplars for reporting systematic reviews. BMJ 2021;372:n160. doi: 10.1136/bmj.n160
- Select activity Additional resources: GRADE Methodology: http:/...
  
  Additional resources:
  
  GRADE Methodology: http://help.magicapp.org/knowledgebase/articles/371159-the-grade-handbook
  
  AMSTAR 2 checklist: https://amstar.ca/Amstar_Checklist.php
  
  The PRISMA Statement and checklist: http://prisma-statement.org/PRISMAStatement/

Section outline

Thursday, March 31, 2022; 8:30 -10:00 am

Thursday, April 7, 2022; 8:30 -10:00 am

Thursday, April 14, 2022; 8:30 -10:00 am

Thursday, April 21, 2022; 8:30 -10:00 am

Thursday, April 28, 2022; 8:30 -10:00 am

Thursday, May 5, 2022; 8:30 -10:00 am