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Syllabus

Clinical Epidemiology EPI204

Date/Time Activity Topic/Content Faculty Locations
Thurs 9/24/2009
8:45 AM-10:15 AM		Lecture

Course overview, the diagnostic process, and measures of interobserver agreement

Introduction to the course and how we will teach it; how the reason for making a diagnosis affects the optimal classification scheme; concordance, unweighted Kappa, linear and quadratic weighted Kappa

Required Reading:

  1. EBD Front matter, Chapter 1, and Chapter 2 through page 22.

Optional Reading:

  1. U. C. Faculty Walkout General Info and Links
  2. UCB’s Prof Catherine Cole Open Letter to Students
  3. The Kept University (Atlantic online, 2000) by E Press and J Washburn
  4. Money and the Changing Culture of Medicine

Note/Slide Files: Lec 1 Overview diagnosis kappa_23Sep09.ppt (292 KB)

Assignment Files: HW Set 1 Epi 204_ 2009.doc (30 KB)

STATA Files: KappaNeuroExample.dta (8 KB)

T NewmanCB 6702
Thurs 9/24/2009
1:00 PM-2:30 PM		Section

Review of Chapter 1 problems and "Kappa Game"

Assignment Files: KAPPA GAME DATA COLL FORM.doc (80 KB) KAPPA GAME For EBD Teachers.doc (131 KB)

STATA Files: Appendix 2-1.doc (41 KB)

N Bansal
C Kistler
M Kohn
A Marmor
J Meadows
T Newman
E Terrazas
E Wang		CB 6702
CB 5721
CB 5759
CB 5721
CB 5759
CB 6702
CB 6601
CB 6601
Thurs 10/1/2009
8:45 AM-10:15 AM		Lecture

Dichotomous tests

Sensitivity, specificity, predictive value, prior and posterior probability; 2x2 table method for getting posterior probability; probability and odds; likelihood ratios, the likelihood ratio slide rule, false-positive and false negative confusion; use of X-graphs to understand testing and treatment thresholds

Required Reading:

  1. EBD Chapter 3

Optional Reading:

  1. Testing Threshold Derivations (handwritten and scanned)

Note/Slide Files: Lec 2 Dichotomous Tests_1Oct09.ppt (75 KB)

Tool Files: Cost-Benefit X Graph and calcs for Chapter 3 .xls (58 KB)

T NewmanCB 6702
Thurs 10/1/2009
1:00 PM-2:30 PM		Section

Review of Chapter 2 problems on measures of interobserver agreement

Assignment Files: HW Set 2 Epi 204_ 2009.doc (45 KB)

Assignment Answer Files: epi 204 HW 2 answer key.doc (44 KB)

N Bansal
C Kistler
M Kohn
A Marmor
J Meadows
T Newman
E Terrazas
E Wang		CB 6702
CB 5721
CB 5759
CB 5721
CB 5759
CB 6702
CB 6601
CB 6601
Thurs 10/8/2009
8:45 AM-10:15 AM		Lecture

Multilevel and continuous tests

ROC Curves, multilevel likelihood ratios and the relationship between them; how dichotmozing tests wastes information; the Walking Man approach to ROC curves; choosing cutoffs

Required Reading:

  1. EBD Chapter 4

Note/Slide Files: Lec 3 Multilevel And Continuous Tests_8Oct09.ppt (1237 KB)

M KohnCB 6702
Thurs 10/8/2009
1:00 PM-2:30 PM		Section

Review of Chapter 3 problems on dichotomous tests

Assignment Files: HW Set 3 Epi 204_ 2009.doc (55 KB)

Assignment Answer Files: epi204_HW_3_answer_key.doc (55 KB)

N Bansal
C Kistler
M Kohn
A Marmor
J Meadows
T Newman
E Terrazas
E Wang		CB 6702
CB 5721
CB 6702
CB 5759
CB 5759
CB 6601
CB 5721
CB 6601
Thurs 10/15/2009
8:45 AM-10:15 AM		Lecture

Studies of Diagnostic Tests

Common biases: incorporation bias, verification bias, double gold-standard bias, spectrum bias; Prevalence, spectrum bias and nonindependence; checklist vs systematic approach to critical appraisal of studies of diagnostic tests

Required Reading:

  1. EBD Chapter 5

Note/Slide Files: Lec 4 Studies o f Dx Tests_15Oct09.ppt (946 KB)

T NewmanCB 6702
Thurs 10/15/2009
1:00 PM-2:30 PM		Section

Review of Chapter 4 problems on multilevel and continuous tests

Note/Slide Files: Illustration for Problem 10 on Troponin T.ppt (188 KB)

Assignment Files: HW Set 4 Epi 204_2009.doc (214 KB)

Assignment Answer Files: epi 204 HW 4 answer key TN.doc (257 KB)

N Bansal
C Dehlendorf
C Kistler
M Kohn
A Marmor
J Meadows
T Newman
E Wang		CB 6702
CB 5721
CB 5721
CB 6702
CB 5759
CB 5759
CB 6601
CB 6601
Thurs 10/22/2009
8:45 AM-10:15 AM		Lecture

Screening tests

Need for a more critical approach for screening tests, risk factor vs disease screening; biases in observational studies of screening: lead time bias, length time bias, volunteer bias, stage migration bias, pseudodisease; randomized trials of screening

Required Reading:

  1. EBD Chapter 6

Optional Reading:

  1. Winners and Losers (Dan Merenstein)
  2. NYT Article on Screening Concerns 21Oct09
  3. Metaphors in Medicine article (George Annas)

Note/Slide Files: Lec 5 Screening Tests Slides 1-17.ppt (3068 KB) Lec 5 Screening Tests Slides 18-35.ppt (4361 KB) Lec 5 Screening Tests Slides 36-end.ppt (961 KB)

T NewmanCB 6702
Thurs 10/22/2009
1:00 PM-2:30 PM		Section

Review of Chapter 5 problems on studies of diagnostic tests

Assignment Files: HW Set 5 Epi 204_ 2009.doc (120 KB)

Assignment Answer Files: HW Set 5 with answers Epi 204_ 2009 final.doc (172 KB)

N Bansal
C Kistler
M Kohn
A Marmor
J Meadows
T Newman
E Terrazas
E Wang		CB 6702
CB 5721
CB 6601
CB 6702
CB 5759
CB 5721
CB 5759
CB 6601
Thurs 10/29/2009
8:45 AM-10:15 AM		Lecture

Combining tests and prognostic tests

Prognostic Tests: differences from diagnostic tests; calibration and discrimination; comparing predictions; value of prognostic information. Combining tests/diagnostic models: importance of test non-independence; recursive partitioning; logistic regression; importance of validation separate from derivation

Required Reading:

  1. EBD Chapters 7 and 8

Note/Slide Files: KohnMultipleTestsPrognosticTests_10-29-2009.ppt (1933 KB)

M KohnCB 6702
Thurs 10/29/2009
1:00 PM-2:30 PM		Section

Review of Chapter 6 problems on screening tests

Assignment Files: HW Set 6 Epi 204_ 2009.doc (56 KB)

Assignment Answer Files: HW Set 6 KEY Epi 204_ 2009.doc (72 KB)

N Bansal
C Kistler
M Kohn
A Marmor
J Meadows
T Newman
E Terrazas
E Wang		CB 6702
CB 5721
CB 6704
CB 6702
CB 5759
CB 5721
CB 5759
CB 6704
Thurs 11/5/2009
8:45 AM-10:15 AM		Lecture

Quantifying the benefits and harms of treatments

RCT checklist; importance of baseline incidence; measures of effect size: Relative risk (RR), relative risk reduction (RRR), Odds ratio (OR), Absolute risk reduction (ARR), Number needed to treat (NNT); "Back of the Envelope Cost Effectiveness Analysis"

Required Reading:

  1. EBD Chapter 9
  2. The Articulate Presentation on Marketing Medicines by TN; Slides 1-47 REQUIRED; rest optional

Note/Slide Files: KohnRBTsQuantifyingTreatmentEffects11_5_2009.ppt (3574 KB)

M KohnCB 6702
Thurs 11/5/2009
1:00 PM-2:30 PM		Section

Review of Chapter 7 problems on prognostic tests and Chapter 8 problems on combining tests

Assignment Files: HW 7 (Chs 7 and 8) Epi 204 2009.doc (120 KB)

Assignment Answer Files: HW 7 (Chs 7 and 8) Answers.doc (226 KB)

N Bansal
C Kistler
M Kohn
A Marmor
J Meadows
T Newman
E Terrazas
E Wang		CB 6702
CB 5721
CB 5721
CB 6704
CB 5759
CB 5759
CB 6702
CB 6704
Thurs 11/12/2009
8:45 AM-10:15 AM		Lecture

Alternatives to randomized trials for estimating effects of tests and treatments

When randomized trials are and may not be needed; instrumental variables and natural experiments; measuring additonal predictor and outcome variables to estimate bias; propensity scores

Required Reading:

  1. EBD Chapter 10

Note/Slide Files: Lec 8 Alternatives To RCTs 12Nov09.ppt (2502 KB)

T NewmanCB 6702
Thurs 11/12/2009
1:00 PM-2:30 PM		Section

Review of Chapter 9 problems on quantifying the benefits and harms of treatments

Assignment Files: HW Chapter 9 Epi 204.doc (55 KB)

Assignment Answer Files: Chapter 9 Answer Key.doc (126 KB)

N Bansal
C Dehlendorf
C Kistler
M Kohn
A Marmor
J Meadows
T Newman
E Wang		CB 6702
CB 6702
CB 5721
CB 5721
CB 6704
CB 5759
CB 5759
CB 6704
Thurs 11/19/2009
8:45 AM-10:15 AM		Lecture

What do P-values and confidence intervals really mean?

Introduction and justification: why this Bayesian stuff is important and why we think you can handle it; what P-values and confidence intervals don' t mean; what they do mean: analogy between clinical researchg and diagnostic tests; confidence intervals for negative studies and for proportions with small numerators

Required Reading:

  1. EBD Chapter 11

Optional Reading:

  1. Browner WS, Newman TB. Are all significant P-values created equal? The analogy between diagnostic tests and clinical research. JAMA 1987;257:2459-63
  2. Davidoff, F. Standing statistics right side up. Annals of Internal Medicine 1999; 130: 1019-1021
  3. Goodman, S. Toward evidence-based medical statistics. 1: The P value fallacy. Annals of Internal Medicine 1999; 130: 995-1004
  4. Goodman, S. Toward evidence-based medical statistics. 2: The Bayes factor. Annals of Internal Medicine 1999; 130: 1005-1013
  5. Newman, T. If almost nothing goes wrong, is almost everything all right? JAMA 1995; 274: 1013

Note/Slide Files: Lec 9 Understanding P- values and CI 18Nov09.ppt (234 KB)

T NewmanCB 6702
Thurs 11/19/2009
1:00 PM-2:30 PM		Section

Review of Chapter 10 problems on alternatives to randomized trials for estimating effects of tests and treatments

Assignment Files: HW Ch 10 Epi 204.doc (210 KB)

Assignment Answer Files: Chapter 10 Answers to Problems not in the text.doc (38 KB)

N Bansal
C Kistler
M Kohn
A Marmor
J Meadows
T Newman
E Terrazas
E Wang		CB 6702
CB 5721
CB 5759
CB 5721
CB 5759
CB 6702
CB 6704
CB 6704
Thurs 12/3/2009
8:45 AM-10:15 AM		Lecture

Challenges for Evidence-based Diagnosis and Course Review; Distribute final exam

Criticisms of evidence-based medicine; stories and statistics; psychology of medical decision making: heuristics used to estimate probability. Course review.

Required Reading:

  1. EBD Chapter 12

Optional Reading:

  1. Newman, TB. The Power of Stories over Statistics.BMJ. 2003;327(7429):1424-7
  2. Newman TB, Maisels, MJ. Less Aggressive Treatment of Neonatal Jaundice and Reports of Kernicterus: Lessons About Practice Guidelines. Pediatrics 2000;105:242
  3. Newman TB, Johnston BD, Grossman DC. Effects and costs of requiring child-restraint systems for young children traveling on commercial airplanes.Arch Pediatr Adolesc Med. 2003 Oct;157(10):969-74
  4. Bishai D. Hearts and Minds and Child Restraints on Airplanes. Arch Peds Adol Med 2003;157:953
  5. Merenstein D. Winners & Losers. JAMA 2004;291:242-5
  6. Healy B. Who Says Whats Best? US News World Rept
  7. Newman TB. Universal Bilirubin Screening, Guidelines and Evidence. Pediatrics 2009

Note/Slide Files: Lec10 Challenges for EBM3Dec2009.ppt (1690 KB)

M Kohn
T Newman		CB 6702
CB 6702
Thurs 12/3/2009
1:00 PM-2:30 PM		Section

Review of Chapter 11 problems on P-values and confidence intervals

Note/Slide Files: Lec11 Exam Reivew 8Dec2009.ppt (1668 KB)

Assignment Files: HW Chapter 11 Epi 204_ 2009.doc (48 KB)

Assignment Answer Files: HW Chapter 11 Answer Key Revised 3Dec09.doc (59 KB)

N Bansal
C Kistler
M Kohn
A Marmor
J Meadows
T Newman
E Terrazas
E Wang		CB 6702
CB 5721
CB 6702
CB 5759
CB 5759
CB 6704
CB 5721
CB 6704
Thurs 12/10/2009
8:45 AM-10:15 AM		Lecture

Final examination review

Assignment Answer Files: KEY to Final Examination 2009 Epi 204 .doc (340 KB)

Final Exam Files: Final Examination 2009 Epi 204 .doc (315 KB) FINAL EXAMINATION CLARIFICATIONS 8Dec09.doc (38 KB)

T NewmanCB 6702