biostat/stat 111 an light survival analysis...blooming cherry trees in the quad mount rainier...
TRANSCRIPT
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SISCER Mod 6
Survival AnalysisLecture 5
Ying Qing Chen, Ph.D.
University of Washington
Fred Hutchinson Cancer Research Center
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In Lecture 4
◼ What we discussed
❑ Cox proportional hazards model
◼ Model specification
◼ Interpretation
◼ Estimation by partial likelihood
◼ Stratified Cox proportional hazards model
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Special topic 1: time-varying covariates
◼ Time-varying (time-dependent) covariates
❑ External covariates
◼ Pollen level to asthma attack
◼ Maternal CD4 counts and plasma viral loads to infant HIV-
infections by breast milk feeding
◼ Exposure to second-hand smoking to lung cancer
❑ Internal covariates
◼ Smoking secession because of doctor’s advice on health
status
◼ Blood pressure for death caused by cadio-vascular diseases
◼ Sexual behavior change because of deteriorating HIV
progression
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Extended Cox model
◼ Cox model with time-varying covariates
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◼ What drives the change in covariates?
❑ In general, time-dependent covariates are not as
easy to understand conceptually as time-
independent covariates
❑ This is where the longitudinal data analysis may
need to empirically address the change in time-
dependent covariates
◼ Are the time-varying covariates risk factors?
◼ Or they are biomarkers of disease progression? i.e.,
they are varying because of disease dynamics?
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Example: atomic bomb survivors study
◼ Survival data
❑ Time-to-event outcome: leukemia incidence
❑ Time zero: 1945
❑ Risk factor: in the range of 2.5km or not
◼ Model specification: extended Cox model
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Example: Stanford heart transplant data
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Data split
◼ Construct the so-called “covariate process
data”
Heart transplant
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STATA codes
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With time-varying covariates
Split record
according to
covariate process
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Not age-adjusted Age-adjusted
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Summary
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References
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Special topic 2: assessment of model
adequacy
◼ Most critical assumption for the Cox model
❑ Proportionality between hazard functions
❑ Needs to be carefully examined
◼ Example: Brain cancer trial
❑ Randomized trial of 222 patients with brain tumors
◼ BCNU (Carmustine) medicated polymers
◼ Control polymers
❑ Chen & Wang (2000, Journal of the American
Statistical Association)
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Graphical assessment
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-log-log plot
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STATA codes
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Unadjusted Adjusted
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Comparing observed and expected
survival curves
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Confirmatory goodness-of-fit test
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More techniques: analysis of residuals
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Summary
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Special topics yet to cover
◼ Competing risks
◼ Truncated time-to-event outcomes
◼ Interval-censored outcomes
◼ Measure of surrogacy
◼ Alternative regression models
◼ Model predictiveness
◼ ROC for time-to-event outcomes
◼ Attributable risk functions
◼ Multivariate survival times
◼ Study designs
◼ etc, etc
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Seattle, Seattle, Seattle…
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Thanks to
◼ Our great TA: Eric Morenz
◼ And mostly to: Everyone of You!
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Q & A