S G Baker

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. ncbi request reprint Evaluating markers for the early detection of cancer: overview of study designs and methods
    Stuart G Baker
    National Institutes of Health, Bethesda, MD, USA
    Clin Trials 3:43-56. 2006
  2. pmc Putting risk prediction in perspective: relative utility curves
    Stuart G Baker
    Biometry Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD 20892 7354, USA
    J Natl Cancer Inst 101:1538-42. 2009
  3. pmc Surrogate endpoint analysis: an exercise in extrapolation
    Stuart G Baker
    Corespondence to Stuart G Baker, National Cancer Institute, EPN 3131, 6130 Executive Blvd, MSC 7354, Bethesda, MD 20892 7354
    J Natl Cancer Inst 105:316-20. 2013
  4. ncbi request reprint Biomarkers, subgroup evaluation, and clinical trial design
    Stuart G Baker
    Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland 20892, USA
    Discov Med 13:187-92. 2012
  5. pmc Predicting treatment effect from surrogate endpoints and historical trials: an extrapolation involving probabilities of a binary outcome or survival to a specific time
    Stuart G Baker
    National Cancer Institute, EPN 3131, Bethesda, Maryland 20892 7354, USA
    Biometrics 68:248-57. 2012
  6. doi request reprint Two simple approaches for validating a binary surrogate endpoint using data from multiple trials
    Stuart G Baker
    Biometry Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD 20892 7354, USA
    Stat Methods Med Res 17:505-14. 2008
  7. ncbi request reprint Randomized trials for the real world: making as few and as reasonable assumptions as possible
    Stuart G Baker
    Biometry Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD 20892 7354, USA
    Stat Methods Med Res 17:243-52. 2008
  8. pmc Paradoxes in carcinogenesis: new opportunities for research directions
    Stuart G Baker
    Division of Cancer Prevention, National Cancer Institute, Bethesda, MD, USA
    BMC Cancer 7:151. 2007
  9. pmc Identifying genes that contribute most to good classification in microarrays
    Stuart G Baker
    Biometry Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD 20892 7354, USA
    BMC Bioinformatics 7:407. 2006
  10. pmc Common susceptibility genes for cancer: search for the end of the rainbow
    Stuart G Baker
    National Cancer Institute, Bethesda MD 20892 7354, USA
    BMJ 332:1150-2. 2006

Detail Information

Publications48

  1. ncbi request reprint Evaluating markers for the early detection of cancer: overview of study designs and methods
    Stuart G Baker
    National Institutes of Health, Bethesda, MD, USA
    Clin Trials 3:43-56. 2006
    ..New developments both in the biologic and statistical realms are providing increasing opportunities for evaluation of markers for both early detection and diagnosis of cancer...
  2. pmc Putting risk prediction in perspective: relative utility curves
    Stuart G Baker
    Biometry Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD 20892 7354, USA
    J Natl Cancer Inst 101:1538-42. 2009
    ..To illustrate an application of relative utility curves, an analysis was performed on previously published data involving the addition of breast density to a risk prediction model for invasive breast cancer...
  3. pmc Surrogate endpoint analysis: an exercise in extrapolation
    Stuart G Baker
    Corespondence to Stuart G Baker, National Cancer Institute, EPN 3131, 6130 Executive Blvd, MSC 7354, Bethesda, MD 20892 7354
    J Natl Cancer Inst 105:316-20. 2013
    ..In summary, when using surrogate endpoint analyses, an appreciation of the problems of extrapolation is crucial...
  4. ncbi request reprint Biomarkers, subgroup evaluation, and clinical trial design
    Stuart G Baker
    Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland 20892, USA
    Discov Med 13:187-92. 2012
    ..The adaptive signature design can be usefully extended via the sliding-window subgroup plot that was originally developed for the biomarker-analysis design...
  5. pmc Predicting treatment effect from surrogate endpoints and historical trials: an extrapolation involving probabilities of a binary outcome or survival to a specific time
    Stuart G Baker
    National Cancer Institute, EPN 3131, Bethesda, Maryland 20892 7354, USA
    Biometrics 68:248-57. 2012
    ..To summarize the additional uncertainty from using a predicted instead of true result for the estimated treatment effect, we compute its multiplier of standard error. Software is available for download...
  6. doi request reprint Two simple approaches for validating a binary surrogate endpoint using data from multiple trials
    Stuart G Baker
    Biometry Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD 20892 7354, USA
    Stat Methods Med Res 17:505-14. 2008
    ..96 to a level determined by the relationships between surrogate and true endpoints in the data sets. This elevated critical value could be used for accelerated approval...
  7. ncbi request reprint Randomized trials for the real world: making as few and as reasonable assumptions as possible
    Stuart G Baker
    Biometry Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD 20892 7354, USA
    Stat Methods Med Res 17:243-52. 2008
    ....
  8. pmc Paradoxes in carcinogenesis: new opportunities for research directions
    Stuart G Baker
    Division of Cancer Prevention, National Cancer Institute, Bethesda, MD, USA
    BMC Cancer 7:151. 2007
    ..These paradoxical aspects offer opportunities for new research directions that should not be ignored...
  9. pmc Identifying genes that contribute most to good classification in microarrays
    Stuart G Baker
    Biometry Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD 20892 7354, USA
    BMC Bioinformatics 7:407. 2006
    ..Our strategy is to search for classification rules that perform well with few genes and, if they are found, identify genes that occur relatively frequently under multiple random validation (random splits into training and test samples)...
  10. pmc Common susceptibility genes for cancer: search for the end of the rainbow
    Stuart G Baker
    National Cancer Institute, Bethesda MD 20892 7354, USA
    BMJ 332:1150-2. 2006
  11. ncbi request reprint Simple maximum likelihood estimates of efficacy in randomized trials and before-and-after studies, with implications for meta-analysis
    Stuart G Baker
    Biometry Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD 20892 7354, USA
    Stat Methods Med Res 14:349-67. 2005
    ..Particular attention is paid to estimating efficacy in meta-analysis, where the interpretation is much more straightforward than with intent-to-treat analyses...
  12. pmc Using microarrays to study the microenvironment in tumor biology: the crucial role of statistics
    Stuart G Baker
    Division of Cancer Prevention, National Cancer Institute, Bethesda, MD 20892 7354, USA
    Semin Cancer Biol 18:305-10. 2008
    ..Using these examples we critically discuss three types of analyses: differential gene expression, cluster analysis, and class prediction. We also discuss design issues...
  13. pmc Early reporting for cancer screening trials
    Stuart G Baker
    Division of Cancer Prevention, National Cancer Institute, Bethesda, MD 20892 7354, USA
    J Med Screen 15:122-9. 2008
    ....
  14. pmc Plausibility of stromal initiation of epithelial cancers without a mutation in the epithelium: a computer simulation of morphostats
    Stuart G Baker
    Biometry Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, USA
    BMC Cancer 9:89. 2009
    ..These disrupted interactions are hypothesized to be mediated by molecules, termed morphostats, which diffuse through the tissue to determine cell phenotype and maintain tissue architecture...
  15. pmc Improving the biomarker pipeline to develop and evaluate cancer screening tests
    Stuart G Baker
    Biometry Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD, USA
    J Natl Cancer Inst 101:1116-9. 2009
    ....
  16. pmc Transparency and reproducibility in data analysis: the Prostate Cancer Prevention Trial
    Stuart G Baker
    Biometry Research Group, Division of Cancer Prevention, National Cancer Institute, 6130 Executive Boulevard, Bethesda, MD 20892 7354, USA
    Biostatistics 11:413-8. 2010
    ..With such an important result at stake, a transparent analysis was important...
  17. pmc Estimation and inference for the causal effect of receiving treatment on a multinomial outcome: an alternative approach
    Stuart G Baker
    Biometry Research Group, Division of Cancer Prevention, National Cancer Institute, EPN 3131, 6130 Executive Blvd MSC 7354, Bethesda, Maryland 20892 7354, USA
    Biometrics 67:319-23; discussion 323-5. 2011
    ..We believe this approach is easier to implement, which would facilitate the reproduction of calculations...
  18. pmc Simple and flexible classification of gene expression microarrays via Swirls and Ripples
    Stuart G Baker
    Biometry Research Group, Division of Cancer Prevention, National Cancer Institute, EPN 3131, 6130 Executive Blvd MSC 7354, Bethesda, MD 20892 7354, USA
    BMC Bioinformatics 11:452. 2010
    ....
  19. pmc Designing a randomized clinical trial to evaluate personalized medicine: a new approach based on risk prediction
    Stuart G Baker
    National Cancer Institute, Bethesda, MD 20892 7354, USA
    J Natl Cancer Inst 102:1756-9. 2010
    ....
  20. pmc Systems biology and cancer: promises and perils
    Stuart G Baker
    Division of Cancer Prevention, National Cancer Institute, EPN 3131, 6130 Executive Blvd MSC 7354, Bethesda, MD 20892 7354, USA
    Prog Biophys Mol Biol 106:410-3. 2011
    ..Using illustrative examples we discuss these threads in the context of cancer research...
  21. ncbi request reprint A simple meta-analytic approach for using a binary surrogate endpoint to predict the effect of intervention on true endpoint
    Stuart G Baker
    Biometry Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD 20892 7354, USA
    Biostatistics 7:58-70. 2006
    ..Validation is illustrated using data from multiple randomized trials of patients with advanced colorectal cancer in which the surrogate endpoint was tumor response and the true endpoint was median survival time...
  22. ncbi request reprint Simple adjustments for randomized trials with nonrandomly missing or censored outcomes arising from informative covariates
    Stuart G Baker
    Biometry Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD, USA
    Biostatistics 7:29-40. 2006
    ..We discuss the computations for univariate, survival, and longitudinal outcomes, and present an application involving a randomized study of dual versus triple combinations of HIV-1 reverse transcriptase inhibitors...
  23. pmc Using observational data to estimate an upper bound on the reduction in cancer mortality due to periodic screening
    Stuart G Baker
    Biometry Research Group, Division of Cancer Prevention, National Cancer Institute, USA
    BMC Med Res Methodol 3:4. 2003
    ....
  24. ncbi request reprint The central role of receiver operating characteristic (ROC) curves in evaluating tests for the early detection of cancer
    Stuart G Baker
    Biometry Research Group, National Cancer Institute, National Intitutes of Health, Bethesda, MD 20892 7354, USA
    J Natl Cancer Inst 95:511-5. 2003
  25. pmc The transitive fallacy for randomized trials: if A bests B and B bests C in separate trials, is A better than C?
    Stuart G Baker
    Division of Cancer Prevention, National Cancer Institute
    BMC Med Res Methodol 2:13. 2002
    ..On its surface, this would appear to be a straightforward application of the transitive principle of logic...
  26. pmc Statistical issues in randomized trials of cancer screening
    Stuart G Baker
    Division of Cancer Prevention, National Cancer Institute, Bethesda, MD, USA
    BMC Med Res Methodol 2:11. 2002
    ..Although some of these issues have been discussed previously, we present important recent and new methodologies...
  27. ncbi request reprint Evaluating serial observations of precancerous lesions for further study as a trigger for early intervention
    Stuart G Baker
    Biometry Research Group, Division of Cancer Prevention, National Cancer Institute, EPN 3131, 6130 Executive Blvd MSC 7354, Bethesda, MD 20892 7354, USA
    Stat Med 21:2383-90. 2002
    ..To solve this problem, we propose a Markov chain model in reverse time. The methodology is illustrated using serial observations of precancerous lesions found on sputum cytology...
  28. pmc Markers for early detection of cancer: statistical guidelines for nested case-control studies
    Stuart G Baker
    Division of Cancer Prevention, National Cancer Institute, Bethesda, MD, USA
    BMC Med Res Methodol 2:4. 2002
    ..This has spurred nested case-control studies that involve testing some specimens for various markers that might predict cancer. Until now there has been little guidance in statistical design and analysis of these studies...
  29. pmc The paired availability design for historical controls
    S G Baker
    Division of Cancer Prevention, National Cancer Institute, Bethesda, MD, USA
    BMC Med Res Methodol 1:9. 2001
    ..One alternative, an observational cohort study, can give biased results if it is not possible to adjust for all relevant risk factors...
  30. ncbi request reprint Identifying combinations of cancer markers for further study as triggers of early intervention
    S G Baker
    Biometry Research Group, Division of Cancer Prevention, National Cancer Institute, EPN 344, 6130 Executive Blvd MSC 7354, Bethesda, Maryland 20892 7354, USA
    Biometrics 56:1082-7. 2000
    ..In a separate validation sample, the ROC curve for last total PSA intersected the target region in 77% of bootstrap replications, indicating some promise for further study. We also discussed sample size calculations...
  31. ncbi request reprint Evaluating the age to begin periodic breast cancer screening using data from a few regularly scheduled screenings
    S G Baker
    Biometry Branch, Division of Cancer Prevention, National Cancer Institute, EPN 344, Bethesda, Maryland 20892, USA
    Biometrics 54:1569-78. 1998
    ..This must be weighted against an estimated increase in the number of biopsies that do not detect cancer of 580 per 10,000 with a 95% confidence interval of (520/10,000, 650/10,000)...
  32. pmc A simple method for analyzing data from a randomized trial with a missing binary outcome
    Stuart G Baker
    Biometry Research Group, Division of Cancer Prevention, National Cancer Institute, USA
    BMC Med Res Methodol 3:8. 2003
    ..Although many previous adjustments for missing binary outcomes have been proposed, none of these makes explicit use of randomization to bound the bias when the data are not missing at random...
  33. pmc Randomized trials, generalizability, and meta-analysis: graphical insights for binary outcomes
    Stuart G Baker
    Biometry Research Group, Division of Cancer Prevention, National Cancer Institute, USA
    BMC Med Res Methodol 3:10. 2003
    ..the question, "What would be the effect of treatment on outcome in a population with a possibly different distribution of an unobserved binary baseline variable that does not interact with treatment in its effect on outcome?"..
  34. pmc Estimating the cumulative risk of false positive cancer screenings
    Stuart G Baker
    Biometry Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland, USA
    BMC Med Res Methodol 3:11. 2003
    ..A previous approach to estimate the probability of at least one false positive in n screenings unrealistically assumed that the probability of dropout does not depend on prior false positives...
  35. ncbi request reprint A sensitivity analysis for nonrandomly missing categorical data arising from a national health disability survey
    Stuart G Baker
    Biometry Research Group, Division of Cancer Prevention, National Cancer Institute, EPN 3131, 6130 Executive Blvd MSC 7354, Bethesda, MD 20892 7354, USA
    Biostatistics 4:41-56. 2003
    ..2 with 95% CI of (3.9, 4.6). Under one nonignorable missing-data model, the odds ratio was 7.4 with 95% CI of (6.3, 8.6). This is the first analysis to find a strong association between balance difficulties and frequent depression...
  36. ncbi request reprint Genetic susceptibility to prostate, breast, and colorectal cancer among Nordic twins
    Stuart G Baker
    Biometry Research Group, Division of Cancer Prevention, National Cancer Institute, EPN 3131, 6130 Executive Boulevard, MSC 7354, Bethesda, Maryland 20892 7354, USA
    Biometrics 61:55-63. 2005
    ..12 to 0.30 for breast cancer, and 0.08 to 0.27 for colorectal cancer. We conclude that genetic susceptibility makes only a small to moderate contribution to the incidence of prostate, breast, and colorectal cancer...
  37. pmc A perfect correlate does not a surrogate make
    Stuart G Baker
    Biometry Research Group, Division of Cancer Prevention, National Cancer Institute, USA
    BMC Med Res Methodol 3:16. 2003
    ..We investigate this belief when the potential surrogate and unobserved true endpoints are perfectly correlated within each randomization group...
  38. pmc The fallacy of enrolling only high-risk subjects in cancer prevention trials: is there a "free lunch"?
    Stuart G Baker
    Biometry Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland, USA
    BMC Med Res Methodol 4:24. 2004
    ..We critically investigate the plausibility of these assumptions...
  39. pmc Comparing breast cancer mortality rates before-and-after a change in availability of screening in different regions: extension of the paired availability design
    Stuart G Baker
    Biometry Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD 20892 7354, USA
    BMC Med Res Methodol 4:12. 2004
    ..The original formulation involved short-term outcomes; the challenge here is accommodating long-term outcomes...
  40. ncbi request reprint Development tracks for cancer prevention markers
    Stuart G Baker
    Biometry Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD 20892 7354, USA
    Dis Markers 20:97-102. 2004
    ..We provide a general framework for describing various roles for biomarkers in cancer prevention research (early detection, surrogate endpoint, and cohort identification for primary prevention) and the phases in their evaluation...
  41. ncbi request reprint The partial testing design: a less costly way to test equivalence for sensitivity and specificity
    S G Baker
    Biometry Branch, National Cancer Institute, Bethesda, MD 20892 7354, USA
    Stat Med 17:2219-32. 1998
    ..The design differs from a double sampling design because it compares two imperfect tests instead of combining information from a perfect and imperfect test...
  42. doi request reprint Cumulative incidence of false-positive test results in lung cancer screening: a randomized trial
    Jennifer M Croswell
    National Institutes of Health, National Cancer Institute, Bethesda, and Information Management Services, Rockville, Maryland 20892, USA
    Ann Intern Med 152:505-12, W176-80. 2010
    ..However, screening exposes healthy persons to potential harms, and cumulative false-positive rates for low-dose CT have never been formally reported...
  43. pmc Cumulative incidence of false-positive results in repeated, multimodal cancer screening
    Jennifer Miller Croswell
    Office of the Director, Office of Disease Prevention, National Institutes of Health, 6100 Executive Blvd, Suite 2B 03, Bethesda, MD 20892, USA
    Ann Fam Med 7:212-22. 2009
    ..We sought to determine the cumulative risk of a false-positive screening result and the resulting risk of a diagnostic procedure for an individual participating in a multimodal cancer screening program...
  44. doi request reprint Estimating the cumulative risk of a false-positive under a regimen involving various types of cancer screening tests
    Stuart G Baker
    Division of Cancer Prevention, National Cancer Institute, 6130 Executive Blvd MSC 7354, Bethesda, MD 20892 7354, USA
    J Med Screen 15:18-22. 2008
    ..Previous methods for estimating cumulative risk of FPs with a single type of test are not directly applicable, so a new approach was developed...
  45. ncbi request reprint Good for women, good for men, bad for people: Simpson's paradox and the importance of sex-specific analysis in observational studies
    S G Baker
    Division of Cancer Prevention, National Cancer Institute, EPN 3131, 6130 Executive Boulevard, MSC 7354, Bethesda, MD 20892-7354, USA
    J Womens Health Gend Based Med 10:867-72. 2001
    ..To better understand why Simpson's paradox and the related result occur, we present a graphic explanation...
  46. ncbi request reprint Surrogate endpoints: wishful thinking or reality?
    Stuart G Baker
    J Natl Cancer Inst 98:502-3. 2006
  47. ncbi request reprint Re: Commonly studied single-nucleotide polymorphisms and breast cancer: results from the Breast Cancer Association Consortium
    Stuart G Baker
    J Natl Cancer Inst 99:487-8; author reply 488-9. 2007
  48. ncbi request reprint Screening and breast cancer
    Stuart G Baker
    N Engl J Med 354:767-9; author reply 767-9. 2006