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  1. Article ; Online: Evaluating Risk Prediction with Data Collection Costs: Novel Estimation of Test Tradeoff Curves.

    Baker, Stuart G

    Medical decision making : an international journal of the Society for Medical Decision Making

    2023  Volume 44, Issue 1, Page(s) 53–63

    Abstract: Background: The test tradeoff curve helps investigators decide if collecting data for risk prediction is worthwhile when risk prediction is used for treatment decisions. At a given benefit-cost ratio (the number of false-positive predictions one would ... ...

    Abstract Background: The test tradeoff curve helps investigators decide if collecting data for risk prediction is worthwhile when risk prediction is used for treatment decisions. At a given benefit-cost ratio (the number of false-positive predictions one would trade for a true positive prediction) or risk threshold (the probability of developing disease at indifference between treatment and no treatment), the test tradeoff is the minimum number of data collections per true positive to yield a positive maximum expected utility of risk prediction. For example, a test tradeoff of 3,000 invasive tests per true-positive prediction of cancer may suggest that risk prediction is not worthwhile. A test tradeoff curve plots test tradeoff versus benefit-cost ratio or risk threshold. The test tradeoff curve evaluates risk prediction at the optimal risk score cutpoint for treatment, which is the cutpoint of the risk score (the estimated risk of developing disease) that maximizes the expected utility of risk prediction when the receiver-operating characteristic (ROC) curve is concave.
    Methods: Previous methods for estimating the test tradeoff required grouping risk scores. Using individual risk scores, the new method estimates a concave ROC curve by constructing a concave envelope of ROC points, taking a slope-based moving average, minimizing a sum of squared errors, and connecting successive ROC points with line segments.
    Results: The estimated concave ROC curve yields an estimated test tradeoff curve. Analyses of 2 synthetic data sets illustrate the method.
    Conclusion: Estimating the test tradeoff curve based on individual risk scores is straightforward to implement and more appealing than previous estimation methods that required grouping risk scores.
    Highlights: The test tradeoff curve helps investigators decide if collecting data for risk prediction is worthwhile when risk prediction is used for treatment decisions.At a given benefit-cost ratio or risk threshold, the test tradeoff is the minimum number of data collections per true positive to yield a positive maximum expected utility of risk prediction.Unlike previous estimation methods that grouped risk scores, the method uses individual risk scores to estimate a concave ROC curve, which yields an estimated test tradeoff curve.
    MeSH term(s) Humans ; Risk Factors ; ROC Curve
    Language English
    Publishing date 2023-11-22
    Publishing country United States
    Document type Journal Article
    ZDB-ID 604497-9
    ISSN 1552-681X ; 0272-989X
    ISSN (online) 1552-681X
    ISSN 0272-989X
    DOI 10.1177/0272989X231208673
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Prediagnostic evaluation of multicancer detection tests: Design and analysis considerations.

    Baker, Stuart G / Etzioni, Ruth

    Journal of the National Cancer Institute

    2024  

    Abstract: There is growing interest in multicancer detection (MCD) tests, which identify molecular signals in the blood indicating a potential preclinical cancer. A key stage in evaluating MCD tests is a prediagnostic performance study, in which investigators ... ...

    Abstract There is growing interest in multicancer detection (MCD) tests, which identify molecular signals in the blood indicating a potential preclinical cancer. A key stage in evaluating MCD tests is a prediagnostic performance study, in which investigators store specimens from asymptomatic persons and later test stored specimens from cancer cases and a random sample of controls to determine predictive performance. Performance metrics include cancer-specific true and false positive rates and a cancer-specific positive predictive value, with the latter compared to a decision-analytic threshold. The sample size tradeoff method, which trades imprecise targeting of the true positive rate for precise targeting of a zero false positive rate can substantially reduce sample size while increasing the lower bound of positive predictive value. For a 1-year follow-up, with ovarian cancer as the rarest cancer considered, the sample size tradeoff method yields a sample size of 163,000 compared with a sample size of 720,000 based on standard calculations. These design and analysis recommendations should be considered in planning a specimen repository and in the prediagnostic evaluation of MCD tests.
    Language English
    Publishing date 2024-02-28
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2992-0
    ISSN 1460-2105 ; 0027-8874 ; 0198-0157
    ISSN (online) 1460-2105
    ISSN 0027-8874 ; 0198-0157
    DOI 10.1093/jnci/djae050
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: The case for a cancer paradox initiative.

    Baker, Stuart G

    Carcinogenesis

    2021  Volume 42, Issue 8, Page(s) 1023–1025

    MeSH term(s) Carcinogenesis ; Humans ; Mutation ; Neoplasms/etiology ; Neoplasms/genetics ; Neoplasms/pathology
    Language English
    Publishing date 2021-07-07
    Publishing country England
    Document type Journal Article
    ZDB-ID 603134-1
    ISSN 1460-2180 ; 0143-3334
    ISSN (online) 1460-2180
    ISSN 0143-3334
    DOI 10.1093/carcin/bgab052
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: The Predictive Approaches to Treatment effect Heterogeneity (PATH) Statement.

    Baker, Stuart G

    Annals of internal medicine

    2020  Volume 172, Issue 11, Page(s) 775–776

    Language English
    Publishing date 2020-06-30
    Publishing country United States
    Document type Letter ; Comment
    ZDB-ID 336-0
    ISSN 1539-3704 ; 0003-4819
    ISSN (online) 1539-3704
    ISSN 0003-4819
    DOI 10.7326/L20-0426
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: CACE and meta-analysis (Letter to the Editor).

    Baker, Stuart G

    Biometrics

    2020  Volume 76, Issue 4, Page(s) 1383–1384

    MeSH term(s) Bayes Theorem ; Patient Compliance ; Randomized Controlled Trials as Topic
    Language English
    Publishing date 2020-02-28
    Publishing country United States
    Document type Letter ; Comment
    ZDB-ID 213543-7
    ISSN 1541-0420 ; 0099-4987 ; 0006-341X
    ISSN (online) 1541-0420
    ISSN 0099-4987 ; 0006-341X
    DOI 10.1111/biom.13240
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Deriving Real-World Insights From Real-World Data.

    Baker, Stuart G

    Annals of internal medicine

    2019  Volume 170, Issue 9, Page(s) 664–665

    MeSH term(s) Biostatistics
    Language English
    Publishing date 2019-05-03
    Publishing country United States
    Document type Letter ; Comment
    ZDB-ID 336-0
    ISSN 1539-3704 ; 0003-4819
    ISSN (online) 1539-3704
    ISSN 0003-4819
    DOI 10.7326/L19-0084
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Latent class instrumental variables and the monotonicity assumption.

    Baker, Stuart G

    Emerging themes in epidemiology

    2020  Volume 17, Page(s) 2

    Abstract: ... The purpose of this letter is to note that Baker and Lindeman and Imbens and Angrist independently introduced ...

    Abstract A key aspect of the article by Lousdal on instrumental variables was a discussion of the monotonicity assumption. However, there was no mention of the history of the development of this assumption. The purpose of this letter is to note that Baker and Lindeman and Imbens and Angrist independently introduced the monotonicity assumption into the analysis of instrumental variables. The letter also places the monotonicity assumption in the context of the method of latent class instrumental variables.
    Language English
    Publishing date 2020-03-19
    Publishing country England
    Document type Journal Article ; Comment
    ISSN 1742-7622
    ISSN 1742-7622
    DOI 10.1186/s12982-020-00088-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Metrics for Evaluating Polygenic Risk Scores.

    Baker, Stuart G

    JNCI cancer spectrum

    2020  Volume 5, Issue 1

    Abstract: There is growing interest in the use of polygenic risk scores based on genetic variants to predict cancer incidence. The type of metric used to evaluate the predictive performance of polygenic risk scores plays a crucial role in their interpretation. I ... ...

    Abstract There is growing interest in the use of polygenic risk scores based on genetic variants to predict cancer incidence. The type of metric used to evaluate the predictive performance of polygenic risk scores plays a crucial role in their interpretation. I compare 3 metrics for this evaluation: the area under the receiver operating characteristic curve (AUC), the probability of cancer in a high-risk subset divided by the prevalence of cancer in the population, which I call the subset relative risk (SRR), and the minimum test tradeoff, which is the minimum number of genetic variant ascertainments (one per person) for each correct prediction of cancer to yield a positive expected clinical utility. I show that SRR is a relabeling of AUC. I recommend the minimum test tradeoff for the evaluation of polygenic risk scores because, unlike AUC and SRR, it is directly related to the expected clinical utility.
    MeSH term(s) Breast Neoplasms/epidemiology ; Breast Neoplasms/genetics ; Clinical Decision Rules ; Costs and Cost Analysis ; Female ; Genetic Variation ; Humans ; Neoplasms/epidemiology ; Neoplasms/genetics ; Prevalence ; Probability ; ROC Curve ; Risk ; Risk Factors
    Language English
    Publishing date 2020-12-23
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ISSN 2515-5091
    ISSN (online) 2515-5091
    DOI 10.1093/jncics/pkaa106
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Decision Curves and Relative Utility Curves.

    Baker, Stuart G

    Medical decision making : an international journal of the Society for Medical Decision Making

    2019  Volume 39, Issue 5, Page(s) 489–490

    MeSH term(s) Decision Making ; Decision Support Techniques ; Family
    Language English
    Publishing date 2019-05-20
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 604497-9
    ISSN 1552-681X ; 0272-989X
    ISSN (online) 1552-681X
    ISSN 0272-989X
    DOI 10.1177/0272989X19850762
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Rethinking carcinogenesis: The detached pericyte hypothesis.

    Baker, Stuart G

    Medical hypotheses

    2020  Volume 144, Page(s) 110056

    Abstract: The limiting step in cancer prevention is a lack of understanding of cancer biology. This limitation is exacerbated by a focus on the dominant somatic mutation theory (that driver mutations cause cancer) with little consideration of alternative theories ... ...

    Abstract The limiting step in cancer prevention is a lack of understanding of cancer biology. This limitation is exacerbated by a focus on the dominant somatic mutation theory (that driver mutations cause cancer) with little consideration of alternative theories of carcinogenesis. The recently proposed detached pericyte hypothesis explains many puzzling phenomena in cancer biology for which the somatic mutation theory offers no obvious explanation. These puzzling phenomena include foreign-body tumorigenesis, the link between denervation and cancer, tumors in transgenic mice that lack the inducing mutation, and non-genotoxic carcinogens. The detached pericyte hypothesis postulates that (1) a carcinogen or chronic inflammation causes pericytes to detach from blood cell walls, (2) some detached pericytes develop into myofibroblasts which alter the extracellular matrix (3) some detached pericytes develop into mesenchymal stem cells, (4) some of the mesenchymal stem cells adhere to the altered extracellular matrix (5) the altered extracellular matrix disrupts regulatory controls, causing the adjacent mesenchymal stem cells to develop into tumors. Results from experimental studies support the detached pericyte hypothesis. If the detached pericyte hypothesis is correct, pericytes should play a key role in metastasis - a testable prediction. Recent experimental results confirm this prediction and motivate a proposed experiment to partially test the detached pericyte hypothesis. If the detached pericyte hypothesis is correct, it could lead to new strategies for cancer prevention.
    MeSH term(s) Animals ; Carcinogenesis ; Mesenchymal Stem Cells ; Mice ; Mice, Transgenic ; Myofibroblasts ; Pericytes
    Language English
    Publishing date 2020-06-30
    Publishing country United States
    Document type Journal Article
    ZDB-ID 193145-3
    ISSN 1532-2777 ; 0306-9877
    ISSN (online) 1532-2777
    ISSN 0306-9877
    DOI 10.1016/j.mehy.2020.110056
    Database MEDical Literature Analysis and Retrieval System OnLINE

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