Reclassification of predictions for uncovering subgroup specific improvement.

Abstract:

:Risk prediction models play an important role in prevention and treatment of several diseases. Models that are in clinical use are often refined and improved. In many instances, the most efficient way to improve a successful model is to identify subgroups for which there is a specific biological rationale for improvement and tailor the improved model to individuals in these subgroups, an approach especially in line with personalized medicine. At present, we lack statistical tools to evaluate improvements targeted to specific subgroups. Here, we propose simple tools to fill this gap. First, we extend a recently proposed measure, the Integrated Discrimination Improvement, using a linear model with covariates representing the subgroups. Next, we develop graphical and numerical tools that compare reclassification of two models, focusing only on those subjects for whom the two models reclassify differently. We apply these approaches to BRCAPRO, a genetic risk prediction model for breast and ovarian cancer, using data from MD Anderson Cancer Center. We also conduct a simulation study to investigate properties of the new reclassification measure and compare it with currently used measures. Our results show that the proposed tools can successfully uncover subgroup specific model improvements.

journal_name

Stat Med

journal_title

Statistics in medicine

authors

Biswas S,Arun B,Parmigiani G

doi

10.1002/sim.6077

subject

Has Abstract

pub_date

2014-05-20 00:00:00

pages

1914-27

issue

11

eissn

0277-6715

issn

1097-0258

journal_volume

33

pub_type

杂志文章
  • Goodman and Kruskal's lambda: a new look at an old measure of association.

    abstract::We examine Goodman and Kruskal's lambda using Efron's approach to regression and analysis of variance (ANOVA) for zero-one outcome data. For a binary response cross-classified by a single nominal predictor, we present a computationally simple ANOVA table in which lambda is analogous to Pearson's R-square. We character...

    journal_title:Statistics in medicine

    pub_type: 杂志文章

    doi:10.1002/sim.4780080511

    authors: Makuch RW,Rosenberg PS,Scott G

    更新日期:1989-05-01 00:00:00

  • Comparisons of the performance of different statistical tests for time-to-event analysis with confounding factors: practical illustrations in kidney transplantation.

    abstract::Confounding factors are commonly encountered in observational studies. Several confounder-adjusted tests to compare survival between differently exposed subjects were proposed. However, only few studies have compared their performances regarding type I error rates, and no study exists evaluating their type II error ra...

    journal_title:Statistics in medicine

    pub_type: 杂志文章

    doi:10.1002/sim.6777

    authors: Le Borgne F,Giraudeau B,Querard AH,Giral M,Foucher Y

    更新日期:2016-03-30 00:00:00

  • The effects of measurement error in response variables and tests of association of explanatory variables in change models.

    abstract::Biomedical studies often measure variables with error. Examples in the literature include investigation of the association between the change in some outcome variable (blood pressure, cholesterol level etc.) and a set of explanatory variables (age, smoking status etc.). Typically, one fits linear regression models to ...

    journal_title:Statistics in medicine

    pub_type: 杂志文章

    doi:10.1002/(sici)1097-0258(19981130)17:22<2597::aid-s

    authors: Yanez ND 3rd,Kronmal RA,Shemanski LR

    更新日期:1998-11-30 00:00:00

  • Random models for margins of a 2 x 2 contingency table and application to pharmacovigilance.

    abstract::The identification of new adverse drug reactions is often tricky. For a given case, the relationship between drug exposure and symptom occurrence is usually questionable. It could be investigated statistically from a series of drug-event association cases with an independence test between the two variables. Analysing ...

    journal_title:Statistics in medicine

    pub_type: 杂志文章

    doi:10.1002/sim.4780100621

    authors: Tubert P,Begaud B

    更新日期:1991-06-01 00:00:00

  • Development and applications of a city-level alcohol availability and alcohol problems database.

    abstract::Data on alcohol availability and problems in all cities in Los Angeles County were collected from several different sources and linked together to form a Local Alcohol Availability Database (LAAD). The two major purposes of the project are to provide a city-level alcohol availability and alcohol-related problems datab...

    journal_title:Statistics in medicine

    pub_type: 杂志文章

    doi:10.1002/sim.4780140517

    authors: MacKinnon DP,Scribner R,Taft KA

    更新日期:1995-03-15 00:00:00

  • Association models for periodontal disease progression: a comparison of methods for clustered binary data.

    abstract::We investigate population-averaged (PA) and cluster-specific (CS) associations for clustered binary logistic regression in the context of a longitudinal clinical trial that investigated the association between tooth-specific visual elastase kit results and periodontal disease progression within 26 weeks of follow-up. ...

    journal_title:Statistics in medicine

    pub_type: 杂志文章

    doi:10.1002/sim.4780140407

    authors: Ten Have TR,Landis JR,Weaver SL

    更新日期:1995-02-28 00:00:00

  • An improved algorithm for outbreak detection in multiple surveillance systems.

    abstract::In England and Wales, a large-scale multiple statistical surveillance system for infectious disease outbreaks has been in operation for nearly two decades. This system uses a robust quasi-Poisson regression algorithm to identify abberrances in weekly counts of isolates reported to the Health Protection Agency. In this...

    journal_title:Statistics in medicine

    pub_type: 杂志文章

    doi:10.1002/sim.5595

    authors: Noufaily A,Enki DG,Farrington P,Garthwaite P,Andrews N,Charlett A

    更新日期:2013-03-30 00:00:00

  • Rank-based principal stratum sensitivity analyses.

    abstract::We describe rank-based approaches to assess principal stratification treatment effects in studies where the outcome of interest is only well-defined in a subgroup selected after randomization. Our methods are sensitivity analyses, in that estimands are identified by fixing a parameter and then we investigate the sensi...

    journal_title:Statistics in medicine

    pub_type: 杂志文章

    doi:10.1002/sim.5849

    authors: Lu X,Mehrotra DV,Shepherd BE

    更新日期:2013-11-20 00:00:00

  • A method to test for a recent increase in HIV-1 seroconversion incidence: results from the Multicenter AIDS Cohort Study (MACS).

    abstract::We have formulated the problem of determining whether there has been an upturn in HIV-1 seroconversion incidence over the first five years of follow-up in the Multicenter AIDS Cohort Study (MACS) as that of locating the minimum of a quadratic regression or examination of two-knot piecewise spline models. Under a quadr...

    journal_title:Statistics in medicine

    pub_type: 杂志文章,多中心研究

    doi:10.1002/sim.4780120207

    authors: Zhou SY,Kingsley LA,Taylor JM,Chmiel JS,He DY,Hoover DR

    更新日期:1993-01-30 00:00:00

  • Statistical inferences for a twin correlation with multinomial outcomes.

    abstract::Current methods for statistical analysis of twin studies focus on continuous and dichotomous data, while only limited methodology exists for analysing multinomial data. As a consequence, investigators are often tempted to collapse multinomial data into two categories simply to facilitate the analysis. We address this ...

    journal_title:Statistics in medicine

    pub_type: 杂志文章

    doi:10.1002/1097-0258(20010130)20:2<249::aid-sim641>3.

    authors: Bartfay E,Donner A

    更新日期:2001-01-30 00:00:00

  • Investigating the prediction ability of survival models based on both clinical and omics data: two case studies.

    abstract::In biomedical literature, numerous prediction models for clinical outcomes have been developed based either on clinical data or, more recently, on high-throughput molecular data (omics data). Prediction models based on both types of data, however, are less common, although some recent studies suggest that a suitable c...

    journal_title:Statistics in medicine

    pub_type: 杂志文章

    doi:10.1002/sim.6246

    authors: De Bin R,Sauerbrei W,Boulesteix AL

    更新日期:2014-12-30 00:00:00

  • Statistical models for longitudinal biomarkers of disease onset.

    abstract::We consider the analysis of serial biomarkers to screen and monitor individuals in a given population for onset of a specific disease of interest. The biomarker readings are subject to error. We survey some of the existing literature and concentrate on two recently proposed models. The first is a fully Bayesian hierar...

    journal_title:Statistics in medicine

    pub_type: 杂志文章

    doi:10.1002/(sici)1097-0258(20000229)19:4<617::aid-sim

    authors: Slate EH,Turnbull BW

    更新日期:2000-02-29 00:00:00

  • Four-fold table cell frequencies imputation in meta analysis.

    abstract::Meta analysis is a collection of quantitative methods devoted to combine summary information from related but independent studies. Because research reports usually present only data reductions and summary statistics rather than detailed data, the reviewer must often resort to rather crude methods for constructing summ...

    journal_title:Statistics in medicine

    pub_type: 杂志文章

    doi:10.1002/sim.2287

    authors: Di Pietrantonj C

    更新日期:2006-07-15 00:00:00

  • Sample size planning for survival prediction with focus on high-dimensional data.

    abstract::Sample size planning should reflect the primary objective of a trial. If the primary objective is prediction, the sample size determination should focus on prediction accuracy instead of power. We present formulas for the determination of training set sample size for survival prediction. Sample size is chosen to contr...

    journal_title:Statistics in medicine

    pub_type: 杂志文章

    doi:10.1002/sim.5550

    authors: Götte H,Zwiener I

    更新日期:2013-02-28 00:00:00

  • Bounding the bias of unmeasured factors with confounding and effect-modifying potentials.

    abstract::Confounding is a major concern in observational studies. To adjust for confounding bias, the potential confounder(s) for a study must first be identified and measured. But this is not always possible. The unmeasured factors may also exhibit effect modification, and this further complicates the situation. In this paper...

    journal_title:Statistics in medicine

    pub_type: 杂志文章

    doi:10.1002/sim.4151

    authors: Lee WC

    更新日期:2011-04-30 00:00:00

  • Designs for phase I trials in ordered groups.

    abstract::We propose a new design for dose finding for cytotoxic agents in two ordered groups of patients. By ordered groups, we mean that prior to the study there is clinical information that would indicate that for a given dose one group would be more susceptible to toxicities than patients in the other group. The designs are...

    journal_title:Statistics in medicine

    pub_type: 杂志文章

    doi:10.1002/sim.7133

    authors: Conaway MR,Wages NA

    更新日期:2017-01-30 00:00:00

  • Fast linear mixed model computations for genome-wide association studies with longitudinal data.

    abstract::Genome-wide association studies are characterized by a huge number of statistical tests performed to discover new disease-related genetic variants [in the form of single-nucleotide polymorphisms (SNPs)] in human DNA. Many SNPs have been identified for cross-sectionally measured phenotypes. However, there is a growing ...

    journal_title:Statistics in medicine

    pub_type: 杂志文章

    doi:10.1002/sim.5517

    authors: Sikorska K,Rivadeneira F,Groenen PJ,Hofman A,Uitterlinden AG,Eilers PH,Lesaffre E

    更新日期:2013-01-15 00:00:00

  • True verification probabilities should not be used in estimating the area under receiver operating characteristic curve.

    abstract::In medical research, a two-phase study is often used for the estimation of the area under the receiver operating characteristic curve (AUC) of a diagnostic test. However, such a design introduces verification bias. One of the methods to correct verification bias is inverse probability weighting (IPW). Since the probab...

    journal_title:Statistics in medicine

    pub_type: 杂志文章

    doi:10.1002/sim.8700

    authors: Wu Y

    更新日期:2020-11-30 00:00:00

  • Logistic regression with incompletely observed categorical covariates--investigating the sensitivity against violation of the missing at random assumption.

    abstract::Missing values in the covariates are a widespread complication in the statistical inference of regression models. The maximum likelihood principle requires specification of the distribution of the covariates, at least in part. For categorical covariates, log-linear models can be used. Additionally, the missing at rand...

    journal_title:Statistics in medicine

    pub_type: 杂志文章

    doi:10.1002/sim.4780141205

    authors: Vach W,Blettner M

    更新日期:1995-06-30 00:00:00

  • Combining individual and aggregated data to investigate the role of socioeconomic disparities on cancer burden in Italy.

    abstract::Quantifying socioeconomic disparities and understanding the roots of inequalities are growing topics in cancer research. However, socioeconomic differences are challenging to investigate mainly due to the lack of accurate data at individual-level, while aggregate indicators are only partially informative. We implement...

    journal_title:Statistics in medicine

    pub_type: 杂志文章

    doi:10.1002/sim.8392

    authors: Mezzetti M,Palli D,Dominici F

    更新日期:2020-01-15 00:00:00

  • Sample size calculation for stepped wedge and other longitudinal cluster randomised trials.

    abstract::The sample size required for a cluster randomised trial is inflated compared with an individually randomised trial because outcomes of participants from the same cluster are correlated. Sample size calculations for longitudinal cluster randomised trials (including stepped wedge trials) need to take account of at least...

    journal_title:Statistics in medicine

    pub_type: 杂志文章

    doi:10.1002/sim.7028

    authors: Hooper R,Teerenstra S,de Hoop E,Eldridge S

    更新日期:2016-11-20 00:00:00

  • Study control, violators, inclusion criteria and defining explanatory and pragmatic trials.

    abstract::Important differences between explanatory and pragmatic studies were originally argued by Schwartz and Lellouch. Three important differences between the two types of study involve study control, study violators and inclusion criteria. It was originally argued that explanatory studies are highly controlled, and pragmat...

    journal_title:Statistics in medicine

    pub_type: 杂志文章

    doi:10.1002/sim.1120

    authors: McMahon AD

    更新日期:2002-05-30 00:00:00

  • A standardization method to adjust for the effect of patient selection in phase II clinical trials.

    abstract::New combination regimens evaluated in phase II cancer clinical trials often show promising results compared to the standard therapy for a disease system. Selection of patients with a better prognosis can be a prominent factor for this optimism. For most disease systems, prognostic variables that are related to the out...

    journal_title:Statistics in medicine

    pub_type: 杂志文章

    doi:10.1002/sim.706

    authors: Mazumdar M,Fazzari M,Panageas KS

    更新日期:2001-03-30 00:00:00

  • Exact test size and power of a Gaussian error linear model for an internal pilot study.

    abstract::Wittes and Brittain recommended using an 'internal pilot study' to adjust sample size. The approach involves five steps in testing a general linear hypothesis for a general linear univariate model, with Gaussian errors. First, specify the design, hypothesis, desired test size, power, a smallest 'clinically meaningful'...

    journal_title:Statistics in medicine

    pub_type: 杂志文章

    doi:10.1002/(sici)1097-0258(19990530)18:10<1199::aid-s

    authors: Coffey CS,Muller KE

    更新日期:1999-05-30 00:00:00

  • A flexible, interpretable framework for assessing sensitivity to unmeasured confounding.

    abstract::When estimating causal effects, unmeasured confounding and model misspecification are both potential sources of bias. We propose a method to simultaneously address both issues in the form of a semi-parametric sensitivity analysis. In particular, our approach incorporates Bayesian Additive Regression Trees into a two-p...

    journal_title:Statistics in medicine

    pub_type: 杂志文章

    doi:10.1002/sim.6973

    authors: Dorie V,Harada M,Carnegie NB,Hill J

    更新日期:2016-09-10 00:00:00

  • Sample size calculation for clinical trials with correlated count measurements based on the negative binomial distribution.

    abstract::Statistical inference based on correlated count measurements are frequently performed in biomedical studies. Most of existing sample size calculation methods for count outcomes are developed under the Poisson model. Deviation from the Poisson assumption (equality of mean and variance) has been widely documented in pra...

    journal_title:Statistics in medicine

    pub_type: 杂志文章

    doi:10.1002/sim.8378

    authors: Li D,Zhang S,Cao J

    更新日期:2019-12-10 00:00:00

  • Flexible design clinical trial methodology in regulatory applications.

    abstract::Adaptive designs or flexible designs in a broader sense have increasingly been considered in planning pivotal registration clinical trials. Sample size reassessment design and adaptive selection design are two of such designs that appear in regulatory applications. At the design stage, consideration of sample size rea...

    journal_title:Statistics in medicine

    pub_type: 杂志文章

    doi:10.1002/sim.4021

    authors: Hung HM,Wang SJ,O'Neill R

    更新日期:2011-06-15 00:00:00

  • Accounting for competing risks in randomized controlled trials: a review and recommendations for improvement.

    abstract::In studies with survival or time-to-event outcomes, a competing risk is an event whose occurrence precludes the occurrence of the primary event of interest. Specialized statistical methods must be used to analyze survival data in the presence of competing risks. We conducted a review of randomized controlled trials wi...

    journal_title:Statistics in medicine

    pub_type: 杂志文章,评审

    doi:10.1002/sim.7215

    authors: Austin PC,Fine JP

    更新日期:2017-04-15 00:00:00

  • Selection of patients for randomized controlled trials: implications of wide or narrow eligibility criteria.

    abstract::This paper discusses the various philosophies that influence the selection of patients for entry into randomized controlled trials. Although a number of different and often competing issues have to be considered depending upon the trial, keeping entry criteria simple, wide and at times even flexible is usually prefera...

    journal_title:Statistics in medicine

    pub_type: 杂志文章

    doi:10.1002/sim.4780090114

    authors: Yusuf S,Held P,Teo KK,Toretsky ER

    更新日期:1990-01-01 00:00:00

  • Marker values at the time of an AIDS diagnosis.

    abstract::In this paper statistical methods are proposed to estimate the distribution of a CD4 T-cell number at the time of a clinical AIDS endpoint from serial measurements of CD4 T-cell values in a cohort study. The statistical formulation of the problem is that of survival analysis with interval censored data, but in which t...

    journal_title:Statistics in medicine

    pub_type: 杂志文章

    doi:10.1002/sim.4780131915

    authors: Taylor JM,Kim DK

    更新日期:1994-10-15 00:00:00