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Article ; Online: Assigning readers to cases in imaging studies using balanced incomplete block designs.

Huang, Erich P / Shih, Joanna H

2021 Volume 30, Issue 10, Page(s) 2288–2312

Abstract: In many imaging studies, each case is reviewed by human readers and characterized according to one or more features. Often, the inter-reader agreement of the feature indications is of interest in addition to their diagnostic accuracy or association with ... ...

Abstract	In many imaging studies, each case is reviewed by human readers and characterized according to one or more features. Often, the inter-reader agreement of the feature indications is of interest in addition to their diagnostic accuracy or association with clinical outcomes. Complete designs in which all participating readers review all cases maximize efficiency and guarantee estimability of agreement metrics for all pairs of readers but often involve a heavy reading burden. Assigning readers to cases using balanced incomplete block designs substantially reduces reading burden by having each reader review only a subset of cases, while still maintaining estimability of inter-reader agreement for all pairs of readers. Methodology for data analysis and power and sample size calculations under balanced incomplete block designs is presented and applied to simulation studies and an actual example. Simulation studies results suggest that such designs may reduce reading burdens by >40% while in most scenarios incurring a <20% increase in the standard errors and a <8% and <20% reduction in power to detect between-modality differences in diagnostic accuracy and
MeSH term(s)	Humans ; Magnetic Resonance Imaging/methods ; Observer Variation ; Reproducibility of Results ; Sensitivity and Specificity
Language	English
Publishing date	2021-09-01
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	1136948-6
ISSN	1477-0334 ; 0962-2802
ISSN (online)	1477-0334
ISSN	0962-2802
DOI	10.1177/09622802211037074
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Article ; Online: An imputation approach for a time-to-event analysis subject to missing outcomes due to noncoverage in disease registries.

Shih, Joanna H / Albert, Paul S / Fine, Jason / Liu, Danping

Biostatistics (Oxford, England)

2022 Volume 25, Issue 1, Page(s) 117–133

Abstract: Disease incidence data in a national-based cohort study would ideally be obtained through a national disease registry. Unfortunately, no such registry currently exists in the United States. Instead, the results from individual state registries need to be ...

Abstract	Disease incidence data in a national-based cohort study would ideally be obtained through a national disease registry. Unfortunately, no such registry currently exists in the United States. Instead, the results from individual state registries need to be combined to ascertain certain disease diagnoses in the United States. The National Cancer Institute has initiated a program to assemble all state registries to provide a complete assessment of all cancers in the United States. Unfortunately, not all registries have agreed to participate. In this article, we develop an imputation-based approach that uses self-reported cancer diagnosis from longitudinally collected questionnaires to impute cancer incidence not covered by the combined registry. We propose a two-step procedure, where in the first step a mover-stayer model is used to impute a participant's registry coverage status when it is only reported at the time of the questionnaires given at 10-year intervals and the time of the last-alive vital status and death. In the second step, we propose a semiparametric working model, fit using an imputed coverage area sample identified from the mover-stayer model, to impute registry-based survival outcomes for participants in areas not covered by the registry. The simulation studies show the approach performs well as compared with alternative ad hoc approaches for dealing with this problem. We illustrate the methodology with an analysis that links the United States Radiologic Technologists study cohort with the combined registry that includes 32 of the 50 states.
MeSH term(s)	Humans ; United States/epidemiology ; Cohort Studies ; Registries ; Neoplasms/epidemiology ; Computer Simulation ; Incidence
Language	English
Publishing date	2022-12-09
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Intramural
ZDB-ID	2031500-4
ISSN	1468-4357 ; 1465-4644
ISSN (online)	1468-4357
ISSN	1465-4644
DOI	10.1093/biostatistics/kxac049
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Article ; Online: Absolute and relative risk estimation in the presence of outcome ascertainment gaps and competing risks.

Liu, Danping / Wu, Emily / Shih, Joanna H / Kitahara, Cari M / Cheung, Li C

Statistics in medicine

2023 Volume 42, Issue 8, Page(s) 1263–1276

Abstract: Incomplete coverage by cancer registries can lead to an underreporting of cancers and a resulting bias in risk estimates. When registries are defined by geographic region, gaps in observation can arise for individuals who reside outside of or migrate ... ...

Abstract	Incomplete coverage by cancer registries can lead to an underreporting of cancers and a resulting bias in risk estimates. When registries are defined by geographic region, gaps in observation can arise for individuals who reside outside of or migrate from the total registry catchment area. Moreover, the exact periods of non-observation for an individual may be unknown due to intermittent reporting of residential histories. The motivating example for this work is the U.S. Radiologic Technologist (USRT) study which ascertained cancer outcomes for a national cohort through 43 state/regional registries; similar gaps in outcome ascertainment can appear in other registry or electronic health record- based cohort studies. We propose a two-step procedure for estimating relative and absolute risk in these settings. First, using a mover stayer model fitted to individuals' known residential history, we obtain individual posterior probabilities of residing outside the registry catchment area each year. Second, we incorporate these probabilities in the survival data likelihood for competing risks to account for unobserved events. We assess the performance of the proposed method in extensive simulation studies. Compared to several simple alternative approaches, the proposed method reduces bias and improves efficiency. Finally, we apply the proposed method to a study of first primary lung cancers in the USRT cohort.
MeSH term(s)	Humans ; Risk ; Probability ; Computer Simulation ; Cohort Studies ; Neoplasms ; Registries
Language	English
Publishing date	2023-01-27
Publishing country	England
Document type	Journal Article
ZDB-ID	843037-8
ISSN	1097-0258 ; 0277-6715
ISSN (online)	1097-0258
ISSN	0277-6715
DOI	10.1002/sim.9668
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Article ; Online: Pearson's chi-square test and rank correlation inferences for clustered data.

Shih, Joanna H / Fay, Michael P

Biometrics

2017 Volume 73, Issue 3, Page(s) 822–834

Abstract: Pearson's chi-square test has been widely used in testing for association between two categorical responses. Spearman rank correlation and Kendall's tau are often used for measuring and testing association between two continuous or ordered categorical ... ...

Abstract	Pearson's chi-square test has been widely used in testing for association between two categorical responses. Spearman rank correlation and Kendall's tau are often used for measuring and testing association between two continuous or ordered categorical responses. However, the established statistical properties of these tests are only valid when each pair of responses are independent, where each sampling unit has only one pair of responses. When each sampling unit consists of a cluster of paired responses, the assumption of independent pairs is violated. In this article, we apply the within-cluster resampling technique to U-statistics to form new tests and rank-based correlation estimators for possibly tied clustered data. We develop large sample properties of the new proposed tests and estimators and evaluate their performance by simulations. The proposed methods are applied to a data set collected from a PET/CT imaging study for illustration.
Language	English
Publishing date	2017-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	213543-7
ISSN	1541-0420 ; 0099-4987 ; 0006-341X
ISSN (online)	1541-0420
ISSN	0099-4987 ; 0006-341X
DOI	10.1111/biom.12653
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Article ; Online: The Problems with the Kappa Statistic as a Metric of Interobserver Agreement on Lesion Detection Using a Third-reader Approach When Locations Are Not Prespecified.

Shih, Joanna H / Greer, Matthew D / Turkbey, Baris

Academic radiology

2018 Volume 25, Issue 10, Page(s) 1325–1332

Abstract: Rationale and objectives: To point out the problems with Cohen kappa statistic and to explore alternative metrics to determine interobserver agreement on lesion detection when locations are not prespecified.: Materials and methods: Use of kappa and ... ...

Abstract	Rationale and objectives: To point out the problems with Cohen kappa statistic and to explore alternative metrics to determine interobserver agreement on lesion detection when locations are not prespecified. Materials and methods: Use of kappa and two alternative methods, namely index of specific agreement (ISA) and modified kappa, for measuring interobserver agreement on the location of detected lesions are presented. These indices of agreement are illustrated by application to a retrospective multireader study in which nine readers detected and scored prostate cancer lesions in 163 consecutive patients (n = 110 cases, n = 53 controls) using the guideline of Prostate Imaging Reporting and Data System version 2 on multiparametric magnetic resonance imaging. Results: The proposed modified kappa, which properly corrects for the amount of agreement by chance, is shown to be approximately equivalent to the ISA. In the prostate cancer data, average kappa, modified kappa, and ISA equaled 30%, 55%, and 57%, respectively, for all lesions and 20%, 87%, and 87%, respectively, for index lesions. Conclusions: The application of kappa could result in a substantial downward bias in reader agreement on lesion detection when locations are not prespecified. ISA is recommended for assessment of reader agreement on lesion detection.
MeSH term(s)	Aged ; Humans ; Magnetic Resonance Imaging ; Male ; Middle Aged ; Observer Variation ; Predictive Value of Tests ; Prostatic Neoplasms/diagnostic imaging ; Prostatic Neoplasms/pathology ; Retrospective Studies
Language	English
Publishing date	2018-03-16
Publishing country	United States
Document type	Journal Article ; Multicenter Study
ZDB-ID	1355509-1
ISSN	1878-4046 ; 1076-6332
ISSN (online)	1878-4046
ISSN	1076-6332
DOI	10.1016/j.acra.2018.01.030
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Article: Rank correlation inferences for clustered data with small sample size.

Hunsberger, Sally / Long, Lori / Reese, Sarah E / Hong, Gloria H / Myles, Ian A / Zerbe, Christa S / Chetchotisakd, Pleonchan / Shih, Joanna H

Statistica Neerlandica

2022 Volume 76, Issue 3, Page(s) 309–330

Abstract: This paper develops methods to test for associations between two variables with clustered data using ... ...

Abstract	This paper develops methods to test for associations between two variables with clustered data using a
Language	English
Publishing date	2022-01-12
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1466958-4
ISSN	1467-9574 ; 0039-0402
ISSN (online)	1467-9574
ISSN	0039-0402
DOI	10.1111/stan.12261
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Article: Pearson's chiâsquare test and rank correlation inferences for clustered data

Shih, Joanna H / Michael P. Fay

Biometrics. 2017 Sept., v. 73, no. 3

2017

Abstract: Pearson's chiâsquare test has been widely used in testing for association between two categorical responses. Spearman rank correlation and Kendall's tau are often used for measuring and testing association between two continuous or ordered categorical ... ...

Abstract	Pearson's chiâsquare test has been widely used in testing for association between two categorical responses. Spearman rank correlation and Kendall's tau are often used for measuring and testing association between two continuous or ordered categorical responses. However, the established statistical properties of these tests are only valid when each pair of responses are independent, where each sampling unit has only one pair of responses. When each sampling unit consists of a cluster of paired responses, the assumption of independent pairs is violated. In this article, we apply the withinâcluster resampling technique to Uâstatistics to form new tests and rankâbased correlation estimators for possibly tied clustered data. We develop large sample properties of the new proposed tests and estimators and evaluate their performance by simulations. The proposed methods are applied to a data set collected from a PET/CT imaging study for illustration.
Keywords	biometry ; chi-square distribution ; data collection ; image analysis
Language	English
Dates of publication	2017-09
Size	p. 822-834.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	213543-7
ISSN	0099-4987 ; 0006-341X
ISSN	0099-4987 ; 0006-341X
DOI	10.1111/biom.12653
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Modelling batched Gaussian longitudinal weight data in mice subject to informative dropout.

Albert, Paul S / Shih, Joanna H

Statistical methods in medical research

2014 Volume 23, Issue 3, Page(s) 203–217

Abstract: Modelling longitudinal data subject to informative dropout is an active area in statistical research. This article focuses on modelling such longitudinal data when the outcome at each follow-up time is collected in batches rather than individually ... ...

Abstract	Modelling longitudinal data subject to informative dropout is an active area in statistical research. This article focuses on modelling such longitudinal data when the outcome at each follow-up time is collected in batches rather than individually collected. The problem occurred in a study that compared the weight of mice over time between a control and a treatment group, where animal weight was measured in batches of five animals per cage. We develop both a shared parameter and a pattern mixture modelling approach for accounting for potentially informative dropout due to an animal's death. Our methodology suggests that animals receiving the treatment have a lower weight in mid-life, and have a slower decline in weight in the later period of life. Our simulations suggest that both the shared random parameter and pattern mixture modelling approaches work well under a correctly specified model. However, the pattern mixture model is more robust against model misspecification than the shared random parameter model, but the shared random parameter model parameters have a more direct interpretation than those of the pattern mixture modelling approach.
MeSH term(s)	Animals ; Body Weight ; Data Interpretation, Statistical ; Death ; Longitudinal Studies ; Mice ; Models, Statistical ; Normal Distribution
Language	English
Publishing date	2014
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Intramural
ZDB-ID	1136948-6
ISSN	1477-0334 ; 0962-2802
ISSN (online)	1477-0334
ISSN	0962-2802
DOI	10.1177/0962280210397886
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Article ; Online: Weighted logrank tests for interval censored data when assessment times depend on treatment.

Fay, Michael P / Shih, Joanna H

Statistics in medicine

2012 Volume 31, Issue 28, Page(s) 3760–3772

Abstract: We consider weighted logrank tests for interval censored data when assessment times may depend on treatment, and for each individual, we only use the two assessment times that bracket the event of interest. It is known that treating finite right ... ...

Abstract	We consider weighted logrank tests for interval censored data when assessment times may depend on treatment, and for each individual, we only use the two assessment times that bracket the event of interest. It is known that treating finite right endpoints as observed events can substantially inflate the type I error rate under assessment-treatment dependence (ATD), but the validity of several other implementations of weighted logrank tests (score tests, permutation tests, multiple imputation tests) has not been studied in this situation. With a bounded number of unique assessment times, the score test under the grouped continuous model retains the type I error rate asymptotically under ATD; however, although the approximate permutation test based on the permutation central limit theorem is not asymptotically valid under every ATD scenario, we show through simulation that in many ATD scenarios, it retains the type I error rate better than the score test. We show a case where the approximate permutation test retains the type I error rate when the exact permutation test does not. We study and modify the multiple imputation logrank tests of Huang, Lee, and Yu (2008, Statistics in Medicine, 27: 3217-3226), showing that the distribution of the rank-like scores asymptotically does not depend on the assessment times. We show through simulations that our modifications of the multiple imputation logrank tests retain the type I error rate in all cases studied, even with ATD and a small number of individuals in each treatment group. Simulations were performed using the interval R package.
MeSH term(s)	Antineoplastic Agents, Alkylating/administration & dosage ; Antineoplastic Agents, Alkylating/therapeutic use ; Bias ; Biometry/methods ; Cluster Analysis ; Computer Simulation ; Data Interpretation, Statistical ; Endpoint Determination ; Humans ; Likelihood Functions ; Logistic Models ; Longitudinal Studies ; Models, Statistical ; Neoplasm Recurrence, Local/diagnosis ; Neoplasm Recurrence, Local/prevention & control ; Proportional Hazards Models ; Randomized Controlled Trials as Topic ; Survival Analysis ; Thiotepa/administration & dosage ; Thiotepa/therapeutic use ; Time Factors ; Urinary Bladder Neoplasms/diagnosis ; Urinary Bladder Neoplasms/drug therapy ; Urinary Bladder Neoplasms/surgery ; Veterans Health
Chemical Substances	Antineoplastic Agents, Alkylating ; Thiotepa (905Z5W3GKH)
Language	English
Publishing date	2012-07-11
Publishing country	England
Document type	Journal Article
ZDB-ID	843037-8
ISSN	1097-0258 ; 0277-6715
ISSN (online)	1097-0258
ISSN	0277-6715
DOI	10.1002/sim.5447
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Article ; Online: Prospective Evaluation of PI-RADS Version 2.1 for Prostate Cancer Detection and Investigation of Multiparametric MRI-derived Markers.

Yilmaz, Enis C / Shih, Joanna H / Belue, Mason J / Harmon, Stephanie A / Phelps, Tim E / Garcia, Charisse / Hazen, Lindsey A / Toubaji, Antoun / Merino, Maria J / Gurram, Sandeep / Choyke, Peter L / Wood, Bradford J / Pinto, Peter A / Turkbey, Baris

Radiology

2023 Volume 307, Issue 4, Page(s) e221309

Abstract: Background Data regarding the prospective performance of Prostate Imaging Reporting and Data System (PI-RADS) version 2.1 alone and in combination with quantitative MRI features for prostate cancer detection is limited. Purpose To assess lesion-based ... ...

Abstract	Background Data regarding the prospective performance of Prostate Imaging Reporting and Data System (PI-RADS) version 2.1 alone and in combination with quantitative MRI features for prostate cancer detection is limited. Purpose To assess lesion-based clinically significant prostate cancer (csPCa) rates in different PI-RADS version 2.1 categories and to identify MRI features that could improve csPCa detection. Materials and Methods This single-center prospective study included men with suspected or known prostate cancer who underwent multiparametric MRI and MRI/US-guided biopsy from April 2019 to December 2021. MRI scans were prospectively evaluated using PI-RADS version 2.1. Atypical transition zone (TZ) nodules were upgraded to category 3 if marked diffusion restriction was present. Lesions with an International Society of Urological Pathology (ISUP) grade of 2 or higher (range, 1-5) were considered csPCa. MRI features, including three-dimensional diameter, relative lesion volume (lesion volume divided by prostate volume), sphericity, and surface to volume ratio (SVR), were obtained from lesion contours delineated by the radiologist. Univariable and multivariable analyses were conducted at the lesion and participant levels to determine features associated with csPCa. Results In total, 454 men (median age, 67 years [IQR, 62-73 years]) with 838 lesions were included. The csPCa rates for lesions categorized as PI-RADS 1 (
MeSH term(s)	Male ; Humans ; Aged ; Prostatic Neoplasms/pathology ; Prostate/pathology ; Multiparametric Magnetic Resonance Imaging ; Magnetic Resonance Imaging/methods ; Prospective Studies ; Image-Guided Biopsy/methods ; Retrospective Studies
Language	English
Publishing date	2023-05-02
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	80324-8
ISSN	1527-1315 ; 0033-8419
ISSN (online)	1527-1315
ISSN	0033-8419
DOI	10.1148/radiol.221309
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