An exact trend test for correlated binary data

A permutation-based approach for heterogeneous meta-analyses of rare events

The increasingly widespread use of meta-analysis has led to growing interest in meta-analytic methods for rare events and sparse data. Conventional approaches tend to perform very poorly in such settings. Recent work in this area has provided options for sparse data, but these are still often hampered when heterogeneity across the available studies differs based on treatment group. We propose a permutation-based approach based on conditional logistic regression that accommodates this common contingency, providing more reliable statistical tests when such patterns of heterogeneity are observed. We find that commonly used methods can yield highly inflated Type I error rates, low confidence interval coverage, and bias when events are rare and non-negligible heterogeneity is present. Our method often produces much lower Type I error rates and higher confidence interval coverage than traditional methods in these circumstances. We illustrate the utility of our method by comparing it to several other methods via a simulation study and analyzing an example data set, which assess the use of antibiotics to prevent acute rheumatic fever.

A statistical method for studying correlated rare events and their risk factors

Longitudinal studies of rare events such as cervical high-grade lesions or colorectal polyps that can recur often involve correlated binary data. Risk factor for these events cannot be reliably examined using conventional statistical methods. For example, logistic regression models that incorporate generalized estimating equations often fail to converge or provide inaccurate results when analyzing data of this type. Although exact methods have been reported, they are complex and computationally difficult. The current paper proposes a mathematically straightforward and easy-to-use two-step approach involving (i) an additive model to measure associations between a rare or uncommon correlated binary event and potential risk factors and (ii) a permutation test to estimate the statistical significance of these associations. Simulation studies showed that the proposed method reliably tests and accurately estimates the associations of exposure with correlated binary rare events. This method was then applied to a longitudinal study of human leukocyte antigen (HLA) genotype and risk of cervical high grade squamous intraepithelial lesions (HSIL) among HIV-infected and HIV-uninfected women. Results showed statistically significant associations of two HLA alleles among HIV-negative but not HIV-positive women, suggesting that immune status may modify the HLA and cervical HSIL association. Overall, the proposed method avoids model nonconvergence problems and provides a computationally simple, accurate, and powerful approach for the analysis of risk factor associations with rare/uncommon correlated binary events.

Alteraciones morfológicas de las vellosidades placentarias asociadas a malformaciones fetales múltiples del sistema esquelético

OBJETIVOS: describir y cuantificar alteraciones morfológicas en vellosidades placentarias de embarazadas cuyo feto desarrolló malformaciones esqueléticas múltiples. MÉTODOS: se analizaron cuatro placentas de abortos terapéuticos a las 13, 16, 20 y 38 semanas de gestación. Estas se compararon con placentas normales a la misma edad de gestación de abortos electivos por indicación médico legal. Tinción de hematoxilinaeosina se aplicó a 10 láminas de 5 regiones de cada placenta utilizando un protocolo con 4 variables cuantitativas: madurez, cambios fibrinoides, edema y fibrosis estromal y una variable cualitativa: trombosis. Los resultados cuantitativos se analizaron utilizando el análisis de varianza (ANAVAR) según arreglo completamente aleatorizado y el test de Tukey. Para la variable cualitativa se aplicó la prueba de tendencia para datos correlacionados. Se empleó el software statistix 8.0 y SAS 9.0 para Windows. RESULTADOS: existen diferencias significativas (p<0,05) entre las placentas asociadas a malformaciones múltiples del sistema esquelético y las placentas control en relación a las variables cuantitativas. No se encontraron diferencias significativas (p>0,05) en relación a la variable cualitativa. CONCLUSIONES: la población de vellosidades placentarias asociadas a malformaciones múltiples del sistema esquelético presentó un alto porcentaje de alteraciones indicando que la barrera placentaria está dañada afectando el intercambio de gases, nutrientes y metabolitos durante el desarrollo del feto.

Exact logistic models for nested binary data

The use of logistic models for independent binary data has relied first on asymptotic theory and later on exact distributions for small samples. However, the use of logistic models for dependent analysis based on exact analysis is not as common. Moreover, attention is usually given to one-stage clustering. In this paper, we extend the exact techniques to address hypothesis testing (estimation is not addressed) for data with second-stage and probably higher levels of clustering. The methods are demonstrated through a somewhat generic example using C+ + program.

Prevalence of posterior subcapsular cataracts in volunteer cytapheresis donors

BACKGROUND

Granulocyte donors routinely receive dexamethasone orally before donation. Steroids may increase the risk of posterior subcapsular cataract (PSC) formation.

STUDY DESIGN AND METHODS

We recruited 100 granulocyte donors (four or more granulocyte donations; any number of platelet [PLT] donations) and 100 age- and sex-matched PLT donors (zero to three granulocyte donations, any number of PLT donations) to examine the risk of PSC. PSC was assessed by a masked ophthalmologist and reading center lens photograph gradings or medical record documentation of PSC as the reason for cataract extraction.

RESULTS

Fourteen eyes of 10 granulocyte donors and five eyes of four PLT donors had PSCs (odds ratio [OR], 2.82; 95% confidence interval [CI], 0.83-9.61; p = 0.10). Risk of PSC increased with number of granulocyte donations: compared to zero to three donations (4.0%), the risk for four to nine, 10 to 19, and 20 or more donations was 8.6% (OR, 2.25; 95% CI, 0.31-13.99; p = 0.30), 9.5% (OR, 2.53; 95% CI, 0.44-14.20; p = 0.21), and 13.0% (OR, 3.60; 95% CI, 0.48-22.81; p = 0.11), respectively (p = 0.06 for trend).

CONCLUSION

We did not demonstrate a statistically significant increased risk of PSC associated with granulocyte donation. However, although this makes a large risk unlikely, we cannot rule out a small to moderate risk and there is biologic plausibility that the steroid administration associated with granulocyte donation could be associated with PSC formation. Transfusion medicine professionals should advise granulocyte apheresis donors to maintain an appropriate frequency of eye examinations.

Pregnancy outcome after treatment for Wilms tumor: a report from the national Wilms tumor long-term follow-up study

PURPOSE

This study was undertaken to evaluate the effect of prior treatment with radiation therapy or chemotherapy for unilateral Wilms tumor (WT) diagnosed during childhood on pregnancy complications, birth weight, and the frequency of congenital malformations in live-born offspring.

PATIENTS AND METHODS

We reviewed pregnancy outcomes among female survivors and partners of male survivors of WT treated on National Wilms Tumor Studies 1, 2, 3, and 4 by using a maternal questionnaire and a review of both maternal and offspring medical records.

RESULTS

We received reports of 1,021 pregnancies with duration of 20 weeks or longer, including 955 live-born singletons, for whom 700 sets of maternal and offspring medical records were reviewed. Rates of hypertension complicating pregnancy (International Classification of Diseases [ICD] code 642), early or threatened labor (ICD-644) and malposition of the fetus (ICD-652) increased with increasing radiation dose in female patients. The percentages of offspring weighing less than 2,500 g at birth and of those having less than 37 weeks of gestation also increased with dose. There was no significant trend with radiation dose in the number of congenital anomalies recorded in offspring of female patients.

CONCLUSION

Women who receive flank radiation therapy as part of the treatment for unilateral WT are at increased risk of hypertension complicating pregnancy, fetal malposition, and premature labor. The offspring of these women are at risk for low birth weight and premature (ie, < 37 weeks gestation) birth. These risks must be considered in the obstetrical management of female survivors of WT.

Accounting for within-patient correlation in assessing relative sensitivity of an adjunctive diagnostic test: application to lung cancer

We address the comparison of results between two diagnostic tests applied multiple times to the same subjects. The estimand of interest is the sensitivity of the combined test (primary and adjunct) relative to a primary test. Analytical methods are first described that assume independence between the multiple observations within a subject. In order to account for the within-subject correlation introduced by the multiple measurements, analytical approaches for correlated, categorical response data are described. In the discussion of these methods, we pay particular attention to the presence of a structural zero which results from the decision rule for the combination of diagnostic tests. In a simulation study, we compare the finite sample performances of all analytical approaches in terms of confidence interval coverage rates and median lengths. Our methods are cast in the context of a diagnostic bronchoscopy technology for the detection of lung cancer.

Vaccination with recombinant oncosphere antigens reduces the susceptibility of sheep to infection with Taenia multiceps

Taenia multiceps is a cestode parasite, the larval stage of which encysts in the brain of sheep, goats and cattle causing an often fatal condition. The parasite also causes zoonotic infections in humans. Homologues of the recombinant oncosphere vaccine antigens from Taenia ovis and other Taenia species were identified in T. multiceps. Sequencing of the associated T. multiceps genes and cloning of the encoding mRNA has revealed conserved features in the genes and proteins. The T. multiceps oncosphere proteins, designated Tm16 and Tm18, contain a predicted secretory signal and fibronectin type III domain. The recombinant Tm16 and Tm18 proteins were successfully expressed in Escherichia coli as fusion proteins with GST. The antigens, formulated with Quil A adjuvant, were tested in a vaccine trial in sheep. The antigens stimulated immunity in sheep against challenge infection with T. multiceps eggs. Five of nine control sheep died due to a challenge infection with T. multiceps whereas none of 20 vaccinated animals died as a result of the parasite challenge (P = 0.001). In addition, vaccination with the Tm16 protein, or Tm16 plus Tm18, induced significant protection against the number of parasites encysting in the brain as a result of the challenge infection (P = 0.023, P = 0.015, respectively). No clear relationship was apparent between the level of specific serum antibody in vaccinated animals and either the presence or absence of parasites or the number of parasites that occurred in some of the vaccinated animals. We believe this study is the first description of recombinant vaccine-related investigations for T. multiceps. The recombinant oncosphere antigens identified may allow development of effective vaccination strategies against T. multiceps infection in sheep. They raise the potential for the development of a combined vaccine with the Echinococcus granulosus EG95 antigen for prevention of T. multiceps as well as preventing the transmission of cystic hydatid disease.

An Exact Test for Detecting Inconsistency in Readers Interpretation Over Time in Screening Mammograms

Radiologists' interpretation on screening mammograms is measured by accuracy indices such as sensitivity and specificity. The hypothesis that radiologists' interpretation on screening mammograms is constant across time can be tested by measuring overdispersion. However, small sample sizes are problematic for the accuracy of asymptotic approaches. In this article, we propose an exact conditional distribution for testing overdispersion of the binomial assumption that is assumed for the accuracy indices. An exact p -value can be defined from the developed distribution. We also describe an algorithm for computing this exact test. This proposed method is applied to data from a study in reading screening mammograms in a population of US radiologists (Beam et al., 2003). The exact method is compared analytically with a currently available method based on large sample approximations.

Exact Tests for One Sample Correlated Binary Data

In this paper we developed exact tests for one sample correlated binary data whose cluster sizes are at most two. Although significant progress has been made in the development and implementation of the exact tests for uncorrelated data, exact tests for correlated data are rare. Lack of a tractable likelihood function has made it difficult to develop exact tests for correlated binary data. However, when cluster sizes of binary data are at most two, only three parameters are needed to characterize the problem. One parameter is fixed under the null hypothesis, while the other two parameters can be removed by both conditional and unconditional approaches, respectively, to construct exact tests. We compared the exact and asymptotic p-values in several cases. The proposed method is applied to real-life data.

Exact Analysis of Dose Response for Multiple Correlated Binary Outcomes

The neurotoxicity of a substance is often tested using animal bioassays. In the functional observational battery, animals are exposed to a test agent and multiple outcomes are recorded to assess toxicity, using approximately 40 animals measured on up to 30 different items. This design gives rise to a challenging statistical problem: a large number of outcomes for a small sample of subjects. We propose an exact test for multiple binary outcomes, under the assumption that the correlation among these items is equal. This test is based upon an exponential model described by Molenberghs and Ryan (1999, Environmetrics 10, 279-300) and extends the methods developed by Corcoran et al. (2001, Biometrics 57, 941-948) who developed an exact test for exchangeably correlated binary data for groups (clusters) of correlated observations. We present a method that computes an exact p-value testing for a joint dose-response relationship. An estimate of the parameter for dose response is also determined along with its 95% confidence bound. The method is illustrated using data from a neurotoxicity bioassay for the chemical perchlorethylene.

Design and analysis of group-randomized trials: a review of recent methodological developments

We review recent developments in the design and analysis of group-randomized trials (GRTs). Regarding design, we summarize developments in estimates of intraclass correlation, power analysis, matched designs, designs involving one group per condition, and designs in which individuals are randomized to receive treatments in groups. Regarding analysis, we summarize developments in marginal and conditional models, the sandwich estimator, model-based estimators, binary data, survival analysis, randomization tests, survey methods, latent variable methods and nonlinear mixed models, time series methods, global tests for multiple endpoints, mediation effects, missing data, trial reporting, and software. We encourage investigators who conduct GRTs to become familiar with these developments and to collaborate with methodologists who can strengthen the design and analysis of their trials.