The effects of nonignorable missing data on label-free mass spectrometry proteomics experiments

An idealized version of a label-free discovery mass spectrometry proteomics experiment would provide absolute abundance measurements for a whole proteome, across varying conditions. Unfortunately, this ideal is not realized. Measurements are made on peptides requiring an inferential step to obtain protein level estimates. The inference is complicated by experimental factors that necessitate relative abundance estimation and result in widespread non-ignorable missing data. Relative abundance on the log scale takes the form of parameter contrasts. In a complete-case analysis, contrast estimates may be biased by missing data and a substantial amount of useful information will often go unused. To avoid problems with missing data, many analysts have turned to single imputation solutions. Unfortunately, these methods often create further difficulties by hiding inestimable contrasts, preventing the recovery of interblock information and failing to account for imputation uncertainty. To mitigate many of the problems caused by missing values, we propose the use of a Bayesian selection model. Our model is tested on simulated data, real data with simulated missing values, and on a ground truth dilution experiment where all of the true relative changes are known. The analysis suggests that our model, compared with various imputation strategies and complete-case analyses, can increase accuracy and provide substantial improvements to interval coverage.

Row versus column correlations: avoiding the ecological fallacy in RNA/protein expression studies

Biomedical researchers are often interested in computing the correlation between RNA and protein abundance. However, correlations can be computed between rows of a data matrix or between columns, and the results are not the same. The belief that these two types of correlation are estimating the same phenomenon is a special case of a well-known logical error called the ecological fallacy. In this article, we review different uses of correlation found in the literature, explain the differences between row and column correlations and argue that one of them has an undesirable interpretation in most applications. Through simulation studies and theoretical derivations, we show that the commonly used Pearson's coefficient, computed from protein and transcript data from a single sample, is only loosely related to the biological correlation that most researchers will be interested in studying. Beyond our basic exploration of the ecological fallacy, we examine how correlations are affected by relative quantification proteomics data and common normalization procedures, finding that double normalization is capable of completely masking true correlative relationships. We conclude with guidelines for properly identifying and computing consistent correlation coefficients.

Accelerating high-dimensional clustering with lossless data reduction

MOTIVATION

For cluster analysis, high-dimensional data are associated with instability, decreased classification accuracy and high-computational burden. The latter challenge can be eliminated as a serious concern. For applications where dimension reduction techniques are not implemented, we propose a temporary transformation which accelerates computations with no loss of information. The algorithm can be applied for any statistical procedure depending only on Euclidean distances and can be implemented sequentially to enable analyses of data that would otherwise exceed memory limitations.

RESULTS

The method is easily implemented in common statistical software as a standard pre-processing step. The benefit of our algorithm grows with the dimensionality of the problem and the complexity of the analysis. Consequently, our simple algorithm not only decreases the computation time for routine analyses, it opens the door to performing calculations that may have otherwise been too burdensome to attempt.

AVAILABILITY AND IMPLEMENTATION

R, Matlab and SAS/IML code for implementing lossless data reduction is freely available in the Appendix.

CONTACT

obrienj@hms.harvard.edu.

Divergent Specificity Development of IgG1 and IgG4 Autoantibodies in Endemic Pemphigus Foliaceus (Fogo Selvagem)

We have shown that although the IgG response in fogo selvagem (FS) is mainly restricted to desmoglein (Dsg) 1, other keratinocyte cadherins are also targeted by FS patients and healthy control subjects living in the endemic region of Limão Verde, Brazil (endemic controls). Evaluating nonpathogenic IgG1 and pathogenic IgG4 subclass responses to desmosomal proteins may reveal important differences between pathogenic and nonpathogenic responses, and how these differences relate to the pathogenic IgG4 response and resultant FS. In this study, we tested by ELISA >100 sera from each FS patient, endemic control, and nonendemic control for IgG1 and IgG4 autoantibodies to keratinocyte cadherins besides Dsg1. IgG1 and IgG4 subclass responses in endemic controls are highly correlated between Dsg1 and other keratinocyte cadherins. This correlation persists in the IgG1 response among FS patients, but diminishes in IgG4 response, suggesting that IgG1 binds highly conserved linear epitopes among cadherins, whereas IgG4 binds mainly specific conformational epitopes on Dsg1. A confirmatory test comparing serum samples of 11 individuals before and after their FS onset substantiated our findings that IgG1 recognizes primarily linear epitopes on Dsg1 both before and after disease onset, whereas IgG4 recognizes primarily linear epitopes before disease onset, but recognizes more conformational epitopes on Dsg1 after the onset of disease. This study may provide a mechanism by which a specificity convergence of the IgG4 response to unique Dsg1 epitopes, most likely conformational pathogenic epitopes, leads to the onset of FS disease.

Two-year clinical outcomes of de-intensified chemoradiotherapy for low-risk HPV-associated oropharyngeal squamous cell carcinoma

6044

Background: We here-in report 2 year cancer control outcomes from a prospective phase II clinical trial evaluating de-intensified chemoradiotherapy (CRT) for patients with favorable risk, HPV-associated oropharyngeal squamous cell carcinoma (OPSCC). Methods: The major inclusion criteria were: T0-T3, N0-N2c, M0, HPV or p16 positive, and minimal smoking history. Treatment was limited to 60 Gy intensity modulated radiotherapy with concurrent weekly intravenous cisplatin (30 mg/m2). Patients neither received induction chemotherapy nor definitive surgery. The primary study endpoint was pathologic complete response rate (pCR) based on required biopsy of the primary site and dissection of pretreatment positive lymph node regions, regardless of radiographic response. Secondary endpoint measures included 2 year local control (LC), regional control (RC), cause specific survival (CSS), distant metastasis free survival (DMFS), and overall survival (OS), and patient reported symptoms (PRO-CTCAE) and quality of life (EORTC QLQ-C30 & H&N35). Results: Forty-four patients enrolled and the median f/u was 36 months (range 5-53 months, 93% with > / = 1 year, 88% > / = 2 years). We have previously reported the pCR to be ~ 86%. Two year LC, RC, CSS, DMFS, and OS are the following: 100%, 100%, 100%, 100%, and 95%. All 6 patients who had pathological partial responses are alive with no evidence of disease with a median f/u of 34 months (range 9-48 months). Two patients have died (stroke and glioblastoma). Mean pre and 2-year post EORTC QOL scores were: Global 80/82 (lower worse), Swallowing 11/10 (higher worse), Dry Mouth 16/54, and Sticky Saliva 6/33. 39% of patients required a feeding tube (none permanent) for a median of 15 weeks (5 - 22 weeks). Mean pre and 2 year post PRO-CTCAE (1 to 4 scale, higher worse) scores were: Swallowing 0.4/0.8 and Dry mouth 0.4/1.8. There were no > / = Grade 3 late adverse events. Conclusions: The 2-year clinical outcomes with decreased intensity of therapy with 60 Gy of IMRT and weekly low-dose cisplatin are excellent in favorable risk OPSCC with evidence of better preservation of quality of life as compared to standard therapies. Clinical trial information: NCT01530997 .

Comparison of subject-specific and population averaged models for count data from cluster-unit intervention trials

Maximum likelihood estimation techniques for subject-specific (SS) generalized linear mixed models and generalized estimating equations for marginal or population-averaged (PA) models are often used for the analysis of cluster-unit intervention trials. Although both classes of procedures account for the presence of within-cluster correlations, the interpretations of fixed effects including intervention effect parameters differ in SS and PA models. Furthermore, closed-form mathematical expressions relating SS and PA parameters from the two respective approaches are generally lacking. This paper investigates the special case of correlated Poisson responses where, for a log-linear model with normal random effects, exact relationships are available. Equivalent PA model representations of two SS models commonly used in the analysis of nested cross-sectional cluster trials with count data are derived. The mathematical results are illustrated with count data from a large non-randomized cluster trial to reduce underage drinking. Knowledge of relationships among parameters in the respective mean and covariance models is essential to understanding empirical comparisons of the two approaches.

QuantFusion: Novel Unified Methodology for Enhanced Coverage and Precision in Quantifying Global Proteomic Changes in Whole Tissues

Single quantitative platforms such as label-based or label-free quantitation (LFQ) present compromises in accuracy, precision, protein sequence coverage, and speed of quantifiable proteomic measurements. To maximize the quantitative precision and the number of quantifiable proteins or the quantifiable coverage of tissue proteomes, we have developed a unified approach, termed QuantFusion, that combines the quantitative ratios of all peptides measured by both LFQ and label-based methodologies. Here, we demonstrate the use of QuantFusion in determining the proteins differentially expressed in a pair of patient-derived tumor xenografts (PDXs) representing two major breast cancer (BC) subtypes, basal and luminal. Label-based in-spectra quantitative peptides derived from amino acid-coded tagging (AACT, also known as SILAC) of a non-malignant mammary cell line were uniformly added to each xenograft with a constant predefined ratio, from which Ratio-of-Ratio estimates were obtained for the label-free peptides paired with AACT peptides in each PDX tumor. A mixed model statistical analysis was used to determine global differential protein expression by combining complementary quantifiable peptide ratios measured by LFQ and Ratio-of-Ratios, respectively. With minimum number of replicates required for obtaining the statistically significant ratios, QuantFusion uses the distinct mechanisms to "rescue" the missing data inherent to both LFQ and label-based quantitation. Combined quantifiable peptide data from both quantitative schemes increased the overall number of peptide level measurements and protein level estimates. In our analysis of the PDX tumor proteomes, QuantFusion increased the number of distinct peptide ratios by 65%, representing differentially expressed proteins between the BC subtypes. This quantifiable coverage improvement, in turn, not only increased the number of measurable protein fold-changes by 8% but also increased the average precision of quantitative estimates by 181% so that some BC subtypically expressed proteins were rescued by QuantFusion. Thus, incorporating data from multiple quantitative approaches while accounting for measurement variability at both the peptide and global protein levels make QuantFusion unique for obtaining increased coverage and quantitative precision for tissue proteomes.

Abstract 1999: Proteogenomic characterization of breast cancer sub-types in patient derived xenografts

The goal of this talk is to introduce an integrated quantitative proteogenomic approach to comprehensively map proteomic information back to their encoding genes. We seek evidence from mass spectrometry-based large-scale proteomic data of patient populations in conjunction with patient-centric next-generation sequencing data and unbiased sequencing strategies to study breast cancer (BC) subtypes from a genomic context.

We have obtained global and phosphoproteomic data with matching next generation sequencing data for 18 patient-derived xenografts (PDXs) representing the major clinical subtypes of BC. Our workflow starts with the creation of several protein sequence databases that serve as a template for mass spectrometry database identifications. These databases include 1) completely annotated reference protein sequences, 2) patient-specific databases that were created using next generation sequencing data, 3) isoform databases that contain all possible splicing combinations, and 4) amino acid sequence database resulting from a six-frame translation of the entire human reference and customized genomes. All mass spectrometry raw data are searched against the databases for obtaining identifications at the peptide level, and assembly of peptides for quantification using taxonomy-based label-free quantitation (LFQ) that can specifically quantify unique human peptide sequences found in PDXs. The peptides are then mapped to the human genome and visualized using a genome browser. Quantitative changes across PDXs are presented at the protein level or at the isoform level via peptide role-up to specific exons and visualized as a quantitative data track.

By combining search results from these databases we obtain a comprehensive view of our PDXs. The complementary nature of the databases enable greater proteomic depth, i.e. databases with complete splicing combinations capture proteomic evidence when patient-specific databases fail due to possible erroneous RNA-seq reads. Similarly, 6-frame translated amino acid databases can capture potentially novel coding regions but are unable to detect splicing. Peptide maps are obtained for individual genes or specific protein isoforms covering both knowledge-driven and novel genomic annotation types. We compile peptides carrying variants, splice junctions, fusions, and new coding regions specific to each PDX or in common with a specific BC subtype. Majority of data is mapped back to the genome loci using unmodified peptides via global proteomics while phosphopeptides that contain variants and splicing are also mapped in a similar manner using phosphoproteomic data.

We have currently annotated 455 novel proteogenomic hits covering many examples outlined above for genes related to breast cancer and show how these can be specifically identified and in some instances differentially quantified in the PDX models.

Citation Format: Harsha P. Gunawardena, John A. Wrobel, Jonathon O'Brien, Ling Xie, Petra Erdmann-Gilmore, Sherri R. Davies, Shunqiang Li, Song Cao, Michael McLellan, Kelly V. Ruggles, David Fenyo, R. Reid Townsend, Li Ding, Bahjat F. Qaqish, Matthew J. Ellis, Xian Chen. Proteogenomic characterization of breast cancer sub-types in patient derived xenografts. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1999. doi:10.1158/1538-7445.AM2015-1999

E-cadherin autoantibody profile in patients with pemphigus vulgaris

BACKGROUND

Pemphigus vulgaris (PV) is an autoimmune skin blistering disease. The main targets of autoantibodies are the desmosomal proteins desmoglein (Dsg)3 and Dsg1. Anti-E-cadherin antibody is the second most frequent antibody found in pemphigus foliaceus (fogo selvagem), but the frequency in PV is unknown.

OBJECTIVES

To determine the anti-E-cadherin antibody profile in the two major subtypes of PV: mucosal PV (mPV) and mucocutaneous PV (mcPV).

METHODS

Sera from 80 patients with PV and 80 controls were tested. Patients with PV were subdivided into mPV (n = 18) and mcPV (n = 62). Samples were tested by E-cadherin, Dsg1 and Dsg3 enzyme-linked immunosorbent assays (ELISAs), and immunoprecipitation coupled with Western blotting (IP-WB).

RESULTS

Both mPV and mcPV sera have antibodies against E-cadherin as demonstrated by ELISA and IP-WB. Both subtypes of PV have low levels of anti-E-cadherin antibodies, but significantly higher levels than healthy controls by ELISA (P < 0·0001). No difference exists in antibody levels between subgroups (P = 0·82). By IP-WB, 78% of mcPV sera reacted to E-cadherin, vs. 33% of mPV sera tested. Correlation analysis suggests a moderate correlation between anti-E-cadherin antibodies and Dsg1 antibodies (average r = 0·61), but no correlation with Dsg3 antibodies (average r = 0·19). Patients with mPV can have lower levels of Dsg1 antibodies compared with controls by ELISA (P < 0·0001). A few mPV sera also reacted to Dsg1 protein by IP-WB (17%).

CONCLUSIONS

Anti-E-cadherin antibodies are present in both major subtypes of PV. A moderate correlation exists between E-cadherin and Dsg1 antibodies. Patients with mPV can have low levels of both E-cadherin and Dsg1 antibodies.

ORTH: R and SAS software for regression models of correlated binary data based on orthogonalized residuals and alternating logistic regressions

This article describes a new software for modeling correlated binary data based on orthogonalized residuals, a recently developed estimating equations approach that includes, as a special case, alternating logistic regressions. The software is flexible with respect to fitting in that the user can choose estimating equations for association models based on alternating logistic regressions or orthogonalized residuals, the latter choice providing a non-diagonal working covariance matrix for second moment parameters providing potentially greater efficiency. Regression diagnostics based on this method are also implemented in the software. The mathematical background is briefly reviewed and the software is applied to medical data sets.

Phase II study of de-intensification of radiation and chemotherapy for low-risk HPV-related oropharyngeal squamous cell carcinoma

TPS6097

Background: The prognosis is excellent for low-risk human papillomavirus (HPV) associated oropharyngeal squamous cell carcinoma (OPSCC). Current standard chemoradiotherapy (CRT) regimens cure most patients but cause significant acute (mucositis) and long-term toxicities (xerostomia and dysphagia). Toxicity is primarily determined by the dose of radiotherapy and the intensity of chemotherapy. The aim of this study is to evaluate the pathological complete response (pCR) rate of low-risk HPV-associated OPSCC after de-intensified CRT. Methods: The major inclusion criteria are: 1) T0-T3, N0-N2c, M0, 2) HPV or p16 positive, and 3) </= 10 pack-years smoking history. Patients receive 60 Gy of intensity modulated radiotherapy (IMRT) with concurrent weekly intravenous cisplatinum (30 mg/m2). CT scans are obtained 4 to 8 weeks after completion of CRT to assess response. All patients have a surgical resection of any clinically apparent residual primary tumor or biopsy of the primary site if there is no evidence of residual tumor and a selective neck dissection to encompass at least those nodal level(s) that were positive pre-treatment, within 4 to 14 weeks after CRT. Longitudinal assessments of quality of life (EORTC QLQ-C30 & H&N35, NDII), patient reported outcomes (PRO-CTCAE, EAT-10), and swallowing evaluations (modified barium swallow) are obtained prior to, during, and after CRT. The primary endpoint of this study is the rate of pCR after CRT. The null hypothesis is that the pCR rate for de-intensified CRT is at least 87%, the historical rate (based on the reported 3-year local regional control rate of 87% in the RTOG 0129). Power computations were performed for N=40, with a type I error of 14.2% if the true pCR rate is 0.87. The study will be done in 3 stages with 15+15+10 patients with interim analyses at 15 and 30 patients. The trial will be stopped if the pCR rate is </= 9/15 and 21/30. The null hypothesis will be accepted if the pCR rate is >/= 33/40. Clinical trial information: NCT01530997.

Unanticipated hospital admissions in patients undergoing radiotherapy with or without concurrent chemotherapy: Incidence and predictive factors

114

Background: Unanticipated admissions are burdensome for patients and the healthcare system. An improved understanding of their frequency and predictive factors can inform initiatives to prevent such admissions and mitigate their associated human and financial costs. Methods: Electronic medical records of all patients (n=1144) undergoing external beam radiotherapy (RT) at our center in 2010 were reviewed in this retrospective study. Unanticipated admission within 90 days of initiating RT, and associated clinical factors, were recorded. Chi-squared and uni- and multivariate logistic regression was used to examine factors associated with admission. Results: Unanticipated admissions occurred in 19% (213/1144) of patients, median length of stay was 3 days (range 1-22), and the mean interval between the start of RT till admission was 28 days (1-89 days). The most common indications for admissions were pain (19% of admissions), GI toxicity (18%), and respiratory distress (15%). On univariate analysis, admission rates were higher in patients treated with palliative vs. curative intent (30% vs. 14%, p<0.001), with concurrent chemotherapy (23% vs. 18% RT alone, p=0.047), in those who had a recent admission prior to RT initiation (37% vs. 14% with no prior admission, p<0.001), and patients on their second or third course of RT (27% vs. 16% first treatment course, p<0.001). Multivariable analysis showed treatment intent, chemotherapy, and prior admissions to be associated with unplanned admissions (Table). Conclusions: Rates of unanticipated admissions are ≈20% in patients undergoing RT. Slightly less than 1/3 of patients receiving palliative RT, and nearly 1/4 receiving concurrent chemoradiation, experienced an unplanned admission. Prophylactic measures should be studied in these high-risk patients to reduce admission rates, as unplanned admission may be an important quality of care indicator in oncology. [Table: see text]

Deletion diagnostics for alternating logistic regressions

Deletion diagnostics are introduced for the regression analysis of clustered binary outcomes estimated with alternating logistic regressions, an implementation of generalized estimating equations (GEE) that estimates regression coefficients in a marginal mean model and in a model for the intracluster association given by the log odds ratio. The diagnostics are developed within an estimating equations framework that recasts the estimating functions for association parameters based upon conditional residuals into equivalent functions based upon marginal residuals. Extensions of earlier work on GEE diagnostics follow directly, including computational formulae for one-step deletion diagnostics that measure the influence of a cluster of observations on the estimated regression parameters and on the overall marginal mean or association model fit. The diagnostic formulae are evaluated with simulations studies and with an application concerning an assessment of factors associated with health maintenance visits in primary care medical practices. The application and the simulations demonstrate that the proposed cluster-deletion diagnostics for alternating logistic regressions are good approximations of their exact fully iterated counterparts.

Orthogonalized residuals for estimation of marginally specified association parameters in multivariate binary data

This paper focuses on marginal regression models for correlated binary responses when estimation of the association structure is of primary interest. A new estimating function approach based on orthogonalized residuals is proposed. A special case of the proposed procedure allows a new representation of the alternating logistic regressions method through marginal residuals. The connections between second-order generalized estimating equations, alternating logistic regressions, pseudo-likelihood and other methods are explored. Eficiency comparisons are presented, with emphasis on variable cluster size and on the role of higher-order assumptions. The new method is illustrated with an analysis of data on impaired pulmonary function.

IgG autoantibody response against keratinocyte cadherins in endemic pemphigus foliaceus (fogo selvagem)

It is well established that autoantibodies against desmoglein 3 and desmoglein 1 (Dsg1) are relevant in the pathogenesis of pemphigus vulgaris and pemphigus foliaceus, including its endemic form fogo selvagem (FS). Isolated reports have shown that in certain patients with these diseases, autoantibodies against other desmosomal cadherins and E-cadherin may also be present. The goal of this investigation was to determine whether FS patients and normal individuals living in endemic areas possess autoantibodies against other desmosomal cadherins and E-cadherin. By testing a large number of FS and endemic control sera by ELISA, we found a consistent and specific autoantibody response against Dsg1 and other keratinocyte cadherins in these individuals, which is quite different from healthy individuals from the United States (US controls). Overall, the highest correlations among the autoantibody responses tested were in the endemic controls, followed by FS patients, and lowest in the US controls. These findings suggest that multiple, perhaps cross-reactive, keratinocyte cadherins are recognized by FS patients and endemic controls.

Unanticipated hospital admissions in patients undergoing radiotherapy with or without concurrent chemotherapy: Incidence and predictive factors

6093

Background: Unanticipated admissions are burdensome for patients and the healthcare system. An improved understanding of their frequency and predictive factors can inform initiatives to prevent such admissions and mitigate their associated human and financial costs. Methods: Electronic medical records of 500 patients undergoing external beam radiotherapy (RT) at our center in 2010 were reviewed. Unanticipated admission within 90 days of initiating RT, and associated clinical factors, were recorded. Chi-squared and uni- and multivariate logistic regression was used to examine factors associated with admission. Results: Unanticipated admissions occurred in 20% (101/500) of patients, mean length of stay was 4 days (range 1-16), and the mean interval between the start of RT and admission was 32 days (0-86 days). The most common indications for admissions were pain (19% of admissions), respiratory distress (15%), and neurologic symptoms (13%). On univariable analysis, 33% of patients treated for palliative intent were admitted (vs. 16% of curative intent patients, p<0.001), as were 26% of patients receiving concurrent chemotherapy (vs. 17% receiving RT alone, p=0.02). Multivariable analysis showed treatment intent, chemotherapy, and marital status to be associated with unplanned admissions (Table). A highly variable rate of unanticipated admission per diagnosis was observed (e.g. 4% for breast, 19% for GI/GU/GYN/ENT, and 37% for metastatic sites). Conclusions: Rates of unanticipated admissions are ≈20% in patients undergoing RT. Approximately 1/3 of patients receiving palliative RT, and more than 1/4 receiving concurrent chemoradiation, experienced an unplanned admission. Prophylactic measures should be studied in these high-risk patients to reduce admission rates, as unplanned admission may be an important quality of care indicator in oncology. [Table: see text]

Validation of interobserver agreement in lung cancer assessment: hematoxylin-eosin diagnostic reproducibility for non-small cell lung cancer: the 2004 World Health Organization classification and therapeutically relevant subsets

CONTEXT

Precise subtype diagnosis of non-small cell lung carcinoma is increasingly relevant, based on the availability of subtype-specific therapies, such as bevacizumab and pemetrexed, and based on the subtype-specific prevalence of activating epidermal growth factor receptor mutations.

OBJECTIVES

To establish a baseline measure of interobserver reproducibility for non-small cell lung carcinoma diagnoses with hematoxylin-eosin for the current 2004 World Health Organization classification, to estimate interobserver reproducibility for the therapeutically relevant squamous/nonsquamous subsets, and to examine characteristics that improve interobserver reproducibility.

DESIGN

Primary, resected lung cancer specimens were converted to digital (virtual) slides. Based on a single hematoxylin-eosin virtual slide, pathologists were asked to assign a diagnosis using the 2004 World Health Organization classification. Kappa statistics were calculated for each pathologist-pair for each slide and were summarized by classification scheme, pulmonary pathology expertise, diagnostic confidence, and neoplastic grade.

RESULTS

The 12 pulmonary pathology experts and the 12 community pathologists each independently diagnosed 48 to 96 single hematoxylin-eosin digital slides derived from 96 cases of non-small cell lung carcinoma resection. Overall agreement improved with simplification from the comprehensive 44 World Health Organization diagnoses (κ  =  0.25) to their 10 major header subtypes (κ  =  0.48) and improved again with simplification into the therapeutically relevant squamous/nonsquamous dichotomy (κ  =  0.55). Multivariate analysis showed that higher diagnostic agreement was associated with better differentiation, better slide quality, higher diagnostic confidence, similar years of pathology experience, and pulmonary pathology expertise.

CONCLUSIONS

These data define the baseline diagnostic agreement for hematoxylin-eosin diagnosis of non-small cell lung carcinoma, allowing future studies to test for improved diagnostic agreement with reflex ancillary tests.

Group testing for case identification with correlated responses

This article examines group testing procedures where units within a group (or pool) may be correlated. The expected number of tests per unit (i.e., efficiency) of hierarchical- and matrix-based procedures is derived based on a class of models of exchangeable binary random variables. The effect on efficiency of the arrangement of correlated units within pools is then examined. In general, when correlated units are arranged in the same pool, the expected number of tests per unit decreases, sometimes substantially, relative to arrangements that ignore information about correlation.

Non-small cell lung cancer: prognostic importance of positive FDG PET findings in the mediastinum for patients with N0-N1 disease at pathologic analysis

PURPOSE

To assess the prognostic implications of mediastinal positron emission tomographic (PET) findings in patients undergoing curative resection of non-small cell lung cancer (NSCLC) who have histologically negative mediastinal lymph nodes (LNs), with the hypothesis that positive findings at PET are prognostic even in patients with negative histologic findings in the LNs.

MATERIALS AND METHODS

Records of patients with a preoperative PET undergoing curative surgery, without adjuvant radiation, for pathologic T1-3N0-1 NSCLC at the University of North Carolina between 2000 and 2006 were reviewed as an institutional review board-approved HIPAA-compliant retrospective study. Ninety patients were evaluable (all histologically negative in mediastinum; 44 with both mediastinoscopy and surgery); 13 patients had positive mediastinal PET findings, and 77 had negative mediastinal PET findings. Local-regional and distant failure rates in patients with and those without mediastinal abnormalities at preoperative PET were compared by using logistic regression and log-rank tests.

RESULTS

Median follow-up was 54.3 months (range, 1-99 months). There were higher rates of local-regional (P = .001) and distant (P < .001) failure as well as death (P = .001) in patients with postive PET findings than in patients with negative findings. In multivariable analysis (adjusting for other prognostic factors), positive PET findings in the mediastinum remained prognostic for distant failure (P < .001, hazard ratio = 6.9) and were marginally prognostic for local-regional failure (P = .093, hazard ratio = 1.9).

CONCLUSION

Positive findings at preoperative PET in the mediastinum appear to have prognostic implications despite the mediastinal LNs being histologically negative. The high rate of local-regional and distant failure suggests that postoperative radiation therapy and/or chemotherapy may be particularly helpful in patients with positive mediastinal findings at preoperative PET.

Large vestibular aqueduct syndrome: anatomic and functional parameters

OBJECTIVES/HYPOTHESIS

To correlate imaging and audiologic findings in patients with large vestibular aqueduct syndrome (LVAS).

STUDY DESIGN

Retrospective analysis.

METHODS

Thirty-eight patients with LVAS evident on magnetic resonance imaging with available clinical and audiometric data were selected from the databases of the study institution. Images were analyzed for endolymphatic sac and duct size, evidence of incomplete cochlear partitioning, and endolymphatic sac signal heterogeneity. The endolymphatic duct was measured in two different locations: near the vestibular aperture (ED(VA)) and at the midpoint between the common crus and the operculum (ED(MID)). Imaging data were correlated with audiologic variables.

RESULTS

There was significant correlation between ears for the audiologic and anatomic variables collected. Twenty-one (62%) patients had a fluctuating or progressive hearing loss, and 13 (38%) remained stable (four were not evaluable). At the time of the analysis, 41% of ears had a profound loss. Significant correlation was identified between the presence of endolymphatic signal heterogeneity and worse pure tone average (PTA). ED(VA) measures were significantly larger among ears with a progressive pattern of hearing loss when compared to those that were stable. Also, ED(VA) correlated with PTA and the presence of progressive hearing loss, but ED(MID) had no such a relationship.

CONCLUSIONS

Evidence of endolymphatic sac signal heterogeneity and larger measures of endolymphatic width when measured near the vestibule (ED(VA)) are markers of poorer hearing in these patients. By contrast, midpoint measures of the endolymphatic duct (ED(MID)) have no correlation with audiometric parameters.

An R2 statistic for fixed effects in the linear mixed model

Statisticians most often use the linear mixed model to analyze Gaussian longitudinal data. The value and familiarity of the R(2) statistic in the linear univariate model naturally creates great interest in extending it to the linear mixed model. We define and describe how to compute a model R(2) statistic for the linear mixed model by using only a single model. The proposed R(2) statistic measures multivariate association between the repeated outcomes and the fixed effects in the linear mixed model. The R(2) statistic arises as a 1-1 function of an appropriate F statistic for testing all fixed effects (except typically the intercept) in a full model. The statistic compares the full model with a null model with all fixed effects deleted (except typically the intercept) while retaining exactly the same covariance structure. Furthermore, the R(2) statistic leads immediately to a natural definition of a partial R(2) statistic. A mixed model in which ethnicity gives a very small p-value as a longitudinal predictor of blood pressure (BP) compellingly illustrates the value of the statistic. In sharp contrast to the extreme p-value, a very small R(2) , a measure of statistical and scientific importance, indicates that ethnicity has an almost negligible association with the repeated BP outcomes for the study.

Finite sample adjustments in estimating equations and covariance estimators for intracluster correlations

Bias-corrected covariance estimators are introduced in the context of an estimating equations approach for intracluster correlations among binary outcomes. Simulation study results show that the bias-corrected covariance estimators perform better than uncorrected sandwich estimators in terms of bias and coverage probabilities. Additionally, introduction of a matrix-based bias-correction into the estimating equations considerably improves point and interval estimation for the intracluster correlations. The methods are illustrated using data from a nested cross-sectional cluster trial on reducing underage drinking.

Development of an IgG4-based predictor of endemic pemphigus foliaceus (fogo selvagem)

Fogo selvagem (FS) is mediated by pathogenic, predominantly IgG4, anti-desmoglein 1 (Dsg1) autoantibodies and is endemic in Limao Verde, Brazil. IgG and IgG subclass autoantibodies were tested in a sample of 214 FS patients and 261 healthy controls by Dsg1 ELISA. For model selection, the sample was randomly divided into training (50%), validation (25%), and test (25%) sets. Using the training and validation sets, IgG4 was chosen as the best predictor of FS, with index values above 6.43 classified as FS. Using the test set, IgG4 has sensitivity of 92% (95% confidence interval (95% CI): 82-95%), specificity of 97% (95% CI: 89-100%), and area under the curve of 0.97 (95% CI: 0.94-1.00). The IgG4 positive predictive value (PPV) in Limao Verde (3% FS prevalence) was 49%. The sensitivity, specificity, and PPV of IgG anti-Dsg1 were 87, 91, and 23%, respectively. The IgG4-based classifier was validated by testing 11 FS patients before and after clinical disease and 60 Japanese pemphigus foliaceus patients. It classified 21 of 96 normal individuals from a Limao Verde cohort as having FS serology. On the basis of its PPV, half of the 21 individuals may currently have preclinical FS and could develop clinical disease in the future. Identifying individuals during preclinical FS will enhance our ability to identify the etiological agent(s) triggering FS.

The IgM anti-desmoglein 1 response distinguishes Brazilian pemphigus foliaceus (fogo selvagem) from other forms of pemphigus

Fogo selvagem (FS) and pemphigus foliaceus (PF) possess pathogenic IgG anti-desmoglein 1-(Dsg1) autoantibodies. Although PF occurs sporadically, FS is endemic in Limao Verde (LV), Brazil (3.4% prevalence). IgM anti-Dsg1 were detected in 58% FS LV patients (n=31), 19% of FS patients from Hospital-Campo Grande (n=57), 19% from Hospital-Goiania (n=42), 12% from Hospital-Sao Paulo (n=56), 10% of PF patients from United States (n=20), and 0% of PF patients from Japan (n=20). Pemphigus vulgaris (n=40, USA and Japan), bullous pemphigoid (n=40, USA), and healthy donors (n=55, USA) showed negligible percentages of positive sera. High percentages of positive IgM anti-Dsg1 were found in healthy donors from four rural Amerindian populations (42% of 243) as compared with urban donors (14% of 81; P<0.001). More than 50% of healthy donors from LV (n=99, age 5-20 years) possess IgM anti-Dsg1 across ages, whereas IgG-anti-Dsg1 was detected in 2.9% (age 5-10 years), 7.3% (age 11-15 years), and 29% of donors above age 16. IgM anti-Dsg1 epitopes are Ca2+ and carbohydrate-independent. We propose that IgM anti-Dsg1 are common in FS patients in their native environment and uncommon in other pemphigus phenotypes and in FS patients who migrate to urban hospitals. Recurrent environmental antigenic exposure may lead to IgM and IgG responses that trigger FS. JID JOURNAL CLUB ARTICLE: For questions, answers, and open discussion about this article please go to http://network.nature.com/group/jidclub.

Evidence-based target recall rates for screening mammography

PURPOSE

To retrospectively identify target recall rates for screening mammography on the basis of how sensitivity shifts with recall rate.

MATERIALS AND METHODS

The study group included 1 872 687 subsequent and 171 104 first screening mammograms from 1996 to 2001 from 172 and 139 facilities, respectively, in six sites of the Breast Cancer Surveillance Consortium. Institutional review board (IRB) approval was obtained from each site. Informed consent requirements of the IRBs were followed. The study was HIPAA compliant. Recall rate was defined as the percentage of screening studies for which further work-up was recommended by the radiologist. Sensitivity was defined as the proportion of cancers that were detected at screening mammography. Piecewise linear regression was used to model sensitivity as a function of recall rate. This model allows detection of critical recall rates in which significant changes (shifts) occurred in the rates that sensitivity increased with increasing recall rate. Rates were interpreted as number of additional work-ups per additional cancer detected (AW/ACD) or, in other words, the estimated number of additional women needed to be recalled at a given rate to detect one additional cancer.

RESULTS

For first mammograms, a single shift in the estimated AW/ACD rate occurred at a recall rate of 10.0%, with the rate jumping dramatically from 35 to 172. For subsequent mammograms, four shifts were identified. At a recall rate of 6.7%, the estimated AW/ACD increased from 80 to 132, which rendered it the highest desirable target recall rate. At a recall rate of 12.3%, the estimated AW/ACD was 304, which suggests little benefit for any higher recall rate.

CONCLUSION

Recall rates of 10.0% for first and 6.7% for subsequent mammograms are recommended targets on the basis of their AW/ACD rates (less than 100).

Computed Tomography Reflects Lower Airway Inflammation and Tracks Changes in Early Cystic Fibrosis

RATIONALE

Detecting and tracking early cystic fibrosis (CF) lung disease are difficult due to lack of sensitive markers of airway dysfunction.

OBJECTIVES

The goals were to detect regional distribution of airway disease through high-resolution computed tomography, correlate abnormalities to lower airway inflammation/infection, and compare computed tomography findings before and after intravenous antibiotic therapy in children with CF younger than 4 years experiencing a pulmonary exacerbation.

METHODS

High-resolution computed tomography was performed in 17 children scheduled for bronchoscopy. The radiologist identified the lobes with the "greatest" and "least" disease based on computed tomography, and bronchoalveolar lavage was performed in these areas. In 13 subjects, imaging was repeated after antibiotic completion. Modified Brody scores were assigned by two radiologists.

MEASUREMENTS AND MAIN RESULTS

The lobe with greatest disease was predominantly localized to the right and had higher modified Brody scores, indicating more severe abnormalities (p < 0.01), compared with the lobe with least disease. The total modified Brody score (p < 0.01), hyperinflation subscore (p < 0.01), and bronchial dilatation/bronchiectasis subscore (p < 0.01) improved after antibiotics and intensified airway clearance. Interleukin-8 levels (p < 0.01) and % neutrophils (p = 0.04) were increased in the lobe with greatest disease compared with the lobe with least disease.

CONCLUSIONS

These results indicate that, in young children with CF experiencing a pulmonary exacerbation, computed tomography detects regional differences in airway inflammation, may be a sensitive outcome to evaluate therapeutic interventions, and identifies early lung disease as being more prominent on the right.

Validation of the palliative performance scale in the acute tertiary care hospital setting

BACKGROUND

Physicians are often asked to prognosticate patient survival. However, prediction of survival is difficult, particularly with critically ill and dying patients within the hospitals. The Palliative Performance Scale (PPS) was designed to assess functional status and measure progressive decline in palliative care patients, yet it has not been validated within hospital health care settings.

OBJECTIVE

This study explores the application of the PPS for its predictive ability related to length of survival. Other variables examined were correlates of symptom distress in a tertiary academic setting.

METHODS

Patients were assigned a score on the PPS ranging from 0% to 100% at initial consultation. Standardized symptom assessments were carried out daily, and survival was determined by medical record review and search of the National Death Index.

RESULTS

Of 261 patients seen since January 2002, 157 had cancer and 104 had other diagnoses. PPS scores ranged from 10% to 80% with 92% of the scores between 10% and 40%. Survival ranged from 0 to 30 months, with a median of 9 days. By 90 days, 83% of patients had died. Proportional hazards regression estimates showed that a 10% decrement in PPS score was associated with a hazard ratio of 1.65 (95% confidence interval [CI]: 1.42-1.92). Proportional odds regression models showed that a lower PPS was significantly associated with higher levels of dyspnea.

CONCLUSION

The PPS correlated well with length of survival and with select symptom distress scores. We consider it to be a useful tool in predicting outcomes for palliative care patients.

A Comparison of Two Bias-Corrected Covariance Estimators for Generalized Estimating Equations

Mancl and DeRouen (2001, Biometrics57, 126-134) and Kauermann and Carroll (2001, JASA96, 1387-1398) proposed alternative bias-corrected covariance estimators for generalized estimating equations parameter estimates of regression models for marginal means. The finite sample properties of these estimators are compared to those of the uncorrected sandwich estimator that underestimates variances in small samples. Although the formula of Mancl and DeRouen generally overestimates variances, it often leads to coverage of 95% confidence intervals near the nominal level even in some situations with as few as 10 clusters. An explanation for these seemingly contradictory results is that the tendency to undercoverage resulting from the substantial variability of sandwich estimators counteracts the impact of overcorrecting the bias. However, these positive results do not generally hold; for small cluster sizes (e.g., <10) their estimator often results in overcoverage, and the bias-corrected covariance estimator of Kauermann and Carroll may be preferred. The methods are illustrated using data from a nested cross-sectional cluster intervention trial on reducing underage drinking.

Prevalence of Anti-Desmoglein-3 Antibodies in Endemic Regions of Fogo Selvagem in Brazil

Fogo selvagem (FS), the endemic form of pemphigus foliaceus (PF), is an autoimmune blistering disease characterized by autoantibodies against desmoglein 1. The Terena reservation of Limao Verde in Mato Grosso do Sul, Brazil, is a previously identified focus of disease. Autoantibodies against desmoglein 3 (Dsg3) have also been detected in sera from patients with FS. In an effort to further characterize the serological, geographical, and clinical epidemiology of the disease, we sought to determine the prevalence of anti-Dsg3 autoantibodies in sera from normal subjects living outside of and in an endemic area using an ELISA. Anti-Dsg3 antibodies were detected in 53 of 146 normal subjects from Limao Verde (36%), and in eight of 140 normal subjects from surrounding areas (6%). A significant trend was observed in the proportion of positive tests relative to distance from the endemic area (P < 0.001). Our seroepidemiological observations support the concept that the likely environmental trigger of the antibody response in FS is located in this endemic area, and that the population at risk to develop FS may also be at risk to develop an endemic form of pemphigus vulgaris as reported by our co-investigators from Brasilia.

The molecular portraits of breast tumors are conserved across microarray platforms

BACKGROUND

Validation of a novel gene expression signature in independent data sets is a critical step in the development of a clinically useful test for cancer patient risk-stratification. However, validation is often unconvincing because the size of the test set is typically small. To overcome this problem we used publicly available breast cancer gene expression data sets and a novel approach to data fusion, in order to validate a new breast tumor intrinsic list.

RESULTS

A 105-tumor training set containing 26 sample pairs was used to derive a new breast tumor intrinsic gene list. This intrinsic list contained 1300 genes and a proliferation signature that was not present in previous breast intrinsic gene sets. We tested this list as a survival predictor on a data set of 311 tumors compiled from three independent microarray studies that were fused into a single data set using Distance Weighted Discrimination. When the new intrinsic gene set was used to hierarchically cluster this combined test set, tumors were grouped into LumA, LumB, Basal-like, HER2+/ER-, and Normal Breast-like tumor subtypes that we demonstrated in previous datasets. These subtypes were associated with significant differences in Relapse-Free and Overall Survival. Multivariate Cox analysis of the combined test set showed that the intrinsic subtype classifications added significant prognostic information that was independent of standard clinical predictors. From the combined test set, we developed an objective and unchanging classifier based upon five intrinsic subtype mean expression profiles (i.e. centroids), which is designed for single sample predictions (SSP). The SSP approach was applied to two additional independent data sets and consistently predicted survival in both systemically treated and untreated patient groups.

CONCLUSION

This study validates the "breast tumor intrinsic" subtype classification as an objective means of tumor classification that should be translated into a clinical assay for further retrospective and prospective validation. In addition, our method of combining existing data sets can be used to robustly validate the potential clinical value of any new gene expression profile.

Continuous toxicity monitoring in phase II trials in oncology

The goal of a phase II trial in oncology is to evaluate the efficacy of a new therapy. The dose investigated in a phase II trial is usually an estimate of a maximum-tolerated dose obtained in a preceding phase I trial. Because this estimate is imprecise, stopping rules for toxicity are used in many phase II trials. We give recommendations on how to construct stopping rules to monitor toxicity continuously. A table is provided from which Pocock stopping boundaries can be easily obtained for a range of toxicity rates and sample sizes. Estimation of the probability of toxicity and response is also discussed.

A phase II trial of weekly paclitaxel and gemctiabine infused at a constant rate in patients with advanced non-small cell lung cancer

BACKGROUND

Gemcitabine and paclitaxel both have significant single agent activity in non-small cell lung cancer (NSCLC). Because both are cell cycle and phase specific in their mechanism of action, frequent exposure should optimize activity. Phase I data support that gemcitabine is maximally converted to the active metabolite when it is infused at a rate of 10 mg/(m2 min). Based on this, we designed a phase II trial to examine gemcitabine 800 mg/m2 infused over 80 min with paclitaxel 110 mg/m2 infused over 3 h both on days 1, 8 and 15 every 28 days as first line therapy in patients with advanced NSCLC. The primary objectives were to assess the response rate, toxicity and survival of the combination in advanced NSCLC. Secondary objectives were to determine the effect of paclitaxel on the pharmacokinetic (PK) distribution of gemcitabine, the ability to achieve a concentration of 10-20 microM when gemcitabine was infused at a rate of 10 mg/(m2 min), as well as to assess the quality of life (QOL) with the functional assessment of cancer therapy-lung (FACT-L) questionnaire.

METHODS

Patients with NSCLC, no prior treatment, ECOG performance status (PS) 0-1, adequate bone marrow, renal, and hepatic function were eligible for this trial. Paclitaxel 110 mg/m2 was infused over 3 h, followed by gemcitabine 800 mg/m2 infused over 80 min on days 1, 8, and 15 every 28 days for the first 2 patients, and then amended to days 1 and 8 every 21 days after the first 2 patients required day 15 dose omissions due to myelosupression.

RESULTS

Thirty-nine patients were treated. Nine PS = 0; 28 PS = 1; Stage IIIB = 3, Stage IV = 36; median age 62 (range: 39-77). A median of six cycles (range: 0-10) was delivered. Grade 3-4 toxicities observed in > or =10% of patients included leucopenia in 26%, neutropenia in 28%, dyspnea in 13%, febrile neutropenia in 3% (1 patient). Fourteen of 39 (35%, 95% CI: 21-53%) patients had a partial response (PR), 14 of 39 (35%, 95% CI: 21-53%) had stable disease (SD) and 5 patients (13%, 95% CI: 4-27%) had progressive (PD). Median survival was 10.4 months (95% CI: 5.3-13.6). One-and two-year survival rates were 35% (95% CI: 21-53%) and 5% (95% CI: 0.6-17%), respectively. QOL as measured by the FACT-L and the trial outcome index (TOI) did not change significantly from baseline over the course of therapy.

CONCLUSIONS

Paclitaxel and gemcitabine is an active and well-tolerated combination in advanced NSCLC. Patients on this trial had no significant change in their QOL as assessed by the FACT-L questionnaire.

Anti-Desmoglein-1 Antibodies in Onchocerciasis, Leishmaniasis and Chagas Disease Suggest a Possible Etiological Link to Fogo Selvagem

Pemphigus foliaceus (PF) and the endemic form Fogo Selvagem (FS) are mediated by pathogenic antibodies to the EC1-2 domains of desmoglein-1. There is a preclinical phase with antibodies to only EC5. Based on geographic clustering of cases, FS is thought to have an, as yet unidentified, environmental trigger. In this study we have searched for anti-desmoglein-1 antibodies in sera from parasitic (leishmaniasis, Chagas, and onchocerciasis), and infectious diseases (leprosy and South American (SA) blastomycosis), which are prevalent in the same geographic regions of Brazil as FS. A specific and sensitive desmoglein-1 ELISA detected antibodies in 34 of 41 onchocerciasis (83%), 38 of 88 leishmaniasis (43%), 18 of 31 Chagas disease (58%), 7 of 28 SA blastomycosis (25%), and 14 of 83 leprosy sera (17%). These sera recognized epitopes restricted to the EC5 domain. These findings identify several etiological factors for FS. It is hypothesized that a component of insect vector saliva, rather than the parasite itself may trigger an antibody response to EC-5. In persons with the known HLA susceptibility alleles and living in endemic areas, a response to the EC1-2 domains may subsequently develop by epitope spreading with associated clinical signs of FS.

The role of subclass switching in the pathogenesis of endemic pemphigus foliaceus

Endemic pemphigus foliaceus, like the sporadic form seen in the developed world, is mediated by IgG antibodies to desmoglein-1. We studied an endemic focus in Limao Verde, Brazil, where disease prevalence is 3.4%. We previously detected IgG antibodies to desmoglein-1 in 97% of patients, but also in 55% of normal subjects in the endemic focus, with progressively lower levels in normal subjects in surrounding areas. An environmental trigger is hypothesized to explain these and other findings. In this study we sought to determine if patients and enzyme-linked-immunosorbent-assay-positive normal subjects in Limao Verde differ in IgG subclass response to desmoglein-1. We developed a sensitive and specific subclass enzyme-linked immunosorbent assay using recombinant desmoglein-1 and standardized the assay to enable comparability between the four subclasses. We found that normal subjects have an IgG1 and IgG4 response, whereas patients have similar levels of IgG1 but a mean 19.3-fold higher IgG4 response. Patients in remission have a weak IgG4 response, and a 74.3-fold higher IgG4 response is associated with active disease. Finally, in five patients in whom we had blood samples from both before and after the onset of clinical disease, a mean 103.08-fold rise in IgG4 was associated with onset of clinical disease, but only a mean 3.45-fold rise in IgG1. These results suggest that the early antibody response in normal subjects living in the endemic area and in patients before the onset of clinical disease is mainly IgG1. Acquisition of an IgG4 response is a key step in the development of clinical disease.

Characteristics and quality of Papanicolaou smears obtained by primary care clinicians using a single commercial laboratory

BACKGROUND

Few data are available on factors associated with the quality of Papanicolaou smears performed in primary care.

OBJECTIVE

To identify the patterns and proficiency of cervical cancer screening among different primary care specialties.

MATERIALS AND METHODS

Clinical and cytologic data from 21,833 Papanicolaou smears, submitted to a single large commercial laboratory by 176 clinicians during a 7-month period, were correlated with individual clinician and specialty characteristics according to indexes of specimen quality.

RESULTS

Obstetrician-gynecologists, nurse practitioners, and physician assistants provided screening to a younger population of women compared with family physicians, internists, and general practitioners. Factors positively associated with a greater probability of a "satisfactory" smear or the presence of endocervical cells (as a marker of adequate sampling) were increasing patient age, use of the cytobrush, and the specialty of the obstetrician-gynecologist. Satisfactory smears were not associated with any increased identification of cytologic abnormalities compared with "limited" smears. In contrast, smears with endocervical cells showed a higher proportion of abnormalities compared with specimens without such cells.

CONCLUSIONS

Differences in the performance of obtaining Papanicolaou smears exist between primary care specialties, but need further clarification. The use of the cytobrush and the presence of endocervical cells are criteria that reflect clinician proficiency more realistically than the laboratory criterion of satisfactory smear.

Robust regression for clustered data with application to binary responses

Generalized estimating equations (GEE) can be highly influenced by the presence of unusual data points. A generalization of the GEE procedure, which yields parameter estimates and fitted values that are resistant to influential data, is introduced. Resistant generalized estimating equations (REGEE) include weights in the estimating equations to downweight influential observations or clusters. Influential observations are downweighted according to their leverage or residual in an example of correlated binary regression applied to 137 urinary incontinent elderly patients from 38 medical practices.

Recall and treatment decisions of primary care providers in response to Pap smear reports

INTRODUCTION

Although the frequency of cervical cancer screening has been extensively studied, little is known about how clinicians decide to screen or recall patients for Pap smears. This study reports the management decisions made by office-based clinicians for 10 different Pap smear reports describing adequacy limitations and cytological diagnoses.

METHODS

We surveyed 186 clinicians using a commercial laboratory in the southeastern United States and analyzed results by frequency and comparison statistics.

RESULTS

Our respondents were 148 clinicians (79.6% response rate) from different specialties. There was variation in reported management of inflammation, atypia, and low-grade abnormalities (LGSIL), in regard to recall for repeat or routine testing as well as arranging colposcopy. In only 3 of 10 Pap smear results did more than 50% of respondents agree on a specific test recall interval.

CONCLUSIONS

The variation in responses from office-based clinicians suggests either uncertainty or different opinions in making recall and treatment decisions for smears of limited quality even when associated with cytologic abnormalities. These differences may have relevance to outcomes, clinician workload, and costs of care in cervical cancer screening.

The effect of incarceration during pregnancy on birth outcomes

OBJECTIVE

This study examined the effect of incarceration during pregnancy on infant birth weight.

METHODS

North Carolina prison records were matched to North Carolina birth certificates and health services records to identify 94 women who were incarcerated during one pregnancy but not incarcerated during another pregnancy. Paired analyses examined differences between the pregnancies in terms of the women's characteristics and use of health services. A generalized estimating equations analysis modeled infant birth weight as a function of the number of days that a woman was incarcerated during pregnancy, accounting for the correlation between the birth weights of two infants born to the same mother and several potentially confounding variables.

RESULTS

Since the women were significantly more likely to have been incarcerated during the second of the pair of pregnancies, as a group they were significantly older and had more children at the time of the incarcerated pregnancy than at the time of the home pregnancy. After controlling for important covariates, a higher number of pregnancy days spent incarcerated was found to be associated with higher infant birth weight.

CONCLUSION

These findings suggest that aspects of the prison environment such as shelter and regular meals may enhance pregnancy outcomes among very high risk women. Health professionals should join others in efforts to assure that health-promoting resources such as adequate shelter, nutritional support, and substance abuse treatment programs are available to all pregnant women.

Perceptions and opinions on the performance of Pap smears: a survey of clinicians using a commercial laboratory

Office-based clinicians play a major role in cervical cancer screening in the United States, but little is known about their specific knowledge and understanding of the technical aspects of obtaining an adequate Pap smear. We surveyed 186 office-based clinicians using a major commercial laboratory for cytology services to obtain their opinions regarding the technical adequacy of Pap smears, collection procedures, and methods of communicating test results to patients. There was an 80.1% response rate. Two thirds of the respondents were men. Cytobrush use was reported significantly more by female clinicians. Respondents varied in reported rotation of the cytobrush, from 90 degrees to greater than 360 degrees. More female than male clinicians appropriately indicated that inflammation and heavy vaginal discharge caused sampling difficulties. Approximately half of the respondents believed that errors in cervical screening most often resulted from sampling the cervix or preparation of the Pap smear. Nineteen percent reported that ectocervical cells were not necessary for an adequate smear to be reported. Just over 25% of respondents indicated they did not report normal Pap smear results to the patient. The results indicate differences between clinicians by gender and specialty in reported knowledge, understanding, and technique in cervical cancer screening. The differences suggest that targeted education in this population may be important to improve the quality of cervical cancer screening. Medical Subject Headings (MeSH): screening; neoplasms, cervical; Papanicolaou smear; diagnosis, laboratory.

Concurrent radiation therapy and chemotherapy followed by esophagectomy for localized esophageal carcinoma

PURPOSE

A prospective study was performed to determine the outcome of patients with esophageal cancer who received preoperative radiation therapy and chemotherapy followed by esophagectomy, and to determine the role of preresection esophagogastroduodenoscopy (EGD) in predicting the patients in whom surgery could possibly be omitted, and the impact of surgery on survival.

MATERIALS AND METHODS

Thirty-five patients with localized carcinoma of the esophagus received concurrent external-beam radiotherapy and chemotherapy followed by esophagectomy. Patients received 45 Gy in 25 fractions. Chemotherapy consisted of continuous infusion fluorouracil (5-FU; 1,000 mg/m2/d) on days 1 through 4 and 29 through 32 and cisplatin (100 mg/m2) on day 1. Patients underwent an Ivor-Lewis esophagectomy 18 to 33 days after completion of radiotherapy.

RESULTS

Eighty percent of the patients had squamous cell carcinoma and 20% had adenocarcinoma. In addition, 51% had a pathologic complete response (CR). Twenty-two of the 35 underwent a preresection EGD before resection. Seventeen of the 22 (77%) had negative pathology from the preresection EGD, but seven of the 17 (41%) had residual tumor at surgery. The median survival and disease-free survival rates for all patients were 25.8 months and 32.8 months, respectively. Eighteen patients (51%) had no tumor at resection. The median survival for these patients was 36.8 months; the median disease-free survival time has not been reached. The median survival and disease-free survival rate for the patients with residual tumor in the surgical specimen were 12.9 months and 10.8 months, respectively.

CONCLUSION

Preresection EGD is not reliable for determining the presence of residual disease or the patients in whom surgery could be omitted. Twenty-five percent of the patients with residual tumor in the resected surgical specimen were long-term survivors; this suggests a benefit from esophagectomy after concurrent radiotherapy and chemotherapy.