DiagTest3Grp: An R Package for Analyzing Diagnostic Tests with Three Ordinal Groups

Medical researchers endeavor to identify potentially useful biomarkers to develop markerbased screening assays for disease diagnosis and prevention. Useful summary measures which properly evaluate the discriminative ability of diagnostic markers are critical for this purpose. Literature and existing software, for example, R packages nicely cover summary measures for diagnostic markers used for the binary case (e.g., healthy vs. diseased). An intermediate population at an early disease stage usually exists between the healthy and the fully diseased population in many disease processes. Supporting utilities for threegroup diagnostic tests are highly desired and important for identifying patients at the early disease stage for timely treatments. However, application packages which provide summary measures for three ordinal groups are currently lacking. This paper focuses on two summary measures of diagnostic accuracy—volume under the receiver operating characteristic surface and the extended Youden index, with three diagnostic groups. We provide the R package DiagTest3Grp to estimate, under both parametric and nonparametric assumptions, the two summary measures and the associated variances, as well as the optimal cut-points for disease diagnosis. An omnibus test for multiple markers and a Wald test for two markers, on independent or paired samples, are incorporated to compare diagnostic accuracy across biomarkers. Sample size calculation under the normality assumption can be performed in the R package to design future diagnostic studies. A real world application evaluating the diagnostic accuracy of neuropsychological markers for Alzheimer’s disease is used to guide readers through step-by-step implementation of DiagTest3Grp to demonstrate its utility

Lipidome of mammographic breast density in premenopausal women

BACKGROUND: High mammographic breast density (MBD) is a strong risk factor for breast cancer development, but the biological mechanisms underlying MBD are unclear. Lipids play important roles in cell differentiation, and perturbations in lipid metabolism are implicated in cancer development. Nevertheless, no study has applied untargeted lipidomics to profile the lipidome of MBD. Through this study, our goal is to characterize the lipidome of MBD in premenopausal women. METHODS: Premenopausal women were recruited during their annual screening mammogram at the Washington University School of Medicine in St. Louis, MO. Untargeted lipidomic profiling for 982 lipid species was performed at Metabolon (Durham, NC®), and volumetric measures of MBD (volumetric percent density (VPD), dense volume (DV), and non-dense volume (NDV)) was assessed using Volpara 1.5 (Volpara Health®). We performed multivariable linear regression models to investigate the associations of lipid species with MBD and calculated the covariate-adjusted least square mean of MBD by quartiles of lipid species. MBD measures were log RESULTS: Of the 705 premenopausal women, 72% were non-Hispanic white, and 23% were non-Hispanic black. Mean age, and BMI were 46 years and 30 kg/m CONCLUSIONS: We report novel lipid species that are associated with MBD in premenopausal women. Studies are needed to validate our results and the translational potential

Estimating correlation between multivariate longitudinal data in the presence of heterogeneity

Abstract Background Estimating correlation coefficients among outcomes is one of the most important analytical tasks in epidemiological and clinical research. Availability of multivariate longitudinal data presents a unique opportunity to assess joint evolution of outcomes over time. Bivariate linear mixed model (BLMM) provides a versatile tool with regard to assessing correlation. However, BLMMs often assume that all individuals are drawn from a single homogenous population where the individual trajectories are distributed smoothly around population average. Methods Using longitudinal mean deviation (MD) and visual acuity (VA) from the Ocular Hypertension Treatment Study (OHTS), we demonstrated strategies to better understand the correlation between multivariate longitudinal data in the presence of potential heterogeneity. Conditional correlation (i.e., marginal correlation given random effects) was calculated to describe how the association between longitudinal outcomes evolved over time within specific subpopulation. The impact of heterogeneity on correlation was also assessed by simulated data. Results There was a significant positive correlation in both random intercepts (ρ = 0.278, 95% CI: 0.121–0.420) and random slopes (ρ = 0.579, 95% CI: 0.349–0.810) between longitudinal MD and VA, and the strength of correlation constantly increased over time. However, conditional correlation and simulation studies revealed that the correlation was induced primarily by participants with rapid deteriorating MD who only accounted for a small fraction of total samples. Conclusion Conditional correlation given random effects provides a robust estimate to describe the correlation between multivariate longitudinal data in the presence of unobserved heterogeneity (NCT00000125)

New concepts in breast cancer genomics and genetics

Massively parallel DNA and RNA sequencing approaches have generated data on thousands of breast cancer genomes. In this review, we consider progress largely from the perspective of new concepts and hypotheses raised so far. These include challenges to the multistep model of breast carcinogenesis and the discovery of new defects in DNA repair through sequence analysis. Issues for functional genomics include the development of strategies to differentiate between mutations that are likely to drive carcinogenesis and bystander background mutations, as well as the importance of mechanistic studies that examine the role of mutations in genes with roles in splicing, histone methylation, and long non-coding RNA function. The application of genome-annotated patient-derived breast cancer xenografts as a potentially more reliable preclinical model is also discussed. Finally, we address the challenge of extracting medical value from genomic data. A weakness of many datasets is inadequate clinical annotation, which hampers the establishment of links between the mutation spectra and the efficacy of drugs or disease phenotypes. Tools such as dGene and the DGIdb are being developed to identify possible druggable mutations, but these programs are a work in progress since extensive molecular pharmacology is required to develop successful ‘genome-forward’ clinical trials. Examples are emerging, however, including targeting HER2 in HER2 mutant breast cancer and mutant ESR1 in ESR1 endocrine refractory luminal-type breast cancer. Finally, the integration of DNA- and RNA-based sequencing studies with mass spectrometry-based peptide sequencing and an unbiased determination of post-translational modifications promises a more complete view of the biochemistry of breast cancer cells and points toward a new discovery horizon in our understanding of the pathophysiology of this complex disease. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13058-014-0460-4) contains supplementary material, which is available to authorized users

Does circulating progesterone mediate the associations of single nucleotide polymorphisms in progesterone receptor (PGR)-related genes with mammographic breast density in premenopausal women?

UNLABELLED: Progesterone is a proliferative hormone in the breast but the associations of genetic variations in progesterone-regulated pathways with mammographic breast density (MD) in premenopausal women and whether these associations are mediated through circulating progesterone are not clearly defined. We, therefore, investigated these associations in 364 premenopausal women with a median age of 44 years. We sequenced 179 progesterone receptor (PGR)-related single nucleotide polymorphisms (SNPs). We measured volumetric percent density (VPD) and non-dense volume (NDV) using Volpara. Linear regression models were fit on circulating progesterone or VPD/NDV separately. We performed mediation analysis to evaluate whether the effect of a SNP on VPD/NDV is mediated through circulating progesterone. All analyses were adjusted for confounders, phase of menstrual cycle and the Benjamini-Hochberg false discovery (FDR) adjusted p-value was applied to correct for multiple testing. In multivariable analyses, only PGR rs657516 had a direct effect on VPD (averaged direct effect estimate = - 0.20, 95%CI = - 0.38 ~ - 0.04, p-value = 0.02) but this was not statistically significant after FDR correction and the effect was not mediated by circulating progesterone (mediation effect averaged across the two genotypes = 0.01, 95%CI = - 0.02 ~ 0.03, p-value = 0.70). Five SNPs (PGR rs11571241, rs11571239, rs1824128, rs11571150, PGRMC1 rs41294894) were associated with circulating progesterone but these were not statistically significant after FDR correction. SNPs in PGR-related genes were not associated with VPD, NDV and circulating progesterone did not mediate the associations, suggesting that the effects, if any, of these SNPs on MD are independent of circulating progesterone. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12672-021-00438-1

Measuring Overall Heterogeneity in Meta-Analyses: Application to CSF Biomarker Studies in Alzheimer’s Disease

The interpretations of statistical inferences from meta-analyses depend on the degree of heterogeneity in the meta-analyses. Several new indices of heterogeneity in meta-analyses are proposed, and assessed the variation/difference of these indices through a large simulation study. The proposed methods are applied to biomakers of Alzheimer’s disease

De novo serine biosynthesis from glucose predicts sex-specific response to antifolates in non-small cell lung cancer cell lines

Lung cancer is the leading cause of cancer-related death. Intriguingly, males with non-small cell lung cancer (NSCLC) have a higher mortality rate than females. Here, we investigated the role of serine metabolism as a predictive marker for sensitivity to the antifolate pemetrexed in male and female NSCLC cell lines. Using

ABCG1 maintains high-grade glioma survival in vitro and in vivo

The overall survival for adults with malignant glioma (glioblastoma) remains poor despite advances in radiation and chemotherapy. One of the mechanisms by which cancer cells develop relative resistance to treatment is through de-regulation of endoplasmic reticulum (ER) homeostasis. We have recently shown that ABCG1, an ATP-binding cassette transporter, maintains ER homeostasis and suppresses ER stress-induced apoptosis in low-grade glioma. Herein, we demonstrate that ABCG1 expression is increased in human adult glioblastoma, where it correlates with poor survival in individuals with the mesenchymal subtype. Leveraging a mouse model of mesenchymal glioblastoma (NPcis), shRNA-mediated Abcg1 knockdown (KD) increased CHOP ER stress protein expression and resulted in greater NPcis glioma cell death in vitro. Moreover, Abcg1 KD reduced NPcis glioma growth and increased mouse survival in vivo. Collectively, these results demonstrate that ABCG1 is critical for malignant glioma cell survival, and might serve as a future therapeutic target for these deadly brain cancers