Simulation models for aggregated data meta-analysis: Evaluation of pooling effect sizes and publication biases.

Simulation studies are commonly used to evaluate the performance of newly developed meta-analysis methods. For methodology that is developed for an aggregated data meta-analysis, researchers often resort to simulation of the aggregated data directly, instead of simulating individual participant data from which the aggregated data would be calculated in reality. Clearly, distributional characteristics of the aggregated data statistics may be derived from distributional assumptions of the underlying individual data, but they are often not made explicit in publications. This article provides the distribution of the aggregated data statistics that were derived from a heteroscedastic mixed effects model for continuous individual data and a procedure for directly simulating the aggregated data statistics. We also compare our simulation approach with other simulation approaches used in literature. We describe their theoretical differences and conduct a simulation study for three meta-analysis methods: DerSimonian and Laird method for pooling aggregated study effect sizes and the Trim & Fill and precision-effect test and precision-effect estimate with standard errors method for adjustment of publication bias. We demonstrate that the choice of simulation model for aggregated data may have an impact on (the conclusions of) the performance of the meta-analysis method. We recommend the use of multiple aggregated data simulation models to investigate the sensitivity in the performance of the meta-analysis method. Additionally, we recommend that researchers try to make the individual participant data model explicit and derive from this model the distributional consequences of the aggregated statistics to help select appropriate aggregated data simulation models.

Constitutional BRCA1 and MGMT Methylation Are Significant Risk Factors for Triple-Negative Breast Cancer and High-Grade Serous Ovarian Cancer in Saudi Women.

Breast cancer (BC) and ovarian cancer (OC) are rapidly increasing in Saudi Arabia. BRCA1 and MGMT epimutations have been linked to a higher risk of these malignancies. The present research investigated the impact of these epimutations on the prevalence of BC and OC among Saudi women. DNA methylation was evaluated using methylation-specific PCR, whereas mRNA expression levels were assessed using qRT-PCR. We evaluated white blood cell (WBC)-BRCA1 methylation in 1958 Saudi women (908 BC patients, 223 OC patients, and 827 controls). MGMT methylation was determined in 1534 of the 1958 women (700 BC patients, 223 OC patients, and 611 controls). BRCA1 methylation was detected in 8.6% of the controls and 11% of the BC patients. This epimutation was linked to 13.8% of the early-onset BC patients (p = 0.003) and 20% of the triple-negative breast cancer (TNBC) patients (p = 0.0001). BRCA1 methylation was also detected in 14% of the OC patients (p = 0.011), 19.4% of patients aged <55 years (p = 0.0007), and 23.4% of high-grade serous ovarian cancer (HGSOC) patients. In contrast, the BRCA1 mutation was detected in 24% of the OC patients, 27.4% of patients aged ≥55 years, and 26.7% of the HGSOC patients. However, MGMT methylation was detected in 10% of the controls and 17.4% of the BC patients (p = 0.0003). This epimutation was linked to 26.4% of the late-onset BC patients (p = 0.0001) and 11% of the TNBC patients. MGMT methylation was also found in 15.2% of the OC patients (p = 0.034) and 19.1% of HGSOC patients (p = 0.054). Furthermore, 36% of the BRCA1-methylated patients and 34.5% of the MGMT-methylated patients had a family history of cancer, including breast and ovarian cancer. Notably, BRCA1 and MGMT mRNA levels were greater in the WBC RNA of the BC patients and cancer-free methylation carriers than in that of the OC patients. Our data indicate that BRCA1 and MGMT epimutations significantly contribute to the development of breast cancer and ovarian cancer in Saudi cancer patients. These blood-based biomarkers could help identify female patients at high risk of developing TNBC and HGSOC at an early age.

Identification and characterization of ATM founder mutation in BRCA-negative breast cancer patients of Arab ethnicity.

Breast cancer (BC) is the most prevalent malignancy among women worldwide with germline pathogenic variants/likely pathogenic variants (PVs/LPVs) in BRCA1/2 accounting for a large portion of hereditary cases. Recently, heterozygous PVs/LPVs in the ATM serine/threonine kinase or Ataxia-telangiectasia mutated gene (ATM) has been identified as a moderate susceptibility factor for BC in diverse ethnicities. However, the prevalence of ATM PVs/LPVs in BC susceptibility in Arab populations remains largely unexplored. This study investigated the prevalence of ATM PVs/LPVs among BC patients from Saudi Arabia, employing capture-sequencing technology for ATM PVs/LPVs screening in a cohort of 715 unselected BC patients without BRCA1/2 PVs/LPVs. In addition, founder mutation analysis was conducted using the PHASE program. In our entire cohort, four unique PVs/LPVs in the ATM gene were identified in six cases (0.8%). Notably, one recurrent LPV, c.6115G > A:p.Glu2039Lys was identified in three cases, for which haplotype analysis confirmed as a novel putative founder mutation traced back to 13 generations on average. This founder mutation accounted for half of all identified mutant cases and 0.4% of total screened cases. This study further reveals a significant correlation between the presence of ATM mutation and family history of BC (p = 0.0127). These findings underscore an approximate 0.8% prevalence of ATM germline PVs/LPVs in Arab BC patients without BRCA1/2 PVs/LPVs and suggest a founder effect of specific recurrent ATM mutation. These insights can help in the design of a genetic testing strategy tailored to the local population in Saudi Arabia, thereby, enabling more accurate clinical management and risk prediction.

PLK1 and PARP positively correlate in Middle Eastern breast cancer and their combined inhibition overcomes PARP inhibitor resistance in triple negative breast cancer.

Background: Despite advancements in treatment approaches, patients diagnosed with aggressive breast cancer (BC) subtypes typically face an unfavorable prognosis. Globally, these cancers continue to pose a significant threat to women's health, leading to substantial morbidity and mortality. Consequently, there has been a significant struggle to identify viable molecular targets for therapeutic intervention in these patients. Polo-like Kinase-1 (PLK1) represents one of these molecular targets currently undergoing rigorous scrutiny for the treatment of such tumors. Yet, its role in the pathogenesis of BC in Middle Eastern ethnicity remains unexplored. Methods: We investigated the expression of PLK1 protein in a cohort of more than 1500 Middle Eastern ethnicity BC cases by immunohistochemistry. Association with clinicopathological parameters and prognosis were performed. In vitro studies were conducted using the PLK1 inhibitor volasertib and the PARP inhibitor olaparib, either alone or in combination, in PTC cell lines. Results: Overexpression of PLK1 was detected in 27.4% of all BC cases, and this was notably correlated with aggressive clinicopathological markers. PLK1 was enriched in the triple-negative breast cancer (TNBC) subtype and exhibited poor overall survival (p = 0.0347). Notably, there was a positive correlation between PLK1 and PARP overexpression, with co-expression of PLK1 and PARP observed in 15.7% of cases and was associated with significantly poorer overall survival (OS) compared to the overexpression of either protein alone (p = 0.0050). In vitro, we studied the effect of PLK1 and PARP inhibitors either single or combined treatments in two BRCA mutated, and one BRCA proficient TNBC cell lines. We showed that combined inhibition significantly reduced cell survival and persuaded apoptosis in TNBC cell lines. Moreover, our findings indicate that inhibition of PLK1 can reinstate sensitivity in PARP inhibitor (PARPi) resistant TNBC cell lines. Conclusion: Our results shed light on the role of PLK1 in the pathogenesis and prognosis of Middle Eastern BC and support the potential clinical development of combined inhibition of PLK1 and PARP, a strategy that could potentially broaden the use of PLK1 and PARP inhibitors beyond BC cases lacking BRCA.

MicroRNA-126 expression in the peripheral white blood cells of patients with breast and ovarian cancer is a potential biomarker for the early prediction of cancer risk in the carriers of methylated BRCA1.

Constitutive breast cancer type 1 gene (BRCA1) promoter methylation is associated with increased cancer risk, but its role in cancer-free (CF) female carriers is incompletely understood. MicroRNA (miR) is modulated during early tumorigenesis. The present study assessed the modulation of miR-126 expression in the peripheral white blood cells (WBC) of patients with breast cancer (BC) and ovarian cancer (OC) as a biomarker of cancer risk in BRCA1 methylation carriers. A total of 1,114 female subjects [502 patients with BC, 187 patients with OC and 425 CF volunteers] were involved. Screening for BRCA1 promoter methylation in WBC was performed using the methylation-specific polymerase chain reaction (PCR) assay, BRCA1 mRNA was analyzed using a reverse transcription-quantitative PCR assay and miR-126 expression was analyzed using a stem-loop RT-qPCR assay. WBC BRCA1 promoter methylation status was significantly associated with OC (P=0.0266), early-onset BC (P=0.0003) and triple-negative BC (P=0.0066). Notably, 9.4% of the CF group exhibited WBC BRCA1 promoter methylation. In addition, high levels of miR-126 in WBCs were detected in all three groups. The increased level of miR-126 was significantly associated with a lower risk of distant metastasis (P=0.045) in BC, but a higher risk of disease progression and death (P=0.0029) in OC. There was a positive correlation between BRCA1 mRNA and miR-126 levels in the WBCs of all three groups, regardless of BRCA1 promoter methylation status. Notably, circulating miR-126 level was decreased in the BC and OC groups, but not in the CF group. Together, these results suggest the likely involvement of miR-126 in the constitutional methylation of BRCA1 promoter-related malignancies. Therefore, miR-126 may be a candidate biomarker for the early prediction of BC and OC risk in CF BRCA1 methylation carriers.

Jointly pooling aggregated effect sizes and their standard errors from studies with continuous clinical outcomes.

The DerSimonian-Laird (DL) weighted average method for aggregated data meta-analysis has been widely used for the estimation of overall effect sizes. It is criticized for its underestimation of the standard error of the overall effect size in the presence of heterogeneous effect sizes. Due to this negative property, many alternative estimation approaches have been proposed in the literature. One of the earliest alternative approaches was developed by Hardy and Thompson (HT), who implemented a profile likelihood instead of the moment-based approach of DL. Others have further extended this likelihood approach and proposed higher-order likelihood inferences (e.g., Bartlett-type corrections). In addition, corrections factors for the estimated DL standard error, like the Hartung-Knapp-Sidik-Jonkman (HKSJ) adjustment, and the restricted maximum likelihood (REML) estimation have been suggested too. Although these improvements address the uncertainty in estimating the between-study variance better than the DL method, they all assume that the true within-study standard errors are known and equal to the observed standard errors of the effect sizes. Here, we will treat the observed standard errors as estimators for the within-study variability and we propose a bivariate likelihood approach that jointly estimates the overall effect size, the between-study variance, and the potentially heteroskedastic within-study variances. We study the performance of the proposed method by means of simulation, and compare it to DL (with and without HKSJ), HT, their higher-order likelihood methods, and REML. Our proposed approach seems to have better or similar coverages compared to the other approaches and it appears to be less biased in the case of heteroskedastic within-study variances when this heteroskedasticty is correlated with the effect size.

Tests for publication bias are unreliable in case of heteroscedasticity.

Regression based methods for the detection of publication bias in meta-analysis have been extensively evaluated in literature. When dealing with continuous outcomes, specific hidden factors (e.g., heteroscedasticity) may interfere with the test statistics. In this paper we investigate the influence of residual heteroscedasticity on the performance of four tests for publication bias: the Egger test, the Begg-Mazumdar test and two tests based on weighted regression. In the presence of heteroscedasticity, the Egger test and the weighted regression tests highly inflate the Type I error rate, while the Begg-Mazumdar test deflates the Type I error rate. Although all three tests already have low statistical power, heteroscedasticity typically reduces it further. Our results in combination with earlier discussions on publication bias tests lead us to conclude that application of these tests on continuous treatment effects is not warranted.

Does the Timing of Surgery after Neoadjuvant Therapy in Breast Cancer Patients Affect the Outcome?

BACKGROUND: There is a paucity of literature examining the impact of timing of surgery after neoadjuvant chemotherapy. OBJECTIVE: This study aimed to analyze the impact of the time taken to initiate surgical treatment following completion of neoadjuvant chemotherapy on patients' outcomes by evaluating their pathological response, overall survival (OS), and disease-free survival (DFS). METHODS: This is a retrospective review of 611 patients diagnosed with stage II and III breast cancer that received neoadjuvant chemotherapy and surgery between January 2004 and December 2014. The data was collected from a prospectively gathered registry. The patients were stratified into three cohorts according to the time of surgery after neoadjuvant chemotherapy: <4 weeks, 4-7 weeks, or ≥8 weeks. Outcomes were assessed using Kaplan-Meier curves, and the variables were compared using log-rank statistics. RESULTS: The 5-year OS rate was 89.6% and the 5-year DFS rate was 74%. OS and DFS were not significantly different when stratified according to timing of surgery; however, the trends of OS and DFS were poor when surgery was delayed for ≥8 weeks. Median OS and median DFS have not yet been reached. Of the 17% of patients that had surgery after ≥8 weeks, 12.9% had pathological complete response (pCR), while among those that received surgery 4-7 weeks and <4 weeks after neoadjuvant chemotherapy, 26% and 21% had pCR, respectively (p = 0.02). ER+/HER-2+ patients had a statistically significant decrease in pCR if surgery was performed after ≥8 weeks. CONCLUSION: Our patients showed improved pCR if surgery was performed within 8 weeks, especially for ER+/HER-2+ patients. All patients had better OS and DFS trends if surgery was performed between 4 and 7 weeks after neoadjuvant chemotherapy.

Lying Postures of Dairy Cows in Cubicles and on Pasture.

Cows housed indoors with cubicles are probably more restricted in their choice of lying posture and orientation compared with cows housed on pasture. We therefore compared lying postures on pasture in Uruguay and the Netherlands with lying postures in cubicles in the Netherlands, also recording orientation on pasture in Uruguay and divider and bedding type in Dutch cubicles. We visited one farm with four herds in Uruguay, doing live observations, and 25 Dutch farms, taking pictures of cows. Observations of 205 cows on pasture in Uruguay showed more long postures, lying on their belly with their neck stretched. Two herds preferred lying towards north and south, while one herd preferred west and east. Pictures of 217 cows on pasture in the Netherlands showed more wide postures (lying on the side with three or four legs stretched out). Pictures of 527 cows in cubicles in the Netherlands showed more narrow postures (lying on the side with hind legs folded). More long postures (lying on the belly with a stretched neck) and less short postures (lying with the head folded back) were seen in cubicles with soft floors and English dividers; more narrow postures were seen in cubicles with concrete floors. Wide postures were seen more in cubicles with mattresses and free-hanging dividers. We conclude that since cows in cubicles show more narrow postures than on pasture and cannot choose their orientation, their choice in showing preferred behavior is restricted. More research is needed to study the consequences of restricted choice in lying behavior on the health and welfare of dairy cows.

Primary oral malignant melanoma metastasis to the brain and breast: A case report and literature review.

Primary oral malignant melanoma is a rare tumor, which is estimated to comprise 0.2-8.0% of all melanoma cases. This type of cancer is fairly uncommon, its prognosis is dismal, and it frequently exhibits a biologically aggressive behavior. The common location of primary oral malignant melanoma is the hard palate and maxillary alveolus. In ~85% of cases, the melanoma will metastasize to the liver, lung, bone and brain early in the course of the disease. The present study reports the case of a 50-year-old premenopausal woman who presented with primary oral malignant spindle cell melanoma (T3bN2aM0) and underwent complete surgical resection followed by an adjuvant course of radiation therapy. After 1 year, the patient presented with sudden onset slurred speech, and upon examination, was found to have left-sided hemiparesis and a hard left breast mass. Workup confirmed breast and brain metastasis. The patient developed lung metastasis 4 weeks later and was referred for palliative care.

Clinicopathological features of breast angiosarcoma: A 16-years single-institution experience.

BACKGROUND: Breast Angiosarcoma is a rare type of malignancy arising from endothelial cells lining blood vessels, accounting for 1% of all soft tissue breast tumors. This retrospective study describes the clinical pathological features and clinical management and outcomes of a series of 5 patients with primary and secondary Angiosarcoma of the breast present to King Faisal Specialty Hospital and Research Center during the last 16 years. METHODS: A retrospective review of our institution's pathology database was conducted and all patients who had a pathologically confirmed breast angiosarcoma were included in this study. The patient's data, including demographic characteristics, pathological features, clinical management history and clinical outcomes were collected. RESULTS: Five patients were diagnosed with Breast Angiosarcoma (one secondary and four primary cases). The median age of patients with primary angiosarcoma was 22 years (range 13-25 years). All primary cases were presented late as post-excisional biopsy at local hospitals. Median tumor size was 6cm (range 4.0-17.0cm). All primary angiosarcoma patients had total mastectomy. Three-year disease-free survival (DFS) of patients with primary angiosarcoma was 25%. 5-year surviving rate of primary angiosarcoma was 50%. Recurrence was observed in three of the patients with primary Angiosarcoma and in the case of post irradiation Angiosarcoma. CONCLUSIONS: Our study demonstrates that Breast Angiosarcoma exhibits high recurrence and mortality rates. Early detection, small tumor size, and clear surgical margins seem to be crucial factors for survival. Mastectomy with adequate tumor margin is recommended and close long-term follow-up is of utmost importance. Surgery for local recurrence may be potentially curative.

Impact of Surgery on Survival in Stage IV Breast Cancer.

We aimed to assess retrospectively the survival outcome in patients with stage IV breast cancer who underwent surgery. In a retrospective, nonrandomized study of stage IV breast cancer patients diagnosed in a single institution between 2000 and 2012, we assessed patient's survival in the context of baseline characteristics. A total 678 patients with metastatic breast cancer were included; 412 (60.77%) underwent surgery for the primary tumor (Surgery group), and 266 (39%) did not underwent surgery for the primary tumor (Nonsurgery group), with a median follow-up of 41 months. Patients in the Surgery group had longer survival (41 versus 27 months, p < 0.0029). The 5-year survival rate for Surgery group was 34% compared with 14% for the Nonsurgery group. A multivariate analysis revealed surgery (p = 0.0003), large tumor size (p = 0.0195), ER-positive (p < 0.0001), and metastasis at presentation (p = 0.0032) were prognostic variables. Loco-regional surgery does confer a survival advantage in stage IV breast cancer, however, selection bias cannot be excluded, a well-designed and powerful randomized, controlled trial would be valuable to answer whether surgery can improve survival.

Evaluation of a virtual pet visit system with live video streaming of patient images over the Internet in a companion animal intensive care unit in the Netherlands.

OBJECTIVE: To evaluate the impact of a virtual pet visit system ("TelePet" System, TPS) on owners and staff of a companion animal ICU. DESIGN: Longitudinal interventional study (2010-2013). SETTING: Companion animal ICU at a university veterinary medical teaching hospital. STUDY POPULATIONS: Pet owners, ICU technicians. INTERVENTIONS: The introduction of the TPS, with live video streaming of patient images over the Internet, in a companion animal ICU. MEASUREMENTS AND MAIN RESULTS: Pet owners experienced TPS as a valuable extra service. Most TPS users (72.4%) experienced less anxiety and felt less need (40.4% of TPS users) to visit their hospitalized pet in person. Most users (83.5%) shared TPS access with their family. The introduction of the TPS did not improve overall owner satisfaction, except for the score on "quality of medical treatment." Seven of 26 indicators of owner satisfaction were awarded higher scores by TPS users than by TPS nonusers in the survey after the introduction of the system. However, the lack of randomization of owners might have influenced findings. The enthusiasm of the ICU technicians for the system was tempered by the negative feedback from a small number of owners. Nevertheless they recognized the value of the system for owners. The system was user friendly and ICU staff and TPS users experienced few technical problems. CONCLUSIONS: As veterinary healthcare is moving toward a more client-centered approach, a virtual pet visit system, such as TPS, is a relatively simple application that may improve the well-being of most owners during the hospitalization of their pet.

Combined statistical analyses for long-term stability data with multiple storage conditions: a simulation study.

Shelf-life estimation usually requires that at least three registration batches are tested for stability at multiple storage conditions. The shelf-life estimates are often obtained by linear regression analysis per storage condition, an approach implicitly suggested by ICH guideline Q1E. A linear regression analysis combining all data from multiple storage conditions was recently proposed in the literature when variances are homogeneous across storage conditions. The combined analysis is expected to perform better than the separate analysis per storage condition, since pooling data would lead to an improved estimate of the variation and higher numbers of degrees of freedom, but this is not evident for shelf-life estimation. Indeed, the two approaches treat the observed initial batch results, the intercepts in the model, and poolability of batches differently, which may eliminate or reduce the expected advantage of the combined approach with respect to the separate approach. Therefore, a simulation study was performed to compare the distribution of simulated shelf-life estimates on several characteristics between the two approaches and to quantify the difference in shelf-life estimates. In general, the combined statistical analysis does estimate the true shelf life more consistently and precisely than the analysis per storage condition, but it did not outperform the separate analysis in all circumstances.