Powerful rare variant association testing in a copula-based joint analysis of multiple phenotypes

In genetic association studies of rare variants, the low power of association tests is one of the main challenges. In this study, we propose a new single-marker association test called C-JAMP (Copula-based Joint Analysis of Multiple Phenotypes), which is based on a joint model of multiple phenotypes given genetic markers and other covariates. We evaluated its performance and compared its empirical type I error and power with existing univariate and multivariate single-marker and multi-marker rare-variant tests in extensive simulation studies. C-JAMP yielded unbiased genetic effect estimates and valid type I errors with an adjusted test statistic. When strongly dependent traits were jointly analyzed, C-JAMP had the highest power in all scenarios except when a high percentage of variants were causal with moderate/small effect sizes. When traits with weak or moderate dependence were analyzed, whether C-JAMP or competing approaches had higher power depended on the effect size. When C-JAMP was applied with a misspecified copula function, it still achieved high power in some of the scenarios considered. In a real-data application, we analyzed sequencing data using C-JAMP and performed the first genome-wide association studies of high-molecular-weight and medium-molecular-weight adiponectin plasma concentrations. C-JAMP identified 20 rare variants with p-values smaller than 10⁻⁵, while all other tests resulted in the identification of fewer variants with higher p-values. In summary, the results indicate that C-JAMP is a powerful, flexible, and robust method for association studies, and we identified novel candidate markers for adiponectin. C-JAMP is implemented as an R package and freely available from https://cran.r-project.org/package=CJAMP .     

Clinical and Ultrasonographic Evaluation of Lower-extremity Vein Thrombosis in Behcet Syndrome: An Observational Study

Vascular involvement can be seen in up to 40% of patients with Behcet syndrome (BS), the lower-extremity vein thrombosis (LEVT) being the most common type. The aim of the current study was to compare venous Doppler findings and clinical features between BS patients with LEVT and control patients diagnosed as having LEVT due to other causes.All consecutive 78 patients (71 men, 7 women; mean age 38.6 ± 10.3 years) with LEVT due to BS and 50 control patients (29 men, 21 women; mean age 42.0 ± 12.5 years) who had LEVT due to other causes, or idiopathic, were studied with the help of a Doppler ultrasonography after a detailed clinical examination. Patterns of venous disease were identified by cluster analyses. Clinical features of chronic venous disease were assessed using 2 classification systems. Venous claudication was also assessed.Patients with BS were more likely to be men, had significantly earlier age of onset of thrombosis, and were treated mainly with immunosuppressives and less frequently with anticoagulants. Furthermore, they had significantly more bilateral involvement, less complete recanalization, and more frequent collateral formation. While control patients had a disorganized pattern of venous involvement, BS patients had a contiguous and symmetric pattern, involving all deep and superficial veins of the lower extremities, with less affinity for crural veins. Clinical assessment, as measured by the 2 classification systems, also indicated a more severe disease among the BS patients. In line, 51% of the BS patients suffered from severe post-thrombotic syndrome (PTS) and 32% from venous claudication, whereas these were present in 8% and 12%, respectively, among the controls. Among BS patients, a longer duration of thrombosis, bilateral femoral vein involvement, and using no anticoagulation along with immunosuppressive treatment when first diagnosed were found to be associated independently with severe PTS.Lower-extremity vein thrombosis associated with BS, when compared to LEVT due to other causes, had distinctive demographic and ultrasonographic characteristics, and had clinically a more severe disease course.     

Fasting Blood Glucose Level in Locally Advanced Non-Small Cell Lung Cancer: a New Prognostic Factor?

Hyperglycemia may lead to proliferation, invasion, apoptosis inhibition, migration, and eventually metastasis of cancer cells by several mechanisms. In this study, the effect of hyperglycemia on overall survival (OS), disease-free survival (DFS), and locoregional recurrence (LRR) was investigated in NSCLC. One stage IIIA-IIIB NSCLC patient treated with chemoradiotherapy between 2010 and 2015 was enrolled. Fasting blood glucose (FBG) levels were recorded in pre-treatment, treatment, and post-treatment periods. Median age was 54 years (51–62). Fifty-two patients had squamous cell carcinoma (SCC); 19 had adenocarcinoma. Median follow-up was 19 (11–30), median survival was 19 (13–24), and DFS was 9 (7–11) months. Diabetic patients had shorter survival than non-diabetics 12 (95%CI, 10–14) vs. 25 months (95%CI,18–32), p?= 0.005. Number of patients with LRR was also higher in diabetics compared to non-diabetics (8/12 vs. 11/37, p?=?0.039). OS was shorter in patients with hyperglycemic-FBG and diabetic-FBG levels in pre-treatment period (log-rank p?=?0.03 and 0.023, respectively). Diabetic-FBG level in pre-treatment period was found to be the only independent risk factor for survival. In subgroup analysis, these differences were apparent in SCC (log-rank p?=?0.009 for hyperglicemic, log-rank p?=?0.017 for diabetic-FBG). LRR was 68% in patients with diabetic-FBG, 36.5% in patients with non-diabetic-FBG in post-treatment period (p?=?0.015). Patients with LRR had significantly higher median FBG value in post-treatment period compared to non-relapsing patients, 138 mg/dL (119–228) and 111 mg/dL (99–164), respectively (p?=?0.022). The patients with hyperglycemic and diabetic-FBG levels in pre-treatment period had shorter survival compared to normoglycemic ones. The patients with diabetic-FBG level in post-treatment period had higher LRR, and relapsing patients had higher FBG levels in post-treatment period.     

The effects of experimental varicocele on testicular histology and fertility in monorchic adult rats

OBJECTIVE: To determine the effects of a left-sided experimental varicocele on testicular morphology and fertility in right hemicastrated adult rats. MATERIALS AND METHODS: A double-controlled experimental study was carried out using mature Sprague-Dawley rats, with 12 rats in each treated group and five corresponding controls. Group 1 underwent right orchidectomy, group 2 right orchidectomy and a left varicocele, and group 3 only a left varicocele; each control group underwent a corresponding sham operation. Two months after surgery each rat was placed with two mature female rats for one month to assess fertility. All the rats were then killed and their testes weighed; the mean testicular weight was calculated for each group and the mean seminiferous tubule diameter (STD) measured. Johnsen scores and histological abnormalities were evaluated for each testis using light microscopy. RESULTS: The mean (SEM) testicular weight and STD in group 2 were significantly lower, at 1311 (100) mg and 225 (11) microm, respectively, than in group 1, at 1771 (28) mg and 255 (4) microm (P<0.05). The mean weights of both testes in rats in group 3 were significantly lower than those in group 1 (P<0.05) and although both mean STDs were less than in group 1, the differences were not significant (P>0.05). There were no differences between the Johnsen scores in groups 2 and 3. There were severe histological abnormalities in the left testes in three of nine and two of eight animals in group 2 and 3, respectively; in group 3, changes in the right testis were detected in one rat. Six of nine and seven of eight rats were fertile in group 2 and 3, respectively. CONCLUSION: Experimental left varicocele decreased the left testicular weight and STD in both hemicastrated and intact adult rats. However, the presence of the right testis is important for preserving fertility.     

Cathepsin B, p53 expression and AgNORs in transitional cell carcinoma

The aim of this study was to assess the relation between silver-strained nucleolar organizer regions (AgNOR), tumor stage, tumor grade and p53 expression with cathepsin B staining in transitional cell carcinoma of bladder. Tissue sections from 64 transitional cell carcinomas of the bladder were evaluated for the relation between AgNOR, tumor stage, tumor grade and p53 expression with cathepsin B staining in the neoplastic and stromal cells. Mean AgNOR values were significantly higher and the presence of p53 expression were different in cathepsin B positive and negative tumor and stromal cells. Although the number of cases is limited, this pilot study shows that cathepsin B staining may have a prognostic value in transitional cell carcinoma, but more studies are needed for a definite conclusion.