GMDR: Versatile Software for Detecting Gene-Gene and Gene-Environ- ment Interactions Underlying Complex Traits.

Identification of multifactor gene-gene (G×G) and gene-environment (G×E) interactions underlying complex traits poses one of the great challenges to today's genetic study. Development of the generalized multifactor dimensionality reduction (GMDR) method provides a practicable solution to problems in detection of interactions. To exploit the opportunities brought by the availability of diverse data, it is in high demand to develop the corresponding GMDR software that can handle a breadth of phenotypes, such as continuous, count, dichotomous, polytomous nominal, ordinal, survival and multivariate, and various kinds of study designs, such as unrelated case-control, family-based and pooled unrelated and family samples, and also allows adjustment for covariates. We developed a versatile GMDR package to implement this serial of GMDR analyses for various scenarios (e.g., unified analysis of unrelated and family samples) and large-scale (e.g., genome-wide) data. This package includes other desirable features such as data management and preprocessing. Permutation testing strategies are also built in to evaluate the threshold or empirical p values. In addition, its performance is scalable to the computational resources. The software is available at http://www.soph.uab.edu/ssg/software or http://ibi.zju.edu.cn/software.

Kirschner wire reconstruction of medial and lateral column periosteal hinge in the treatment of multidirectionally unstable supracondylar fracture of the humerus in children.

AIM AND OBJECTIVE: To compare the clinical effect of reconstruction of internal and lateral column periosteal hinge-assisted treatment with Kirschner wire and internal fixation with Kirschner wire in the treatment of multidirectional unstable supracondylar fractures of humerus in children. METHODS: A retrospective cohort study was conducted to analyze the clinical data of 48 patients (31 male, 17 female; mean age: 6.7 ± 2.4 years old) with multidirectionally unstable supracondylar fractures of the humerus treated in our Hospital from August 2020 to August 2022. Twenty-five cases were treated with Kirschner wire reconstruction of the internal and lateral column periosteal hinge assisted by closed reduction and Kirschner wire internal fixation (study group). Twenty-three cases were treated with closed reduction and Kirschner wire internal fixation (control group). The operation time, intraoperative fluoroscopy times, percentage of patients who underwent open reduction after failure of closed reduction, fracture healing time, Baumann angle (BA), shaft-condylar angle (SCA), range of motion (ROM), and Flynn score of elbow at the last follow-up were compared between two groups. Complications such as infection and irritation of Kirschner wire tail were observed in two groups 2 months after the operation. RESULTS: All patients were followed up for 10-22 months ([13.85 ± 2.89] months). The average operation time of the control group was 82.1 min, which was significantly longer than that of the study group 32.3 min (P < 0.05). The number of intraoperative fluoroscopy (29.4 ± 9.2) in the control group was significantly higher than that in the study group (15.2 ± 6.3) (P < 0.05). The incision rate of the control group was 17% while that of the study group was 0 (P < 0.05). According to Flynn score, the excellent and good rate of the elbow joint in the control group was 86.9% (20/23). The excellent and good rate of the elbow joint in the study group was 92.0% (23/25) (P > 0.05). There was no significant difference in fracture healing time, BA, SCA, and ROM between the two groups (P > 0.05). No infection or Kirschner wire tail irritation occurred in the two groups during the 2-month follow-up. CONCLUSION: Reconstruction of internal and lateral periosteal hinges with Kirscher wire has similar effects to closed reduction and Kirschner wire fixation in the treatment of multidirectionally unstable supracondylar fractures of the humerus in children, but it can shorten the operation time and reduce intraoperative fluoroscopy times and incision rate.

The effects of RNA interference mediated VEGF gene silencing on biological behavior of renal cell carcinoma and transplanted renal tumor in nude mice.

OBJECTIVE: This study was to explore the effects of RNA interference mediated vascular endothelial growth factor (VEGF) gene silencing on biological behavior of renal cell carcinoma (RCC), transplanted renal tumor and angiogenesis in nude mice. METHODS: The specific siRNA sequence targeting VEGF were designed and synthesized to construct hVEGF-siRNA plasmid which was transfected into RCC 786-O cells. Reverse transcriptase-polymerase chain reaction (RT-PCR) was used for the detection of VEGF gene expression and western blot was adopted for the examination of VEGF protein expression. The 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay was used to detect cell growth as well as cell migration and invasion. The transplanted renal tumor models in nude mice were established, and the growth condition of nude mice, and VEGF protein expression in transplanted tumor slices and the microvessel density (MVD) were detected. RESULTS: The expression level of VEGF mRNA in VEGF-siRNA group was significant lower than that in the control group and negative group, suggesting that establishment of plasmid specifically inhibited the expression of VEGF gene The expression level of VEGF protein in VEGF-siRNA group was significant lower than that in the control group and negative group. VEGF gene silencing has the significant inhibition effects on proliferation, migration and invasion of RCC 786-O cells. The tumor weight, VEGF protein positive rate and MVD in VEGF-siRNA group were significant lower than those in negative group and blank group. CONCLUSION: The VEGF gene silencing could inhibit the cell proliferation, migration and invasion of RCC 786-O cells; inhibition of VEGF protein expression could prevent transplanted RCC growth and tumor angiogenesis.

Multivariate dimensionality reduction approaches to identify gene-gene and gene-environment interactions underlying multiple complex traits.

The elusive but ubiquitous multifactor interactions represent a stumbling block that urgently needs to be removed in searching for determinants involved in human complex diseases. The dimensionality reduction approaches are a promising tool for this task. Many complex diseases exhibit composite syndromes required to be measured in a cluster of clinical traits with varying correlations and/or are inherently longitudinal in nature (changing over time and measured dynamically at multiple time points). A multivariate approach for detecting interactions is thus greatly needed on the purposes of handling a multifaceted phenotype and longitudinal data, as well as improving statistical power for multiple significance testing via a two-stage testing procedure that involves a multivariate analysis for grouped phenotypes followed by univariate analysis for the phenotypes in the significant group(s). In this article, we propose a multivariate extension of generalized multifactor dimensionality reduction (GMDR) based on multivariate generalized linear, multivariate quasi-likelihood and generalized estimating equations models. Simulations and real data analysis for the cohort from the Study of Addiction: Genetics and Environment are performed to investigate the properties and performance of the proposed method, as compared with the univariate method. The results suggest that the proposed multivariate GMDR substantially boosts statistical power.