GWAB: a web server for the network-based boosting of human genome-wide association data.

During the last decade, genome-wide association studies (GWAS) have represented a major approach to dissect complex human genetic diseases. Due in part to limited statistical power, most studies identify only small numbers of candidate genes that pass the conventional significance thresholds (e.g. P ≤ 5 × 10-8). This limitation can be partly overcome by increasing the sample size, but this comes at a higher cost. Alternatively, weak association signals can be boosted by incorporating independent data. Previously, we demonstrated the feasibility of boosting GWAS disease associations using gene networks. Here, we present a web server, GWAB (www.inetbio.org/gwab), for the network-based boosting of human GWAS data. Using GWAS summary statistics (P-values) for SNPs along with reference genes for a disease of interest, GWAB reprioritizes candidate disease genes by integrating the GWAS and network data. We found that GWAB could more effectively retrieve disease-associated reference genes than GWAS could alone. As an example, we describe GWAB-boosted candidate genes for coronary artery disease and supporting data in the literature. These results highlight the inherent value in sub-threshold GWAS associations, which are often not publicly released. GWAB offers a feasible general approach to boost such associations for human disease genetics.

IMA: Identifying disease-related genes using MeSH terms and association rules.

Genes play an important role in several diseases. Hence, in biology, identifying relationships between diseases and genes is important for the analysis of diseases, because mutated or dysregulated genes play an important role in pathogenesis. Here, we propose a method to identify disease-related genes using MeSH terms and association rules. We identified genes by analyzing the MeSH terms and extracted information on gene-gene interactions based on association rules. By integrating the extracted interactions, we constructed gene-gene networks and identified disease-related genes. We applied the proposed method to study five cancers, including prostate, lung, breast, stomach, and colorectal cancer, and demonstrated that the proposed method is more useful for identifying disease-related and candidate disease-related genes than previously published methods. In this study, we identified 20 genes for each disease. Among them, we presented 34 important candidate genes with evidence that supports the relationship of the candidate genes with diseases.

A Serious Game-Derived Index for Detecting Children With Heterogeneous Developmental Disabilities: Randomized Controlled Trial.

BACKGROUND: Developmental disabilities are a set of heterogeneous delays or difficulties in one or more areas of neuropsychological development. Considering that childhood is an essential stage of brain development and developmental delays lead to personal or social burdens, the early detection of childhood developmental disabilities is important. However, early screening for developmental disabilities has been a challenge because of the fear of positive results, expensive tests, differences in diagnosis depending on examiners' abilities, and difficulty in diagnosis arising from the need for long-term follow-up observation. OBJECTIVE: This study aimed to assess the feasibility of using a serious game-derived index to identify heterogeneous developmental disabilities. This study also examines the correlation between the game-derived index and existing neuropsychological test results. METHODS: The randomized controlled trial involved 48 children with either normal development or developmental disabilities. In this clinical trial, we used 19 features (6 from the Korean-Wechsler Preschool and Primary Scale of Intelligence, 8 from the Psychoeducational Profile Revised, 2 from the Bruininks-Oseretsky Test of Motor Proficiency, Second Edition, and 3 from the Pediatric Evaluation of Disability Inventory) from neuropsychological tests and 9 (7 game scores, path accuracy, and completion rate) from the serious game, DoBrain. The following analysis was conducted based on participants' baseline information and neuropsychological test and game-derived index data for one week: (1) we compared the baseline information between the normal development and developmental disabilities groups; (2) then we measured the correlation between the game-derived index and the neuropsychological test scores for each group; and (3) we built a classifier based on the game-derived index with a Gaussian process method and then compared the area under the curve (AUC) with a model based on neuropsychological test results. RESULTS: A total of 16 children (normal development=9; developmental disabilities=7) were analyzed after selection. Their developmental abilities were assessed before they started to play the serious games, and statistically significant differences were found in both groups. Specifically, the normal development group was more developed than the developmental disabilities group in terms of social function, gross motor function, full-scale IQ, and visual motor imitation, in that order. Similarly, the normal development group obtained a higher score on the game-derived index than the developmental disabilities group. In the correlation analysis between the game-derived index and the neuropsychological tests, the normal development group showed greater correlation with more variables than the developmental disabilities group. The game-derived index-based model had an AUC=0.9, a similar detection value as the neuropsychological test-based model's AUC=0.86. CONCLUSIONS: A game-derived index based on serious games can detect children with heterogenous developmental disabilities. This suggests that serious games can be used as a potential screening tool for developmental disabilities. TRIAL REGISTRATION: Clinical Research Information Service KCT0003247; https://cris.nih.go.kr/cris/en/search/search_result_st01 .jsp?seq=12365.