GeneRiskCalc: a web-based tool for genetic risk association analysis in casecontrol studies

Title

GeneRiskCalc: a web-based tool for genetic risk association analysis in casecontrol studies

Creator

Sudershan, Amrit; Singh, Kuljeet; Kumar, Parvinder

Description

Background: Genetic association studies play a pivotal role in identifying disease-associated variants, but researchers face challenges in performing essential calculations like HardyWeinberg equilibrium testing, odds ratios, and confidence intervals due to reliance on manual methods or multiple software tools. We aimed to develop GeneRiskCalc, an integrated web-based platform that simplifies genetic association analysis by automating HardyWeinberg equilibrium assessment, odds ratios with confidence interval calculation, and visual data presentation in casecontrol studies. Using an HTML/CSS/JavaScript framework, we developed online software with three core functionalities: (1) automated HWE evaluation, (2) odds ratio with 95% confidence interval computation with statistical validation, and (3) dynamic Forest Plot generation for data visualization. The tool was designed with an intuitive interface to minimize prerequisite statistical expertise. Results: The tool, named the Genetic Risk Association Calculator (GeneRiskCalc), demonstrated high computational accuracy in HWE testing (?2 validation) and association metrics (odds ratio and confidence interval). The results were cross-validated against established statistical methods, confirming their reliability. Furthermore, the integrated Forest Plotter enabled immediate visualization of effect sizes across multiple genetic models, facilitating a comprehensive interpretation of genetic associations. Conclusion: By integrating essential analytical steps into a single platform, the GeneRiskCalc, streamlines genetic epidemiology workflows, addressing key challenges in data analysis. Its user-friendly interface enhances accessibility, promotes reproducibility, and accelerates research in genetic association studies. The tool is freely available at GeneRiskCalc (https://sites.google.com/view/GeneRiskCalc/home?authuser=0). The Author(s) 2025.

Source

BMC Bioinformatics;Volume;26;Issue;1;Article No.;213;

Date

01-01-2025

Publisher

BioMed Central Ltd

Subject

Casecontrol studies; Forest plot; Genetic association studies; Genetic epidemiology; HardyWeinberg equilibrium; Odds ratio

Coverage

Sudershan A., Institute of Human Genetics, University of Jammu, Jammu & Kashmir, Jammu, India, Department of Human Genetics, Sri Pratap College, Cluster University Srinagar, Jammu & Kashmir, Kashmir, Srinagar, 190001, India; Singh K., Department of Computer Science, School of Sciences, Christ University, NCR, Delhi, 201003, India; Kumar P., Institute of Human Genetics, University of Jammu, Jammu & Kashmir, Jammu, India, Department of Zoology, University of Jammu, Jammu & Kashmir, Jammu, 180006, India

Rights

All Open Access; Gold Open Access; Green Open Access

Relation

ISSN: 14712105; CODEN: BBMIC

Format

online

Language

English

Type

Article

Identifier

https://doi.org/10.1186/s12859-025-06207-z

https://www.scopus.com/pages/publications/105013688666?origin=resultslist