A bioinformatics toolbox to prioritize causal genetic variants in candidate regions

Šimon, Martin (author), Čater, Maša (author), Kunej, Tanja (author), Morton, Nicholas M. (author), Horvat, Simon (author)

This review addresses the significant challenge of identifying causal genetic variants within quantitative trait loci (QTLs) for complex traits and diseases. Despite progress in detecting the ever-larger number of such loci, establishing causality remains daunting. We advocate for integrating bioinformatics and multiomics analyses to streamline the prioritization of candidate genes’ variants. Our case study on the Pla2g4e gene, identified previously as a positional candidate obesity gene through genetic mapping and expression studies, demonstrates how applying multiomic data filtered through regulatory elements containing SNPs can refine the search for causative variants. This approach can yield results that guide more efficient experimental strategies, accelerating genetic research toward functional validation and therapeutic development.

• Language: English
• Keywords: multiomics analysis, prioritization, causality, regulatory elements, SNP
• Work type: Article
• Typology: 1.02 - Review Article
• Organization: BF - Biotechnical Faculty
• Publication status: Published
• Publication version: Version of Record
• Year: 2025
• Number of pages: Str. 33-46
• Numbering: Vol. 41, iss. 1
• PID: 20.500.12556/RUL-166554
• UDC: 575
• ISSN on article: 1362-4555
• DOI: 10.1016/j.tig.2024.09.007
• COBISS.SI-ID: 211722499
• Publication date in RUL: 17.01.2025

ŠIMON, Martin, ČATER, Maša, KUNEJ, Tanja, MORTON, Nicholas M. and HORVAT, Simon, 2025, A bioinformatics toolbox to prioritize causal genetic variants in candidate regions. Trends in genetics [online]. 2025. Vol. 41, no. 1, p. 33–46. [Accessed 18 May 2025]. DOI 10.1016/j.tig.2024.09.007. Retrieved from: https://repozitorij.uni-lj.si/IzpisGradiva.php?lang=eng&id=166554

Record is a part of a journal

• Title: Trends in genetics
• Publisher: Elsevier
• ISSN: 1362-4555
• COBISS.SI-ID: 520937241

Licences

• License: CC BY 4.0, Creative Commons Attribution 4.0 International
• Link: http://creativecommons.org/licenses/by/4.0/
• Description: This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.

Secondary language

• Language: Slovenian
• Keywords: genetika, bioinformatika, vzročne genetske različice, QTL, kompleksne lastnosti, bolezni