Computational Tools for Prioritizing Candidate Genes: Boosting Disease Gene Discovery

Overview

Journal Nat Rev Genet

Specialty Genetics

Date 2012 Jul 4

PMID 22751426

Citations 210

Authors

Yves Moreau

Leon-Charles Tranchevent

Affiliations

Soon will be listed here.

Abstract

At different stages of any research project, molecular biologists need to choose - often somewhat arbitrarily, even after careful statistical data analysis - which genes or proteins to investigate further experimentally and which to leave out because of limited resources. Computational methods that integrate complex, heterogeneous data sets - such as expression data, sequence information, functional annotation and the biomedical literature - allow prioritizing genes for future study in a more informed way. Such methods can substantially increase the yield of downstream studies and are becoming invaluable to researchers.

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References

Tiffin N, Adie E, Turner F, Brunner H, van Driel M, Oti M . Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes. Nucleic Acids Res. 2006; 34(10):3067-81. PMC: 1475747. DOI: 10.1093/nar/gkl381. View

Van Vooren S, Thienpont B, Menten B, Speleman F, De Moor B, Vermeesch J . Mapping biomedical concepts onto the human genome by mining literature on chromosomal aberrations. Nucleic Acids Res. 2007; 35(8):2533-43. PMC: 1885641. DOI: 10.1093/nar/gkm054. View

Baudot A, Gomez-Lopez G, Valencia A . Translational disease interpretation with molecular networks. Genome Biol. 2009; 10(6):221. PMC: 2718486. DOI: 10.1186/gb-2009-10-6-221. View

Chen J, Xu H, Aronow B, Jegga A . Improved human disease candidate gene prioritization using mouse phenotype. BMC Bioinformatics. 2007; 8:392. PMC: 2194797. DOI: 10.1186/1471-2105-8-392. View

Spinazzola A, Viscomi C, Fernandez-Vizarra E, Carrara F, dAdamo P, Calvo S . MPV17 encodes an inner mitochondrial membrane protein and is mutated in infantile hepatic mitochondrial DNA depletion. Nat Genet. 2006; 38(5):570-5. DOI: 10.1038/ng1765. View

Ebermann I, Scholl H, Charbel Issa P, Becirovic E, Lamprecht J, Jurklies B . A novel gene for Usher syndrome type 2: mutations in the long isoform of whirlin are associated with retinitis pigmentosa and sensorineural hearing loss. Hum Genet. 2006; 121(2):203-11. DOI: 10.1007/s00439-006-0304-0. View

Firth H, Richards S, Bevan A, Clayton S, Corpas M, Rajan D . DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources. Am J Hum Genet. 2009; 84(4):524-33. PMC: 2667985. DOI: 10.1016/j.ajhg.2009.03.010. View

Chen R, Li L, Butte A . AILUN: reannotating gene expression data automatically. Nat Methods. 2007; 4(11):879. PMC: 2716375. DOI: 10.1038/nmeth1107-879. View

Yu W, Wulf A, Liu T, Khoury M, Gwinn M . Gene Prospector: an evidence gateway for evaluating potential susceptibility genes and interacting risk factors for human diseases. BMC Bioinformatics. 2008; 9:528. PMC: 2613935. DOI: 10.1186/1471-2105-9-528. View

10.

Robinson P, Kohler S, Bauer S, Seelow D, Horn D, Mundlos S . The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease. Am J Hum Genet. 2008; 83(5):610-5. PMC: 2668030. DOI: 10.1016/j.ajhg.2008.09.017. View

11.

Antonarakis S, MCKUSICK V . OMIM passes the 1,000-disease-gene mark. Nat Genet. 2000; 25(1):11. DOI: 10.1038/75497. View

12.

Oti M, Ballouz S, Wouters M . Web tools for the prioritization of candidate disease genes. Methods Mol Biol. 2011; 760:189-206. DOI: 10.1007/978-1-61779-176-5_12. View

13.

Cantor R, Lange K, Sinsheimer J . Prioritizing GWAS results: A review of statistical methods and recommendations for their application. Am J Hum Genet. 2010; 86(1):6-22. PMC: 2801749. DOI: 10.1016/j.ajhg.2009.11.017. View

14.

Baron D, Bihouee A, Teusan R, Dubois E, Savagner F, Steenman M . MADGene: retrieval and processing of gene identifier lists for the analysis of heterogeneous microarray datasets. Bioinformatics. 2011; 27(5):725-6. PMC: 3042180. DOI: 10.1093/bioinformatics/btq710. View

15.

Sparrow D, Guillen-Navarro E, Fatkin D, Dunwoodie S . Mutation of Hairy-and-Enhancer-of-Split-7 in humans causes spondylocostal dysostosis. Hum Mol Genet. 2008; 17(23):3761-6. DOI: 10.1093/hmg/ddn272. View

16.

Breitkreutz B, Stark C, Tyers M . The GRID: the General Repository for Interaction Datasets. Genome Biol. 2003; 4(3):R23. PMC: 153463. DOI: 10.1186/gb-2003-4-3-r23. View

17.

Ma X, Lee H, Wang L, Sun F . CGI: a new approach for prioritizing genes by combining gene expression and protein-protein interaction data. Bioinformatics. 2006; 23(2):215-21. DOI: 10.1093/bioinformatics/btl569. View

18.

Huttenhower C, Haley E, Hibbs M, Dumeaux V, Barrett D, Coller H . Exploring the human genome with functional maps. Genome Res. 2009; 19(6):1093-106. PMC: 2694471. DOI: 10.1101/gr.082214.108. View

19.

Hutz J, Kraja A, McLeod H, Province M . CANDID: a flexible method for prioritizing candidate genes for complex human traits. Genet Epidemiol. 2008; 32(8):779-90. PMC: 4420475. DOI: 10.1002/gepi.20346. View

20.

Schuierer S, Tranchevent L, Dengler U, Moreau Y . Large-scale benchmark of Endeavour using MetaCore maps. Bioinformatics. 2010; 26(15):1922-3. DOI: 10.1093/bioinformatics/btq307. View