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Identification of Driver Epistatic Gene Pairs Combining Germline and Somatic Mutations in Cancer.
Rocha, Jairo; Sastre, Jaume; Amengual-Cladera, Emilia; Hernandez-Rodriguez, Jessica; Asensio-Landa, Victor; Heine-Suñer, Damià; Capriotti, Emidio.
Afiliación
  • Rocha J; Department of Mathematics and Computer Science, University of the Balearic Islands, 07122 Palma de Majorca, Spain.
  • Sastre J; Genomics of Health Group, Health Research Institute of the Balearic Islands (IDISBA), 07120 Palma de Majorca, Spain.
  • Amengual-Cladera E; Department of Mathematics and Computer Science, University of the Balearic Islands, 07122 Palma de Majorca, Spain.
  • Hernandez-Rodriguez J; Genomics of Health Group, Health Research Institute of the Balearic Islands (IDISBA), 07120 Palma de Majorca, Spain.
  • Asensio-Landa V; Genomics of Health Group, Health Research Institute of the Balearic Islands (IDISBA), 07120 Palma de Majorca, Spain.
  • Heine-Suñer D; Genomics of Health Group, Health Research Institute of the Balearic Islands (IDISBA), 07120 Palma de Majorca, Spain.
  • Capriotti E; Genomics of Health Group, Health Research Institute of the Balearic Islands (IDISBA), 07120 Palma de Majorca, Spain.
Int J Mol Sci ; 24(11)2023 May 26.
Article en En | MEDLINE | ID: mdl-37298272
Cancer arises from the complex interplay of various factors. Traditionally, the identification of driver genes focuses primarily on the analysis of somatic mutations. We describe a new method for the detection of driver gene pairs based on an epistasis analysis that considers both germline and somatic variations. Specifically, the identification of significantly mutated gene pairs entails the calculation of a contingency table, wherein one of the co-mutated genes can exhibit a germline variant. By adopting this approach, it is possible to select gene pairs in which the individual genes do not exhibit significant associations with cancer. Finally, a survival analysis is used to select clinically relevant gene pairs. To test the efficacy of the new algorithm, we analyzed the colon adenocarcinoma (COAD) and lung adenocarcinoma (LUAD) samples available at The Cancer Genome Atlas (TCGA). In the analysis of the COAD and LUAD samples, we identify epistatic gene pairs significantly mutated in tumor tissue with respect to normal tissue. We believe that further analysis of the gene pairs detected by our method will unveil new biological insights, enhancing a better description of the cancer mechanism.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Adenocarcinoma / Neoplasias del Colon / Adenocarcinoma del Pulmón / Neoplasias Pulmonares Tipo de estudio: Diagnostic_studies / Prognostic_studies Límite: Humans Idioma: En Revista: Int J Mol Sci Año: 2023 Tipo del documento: Article País de afiliación: España Pais de publicación: Suiza
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Adenocarcinoma / Neoplasias del Colon / Adenocarcinoma del Pulmón / Neoplasias Pulmonares Tipo de estudio: Diagnostic_studies / Prognostic_studies Límite: Humans Idioma: En Revista: Int J Mol Sci Año: 2023 Tipo del documento: Article País de afiliación: España Pais de publicación: Suiza