Gene variations related to the hepatocellular carcinoma: Results from a field synopsis and Bayesian revaluation

Abel Penha Mesquita; André Victor Oliveira Monteiro; Alessandro Luiz Araújo Bentes Leal; Larissa Dos Santos Pessoa; José de Siqueira Amorim Júnior; José Rogério Souza Monteiro; Aline Andrade de Sousa; Daniel Fernando Pereira Vasconcelos; Ana Carolina Alves de Oliveira; Adenilson Leão Pereira; Felipe Rodolfo Pereira da Silva

doi:10.1016/j.gene.2023.147392

Gene variations related to the hepatocellular carcinoma: Results from a field synopsis and Bayesian revaluation

Gene. 2023 Jun 15:869:147392. doi: 10.1016/j.gene.2023.147392. Epub 2023 Mar 24.

Affiliations

¹ Medicine College, Altamira University Campus, Federal University of Para, Altamira, PA, Brazil.
² Parnaiba Delta Federal University, Parnaiba, PI, Brazil.
³ Parnaiba Delta Federal University, Parnaiba, PI, Brazil; Laboratory of Histological Analysis and Preparation (LAPHIs), Parnaiba Delta Federal University, Parnaiba, PI, Brazil.
⁴ Medicine College, Altamira University Campus, Federal University of Para, Altamira, PA, Brazil. Electronic address: feliperodolfo.15@hotmail.com.

PMID: 36966980
DOI: 10.1016/j.gene.2023.147392

Abstract

Hepatocellular carcinoma (HCC) is considered as the second cause of cancer-related deaths worldwide. Genetic variations are associated with HCC risk, an issue that has been the subject of several meta-analyses. However, meta-analyses have an important limitation on the likelihood of false positive data. Henceforth, this study aimed to assess the level of noteworthiness in the meta-analyses by means of a Bayesian approach. A systematic search was performed for meta-analyses with associations between gene polymorphisms and HCC. The calculations for the False-Positive Rate Probability (FPRP) and the Bayesian False Discovery Probability (BFDP) were performed to assess the noteworthiness with a statistical power of 1.2 and 1.5 of Odds Ratio at a prior probability of 10^-3 and 10^-5. The quality of studies was evaluated by the Venice criteria. As additional analyses, the gene-gene and protein-protein networks were designed for these genes and products. As results, we found 33 meta-analytic studies on 45 polymorphisms occurring in 35 genes. A total of 1,280 values for FPRP and BFDP were obtained. Seventy-five for FPRP (5.86%) and 95 for BFDP (14.79%) were noteworthy. In conclusion, the polymorphisms in CCND1, CTLA4, EGF, IL6, IL12A, KIF1B, MDM2, MICA, miR-499, MTHFR, PNPLA3, STAT4, TM6SF2, and XPD genes were considered as noteworthy biomarkers for HCC risk.

Keywords: Biomarkers; Hepatic cancer; Liver neoplasms; Polymorphisms; Risk Factors.

MeSH terms

Bayes Theorem
Carcinoma, Hepatocellular* / genetics
Genetic Predisposition to Disease
Humans
Liver Neoplasms* / genetics
Polymorphism, Single Nucleotide