Evaluation of pathogenic variants detected in high homology regions of the PMS2 gene. How effective is long-range PCR?

Autor:	Paixão D; Fleury Medicina e Saúde, Grupo Fleury, São Paulo, Brazil., Lima THA; Fleury Medicina e Saúde, Grupo Fleury, São Paulo, Brazil., de Souza RRF; Fleury Medicina e Saúde, Grupo Fleury, São Paulo, Brazil., Carnavalli JEP; Fleury Medicina e Saúde, Grupo Fleury, São Paulo, Brazil., Picanço-Albuquerque CG; Laboratório de Biologia Molecular, Hospital Haroldo Juaçaba, Instituto do Câncer do Ceará, Fortaleza, Brazil., Silva-Fernandes IJL; Laboratório de Biologia Molecular, Hospital Haroldo Juaçaba, Instituto do Câncer do Ceará, Fortaleza, Brazil., de Barros Silva PG; Laboratório de Biologia Molecular, Hospital Haroldo Juaçaba, Instituto do Câncer do Ceará, Fortaleza, Brazil., Mitne-Neto M; Instituto Paulo Gontijo (IPG), São Paulo, Brazil., Moreira CM; Fleury Medicina e Saúde, Grupo Fleury, São Paulo, Brazil., Baratela WADR; Fleury Medicina e Saúde, Grupo Fleury, São Paulo, Brazil.
Jazyk:	angličtina
Zdroj:	Frontiers in oncology [Front Oncol] 2024 Jun 18; Vol. 14, pp. 1390221. Date of Electronic Publication: 2024 Jun 18 (Print Publication: 2024).
DOI:	10.3389/fonc.2024.1390221
Abstrakt:	Introduction: Lynch syndrome (LS) is an inherited cancer predisposition syndrome characterized by a high risk of colorectal and extracolonic tumors. Germline pathogenic variants (GPV) in the PMS2 gene are associated with <15% of all cases. The PMS2CL pseudogene presents high homology with PMS2 , challenging molecular diagnosis by next-generation sequencing (NGS). Due to the high methodological complexity required to distinguish variants between PMS2 and PMS2CL , most laboratories do not clearly report the origin of this molecular finding. Objective: The aim of this study was to confirm the GPVs detected by NGS in regions of high homology segments of the PMS2 gene in a Brazilian sample. Methods: An orthogonal and gold standard long-range PCR (LR-PCR) methodology to separate variants detected in the PMS2 gene from those detected in the pseudogene. Results: A total of 74 samples with a PMS2 GPV detected by NGS in exons with high homology with PMS2CL pseudogene were evaluated. The most common was NM_000535.6:c.2182_2184delinsG, which was previously described as deleterious mutation in a study of African-American patients with LS and has been widely reported by laboratories as a pathogenic variant associated with the LS phenotype. Of all GPVs identified, only 6.8% were confirmed by LR-PCR. Conversely, more than 90% of GPV were not confirmed after LR-PCR, and the diagnosis of LS was ruled out by molecular mechanisms associated with PMS2. Conclusion: In conclusion, the use of LR-PCR was demonstrated to be a reliable approach for accurate molecular analysis of PMS2 variants in segments with high homology with PMS2CL . We highlight that our laboratory is a pioneer in routine diagnostic complementation of the PMS2 gene in Brazil, directly contributing to a more assertive molecular diagnosis and adequate genetic counseling for these patients and their families. Competing Interests: The following authors are employees received salary and other bonuses of Fleury Medicina e Saude: DP, TL, RS, JC, CM, and WB. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. (Copyright © 2024 Paixão, Lima, de Souza, Carnavalli, Picanço-Albuquerque, Silva-Fernandes, de Barros Silva, Mitne-Neto, Moreira and Baratela.)
Databáze:	MEDLINE
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