Assessing pathogenicity of mismatch repair variants of uncertain significance by molecular tumor analysis

Anne-Sophie van der Werf't Lam; Noah C Helderman; Arnoud Boot; Diantha Terlouw; Hans Morreau; Hailian Mei; Rebecca E E Esveldt-van Lange; Inge M M Lakeman; Christi J van Asperen; Emmelien Aten; Nandy Hofland; Pia A M de Koning Gans; Emily Rayner; Carli Tops; Niels de Wind; Tom van Wezel; Maartje Nielsen

doi:10.1016/j.yexmp.2024.104940

Assessing pathogenicity of mismatch repair variants of uncertain significance by molecular tumor analysis

Exp Mol Pathol. 2024 Oct 21:140:104940. doi: 10.1016/j.yexmp.2024.104940. Online ahead of print.

Authors

Anne-Sophie van der Werf't Lam¹, Noah C Helderman¹, Arnoud Boot², Diantha Terlouw², Hans Morreau², Hailian Mei³, Rebecca E E Esveldt-van Lange¹, Inge M M Lakeman¹, Christi J van Asperen¹, Emmelien Aten¹, Nandy Hofland¹, Pia A M de Koning Gans¹, Emily Rayner⁴, Carli Tops¹, Niels de Wind⁴, Tom van Wezel², Maartje Nielsen⁵

Affiliations

¹ Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands.
² Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands.
³ Sequencing Analysis Support Core, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands.
⁴ Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands.
⁵ Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands. Electronic address: m.nielsen@lumc.nl.

PMID: 39437510
DOI: 10.1016/j.yexmp.2024.104940

Abstract

Functional analyses are the main method to classify mismatch repair (MMR) gene variants of uncertain significance (VUSs). However, the pathogenicity remains unclear for many variants because of conflicting results between clinical, molecular, and functional data. In this study, we evaluated whether whole exome sequencing (WES) could add another layer of evidence to elucidate the pathogenicity of MMR variants with conflicting interpretations. WES was performed on formalin-fixed paraffin-embedded tumor tissue of eight patients with a constitutional MMR VUS (seven families), including eight colorectal and two endometrial carcinomas and one ovarian carcinoma. Cell-free CIMRA assays were performed to assign Odds of Pathogenicity to these VUSs. In four families, seven tumors showed MMR deficiency-associated mutational signatures, supporting the pathogenicity of the VUS. Moreover, somatic (second) MMR hits identified in the WES data were found to explain MMR staining patterns when the MMR staining was discordant with the reported germline MMR gene variant. In conclusion, WES did not significantly reclassify VUS in these cases but clarified some phenotypic aspects such as age of onset and explanations in case of discordant MMR stainings.

Keywords: Lynch syndrome; Mismatch repair deficiency; Mutational signature; Reclassification pathogenicity; Variant of unknown significance; Whole exome sequencing.