Laboratory of Constitutional Genetics for Frequent Cancer HCL-CLB, Centre Léon Bérard, Lyon, France.
Genetic Service, Department of Genetics and Procreation, CHU Grenoble Alpes, Grenoble, France.
Mol Genet Genomic Med. 2023 Sep;11(9):e2231. doi: 10.1002/mgg3.2231. Epub 2023 Jun 23.
The MLH1 gene is one of the DNA mismatch repair genes (MMR), implicated in Lynch syndrome (LS), an autosomal dominant hereditary tumor susceptibility disease. The advent of next-generation sequencing (NGS) technologies has accelerated the diagnosis of inherited diseases and increased the percentage of diagnosis of inherited cancers. However, some complex genomic alterations require the combination of several analytical strategies to allow correct biological interpretations. Here, we describe a novel MLH1 deletion and its pathogenicity determination in a patient suspected of LS.
The index case was a French 73-year-old man diagnosed with colorectal cancer displaying microsatellite instability and the loss of MLH1 and PMS2 expression. NGS analysis was used as the primary method for MMR genes screening. Long-range PCR and reverse transcriptase polymerase chain reaction (RT-PCR) were used for breakpoints and pathogenicity determinations.
A large genomic deletion was detected which removed the last six nucleotides of MLH1 exon 11 together with a large part of intron 11. It was initially considered as a variant of unknown significance (VUS). Genomic breakpoints were subsequently characterized defining the deletion as c.1033_1039-248del. Further RNA analysis demonstrated that this variant activated a cryptic donor splice site at the 5' of the breakpoint, leading to a premature truncated protein: p.Thr345Alafs*13.
Our finding suggested that although NGS technologies have increased variant detection yield, combined approaches were still needed for complex variant characterization and pathogenicity assessment.
MLH1 基因是 DNA 错配修复基因（MMR）之一，与林奇综合征（LS）有关，LS 是一种常染色体显性遗传的肿瘤易感性疾病。下一代测序（NGS）技术的出现加速了遗传性疾病的诊断，并提高了遗传性癌症的诊断比例。然而，一些复杂的基因组改变需要结合几种分析策略，以允许正确的生物学解释。在这里，我们描述了一位疑似 LS 患者中 MLH1 缺失的新发现及其致病性的确定。
该指数病例是一名 73 岁的法国男性，诊断为结直肠癌，表现为微卫星不稳定和 MLH1 和 PMS2 表达缺失。NGS 分析被用作 MMR 基因筛查的主要方法。长距离 PCR 和逆转录聚合酶链反应（RT-PCR）用于确定断裂点和致病性。
检测到一个大的基因组缺失，该缺失去除了 MLH1 外显子 11 的最后六个核苷酸和大部分内含子 11。最初认为它是一种意义不明的变异（VUS）。随后对基因组断点进行了特征描述，将缺失定义为 c.1033_1039-248del。进一步的 RNA 分析表明，该变体激活了断裂点 5'的一个隐秘供体位点，导致一个提前截断的蛋白质：p.Thr345Alafs*13。
我们的发现表明，尽管 NGS 技术提高了变异检测的产量，但对于复杂的变异特征和致病性评估，仍需要结合多种方法。
