Lynch Syndrome via MLPA of PMS2

Lynch syndrome, also known as hereditary nonpolyposis colorectal cancer (HNPCC), is an autosomal dominant inherited cancer syndrome associated with germline pathogenic variants in the DNA mismatch repair (MMR) genes MLH1, MSH2, MSH6, and PMS2 as well as the EPCAM gene (Peltomäki and Vasen. 2004. PubMed ID: 15528792; Idos and Valle. 2021. PubMed ID: 20301390). The prevalence of Lynch syndrome is estimated at 1 per 279 individuals but varies by gene (Win et al. 2017. PubMed ID: 27799157). The prevalence of PMS2-associated Lynch syndrome is estimated at 1 per 714 individuals (Win et al. 2017. PubMed ID: 27799157). Individuals with a monoallelic (heterozygous) PMS2 pathogenic variant have higher lifetime risks of colorectal, endometrial, ovarian, prostate, and other types of cancer compared to individuals in the general population (Idos and Valle. 2021. PubMed ID: 20301390).

Testing asymptomatic and symptomatic individuals at increased risk of a hereditary cancer syndrome, such as Lynch syndrome, may inform genetic counseling, screening, prevention strategies, and treatment (Weitzel et al. 2011. PubMed ID: 21858794; ACOG. 2019. PubMed ID: 31764758). It also may be considered if a positive finding will impact medical management for the individual or their at-risk family members.

Of note, the PMS2 gene is also associated with a rare autosomal recessive cancer-related syndrome called constitutional mismatch repair deficiency syndrome (CMMR-D). CMMR-D is characterized by childhood malignancies, mainly hematological or neurological, and neurofibromatosis-like café au lait spots. Approximately 50% of individuals with CMMR-D have biallelic PMS2 pathogenic variants (Wimmer and Etzler. 2008. PubMed ID: 18709565). For individuals harboring a monoallelic PMS2 pathogenic variant, there may be a risk of CMMR-D in offspring if an individual’s partner is also a carrier of a PMS2 pathogenic variant.

PMS2 is an MMR gene involved in DNA repair and maintenance of genomic integrity (Blount and Prakash. 2018. PubMed ID: 29286535). Most pathogenic variants are inherited from one or both parents.

DNA analysis of the PMS2 gene is complicated due to the presence of several pseudogenes. One particular pseudogene, PMS2CL, has high sequence similarity to PMS2 exons 11 through 15 (Blount and Prakash. 2018. PubMed ID: 29286535). However, deletion and duplication analysis via multiplex ligation-dependent probe amplification (MLPA) is able to able to distinguish between the native PMS2 gene and its pseudogenes, including PMS2CL.

Approximately 5% to 25% of Lynch Syndrome is attributed to pathogenic variants in PMS2 (Idos and Valle. 2021. PubMed ID: 20301390). Of these pathogenic variants, 45% to 80% are single nucleotide substitutions or small insertions and deletion detected via sequence analysis, and 20% to 55% are copy number variants detected via gene-targeted deletions and duplication analysis (Idos and Valle. 2021. PubMed ID: 20301390).

Multiplex ligation-dependent probe amplification (MLPA) enables the detection of deletion and duplications of single and multiple exons within a given gene (Eijk-Van Os and Schouten. 2011. PubMed ID: 20938835). It is a semi-quantitative technique to determine relative copy number using a multiplex PCR-based reaction. Only hybridized and ligated adjacent probe oligonucleotides of approximately 60 nucleotides in length are amplified using PCR and thus are specific for the sequence of interest. A stuffer sequence attached to the probe ensures a particular length for deciphering the probe target. Therefore, MLPA enables the detection of relatively small deletions and duplications within a single exon of a given gene or deletions and duplications encompassing the entire gene. For additional information, please see www.mlpa.com.