Investigation of PMS2-hybrid-alleles

Mismatch repair (MMR) is a process to maintain genome integrity during DNA replication and is involved in the cellular response to DNA damaging agents. Defects in the MMR process lead to the development of cancer. Most importantly truncating germline mutations in the MMR genes causes hereditary non-polyposis colorectal cancer (HNPCC), a tumour predisposition syndrome. But also low-penetrance alleles and polymorphisms in the MMR genes have been found associated with increased cancer susceptibility. The PMS2 gene as the MLH1, MSH2 and MSH6 genes plays an essential role in MMR. However, it is the least studied of these genes both for truncating as well as for low-penetrance alleles. This is to a large part explained by difficulties of analyzing the sequence of this gene that arise from the presence of a number of highly similar PMS2 pseudogenenes. Moreover, "gene conversion" (i.e. sequence exchange) between PMS2 and its pseudogene, PMS2CL, leads to functional PMS2 "hybrid"-alleles that contain sequence variants also present in the PMS2CL pseudogene. Some of these "hybrid"- alleles contain PMS2CL-specific-variants (PSVs) in functional regions of the gene and, hence, may be of biological significance, but their presence/absence can not be studied by assays that are usually applied to study single nucleotide polymorphisms. Therefore, we plan to apply an RNA-based assay that has been developed in our laboratory and that identifies unequivocally PMS2 "hybrid"-alleles containing PSVs with possible biological significance. With the aim develop robust and easy to perform genomic DNA-based assays that test for their presence/absence we will characterize PMS2 "hybrid"-alleles identified in control individuals. Using the developed assays we will assess the frequency of the PMS2 "hybrid"-alleles in large retrospective cancer and control populations, since this will be a first step to uncover the possible role of PSVs as modulators of primary and secondary cancer susceptibility.

Mismatch repair (MMR) is a process to maintain genome integrity during DNA replication and is involved in the cellular response to DNA damaging agents. Defects in the MMR process lead to the development of cancer. Most importantly truncating germline mutations in the MMR genes causes hereditary non-polyposis colorectal cancer (HNPCC), a tumour predisposition syndrome. But also low-penetrance alleles and polymorphisms in the MMR genes have been found associated with increased cancer susceptibility. The PMS2 gene as the MLH1, MSH2 and MSH6 genes plays an essential role in MMR. However, it is the least studied of these genes both for truncating as well as for low-penetrance alleles. This is to a large part explained by difficulties of analyzing the sequence of this gene that arise from the presence of a number of highly similar PMS2 pseudogenenes. Moreover, "gene conversion" (i.e. sequence exchange) between PMS2 and its pseudogene, PMS2CL, leads to functional PMS2 "hybrid"-alleles that contain sequence variants also present in the PMS2CL pseudogene. Some of these "hybrid"- alleles contain PMS2CL-specific-variants (PSVs) in functional regions of the gene and, hence, may be of biological significance, but their presence/absence can not be studied by assays that are usually applied to study single nucleotide polymorphisms. Therefore, we plan to apply an RNA-based assay that has been developed in our laboratory and that identifies unequivocally PMS2 "hybrid"-alleles containing PSVs with possible biological significance. With the aim develop robust and easy to perform genomic DNA-based assays that test for their presence/absence we will characterize PMS2 "hybrid"-alleles identified in control individuals. Using the developed assays we will assess the frequency of the PMS2 "hybrid"-alleles in large retrospective cancer and control populations, since this will be a first step to uncover the possible role of PSVs as modulators of primary and secondary cancer susceptibility.