Extensive gene conversion at thePMS2DNA mismatch repair locus

Abstract

Mutations of the PMS2 DNA repair gene predispose to a characteristic range of malignancies, with either childhood onset (when both alleles are mutated) or a partially penetrant adult onset (if heterozygous). These mutations have been difficult to detect, due to interference from a family of pseudogenes located on chromosome 7. One of these, the PMS2CL pseudogene, lies within a 100-kb inverted duplication (inv dup), 700 kb centromeric to PMS2 itself on 7p22. Here, we show that the reference genomic sequences cannot be relied upon to distinguish PMS2 from PMS2CL, because of sequence transfer between the two loci. The 7p22 inv dup occurred prior to the divergence of modern ape species (15 million years ago [Mya]), but has undergone extensive sequence homogenization. This process appears to be ongoing, since there is considerable allelic diversity within the duplicated region, much of it derived from sequence exchange between PMS2 and PMS2CL. This sequence diversity can result in both false-positive and false-negative mutation analysis at this locus. Great caution is still needed in the design and interpretation of PMS2 mutation screens.

The Clinical Phenotype of Lynch Syndrome Due to Germ-Line PMS2 Mutations

“…In contrast, we previously screened 43 probands whose tumors showed loss of both MLH1 and PMS2 proteins on IHC (MLH1 and PMS2 form a heterodimer) and we detected no deleterious PMS2 mutations in these probands. It should be noted that the possibility of gene conversion events between the 3′ end of PMS2 and the PMS2-CL pseudogene 16 means that in a proportion of probands we may have screened exons 13, 14, and 15 from the pseudogene rather than the true PMS2 locus. Our analysis identified 2 deleterious mutations and 2 variants of uncertain significance in these exons ( figure 1).…”

“…14 With these methods, mutation testing by sequencing is greatly simplified and accurate except for exons [13][14][15] in which pseudogene-related conversion may confound the analysis. [15][16][17] Traditionally, families most likely to have LS have been identified by using previously published classification systems known as the Amsterdam Criteria and the less stringent Bethesda Guidelines. [18][19][20][21] However, many medical centers have adopted the practice of screening colorectal and endometrial tumors for LS at the time of surgical diagnosis, often using immunohistochemistry (IHC) to assess the presence or absence of the mismatch repair proteins.…”

A case of early onset rectal cancer of Lynch syndrome with a novel deleteriousPMS2mutation

“…The Sp2_2CL primers were designed using Primer 3 software (14). The Sp2 primers were manually designed so as to assign their 3′ end to paralogous sequence variants (PSVs) whose base sequences differ between PMS2 and PMS2CL (11,12).…”

“…The PMS2 C-terminus like pseudogene (PMS2CL) lies very close to the PMS2 gene on chromosome 7, band 22 (7p22), and is a result of the inverted duplication of a 100 kb repeat element that includes the 3′ region of PMS2 (exons 9-15 except for exon 10). Sequence exchange between intron 12 to the 3′ end of PMS2 and the corresponding region of PMS2CL is an ongoing process (11). The existence of so many pseudogenes and the occurrence of the described chromosomal region exchange makes assay of PMS2 mutations complicated, and thus extreme caution is required to avoid false-negative or false-positive results (11,12).…”

“…Sequence exchange between intron 12 to the 3′ end of PMS2 and the corresponding region of PMS2CL is an ongoing process (11). The existence of so many pseudogenes and the occurrence of the described chromosomal region exchange makes assay of PMS2 mutations complicated, and thus extreme caution is required to avoid false-negative or false-positive results (11,12). In this report, we describe a 34-year-old Japanese patient with rectal cancer that is associated with a germ line 11 bp deletion mutation of PMS2 that is distinguished from PMS2CL.…”