HUMAN MUTATION 28(5), 424^430, 2007 RESEARCH ARTICLE Extensive Gene Conversion at the PMS2 DNA Mismatch Repair Locus Bruce E. Hayward, Michel De Vos, Elizabeth M.A. Valleley, Ruth S. Charlton, Graham R. Taylor, Eamonn Sheridan, and David T. Bonthron à Leeds Institute of Molecular Medicine, University of Leeds and Yorkshire Regional Genetics Service, St James’s University Hospital, Leeds, United Kingdom Communicated by David Cooper 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. Hum Mutat 28(5), 424–430, 2007. r r 2007 Wiley-Liss, Inc. KEY WORDS: PMS2; gene conversion; paralogous sequence variant; pseudogene; DNA mismatch repair; evolution INTRODUCTION PMS2 (MIM] 600259) is one of four human genes encoding proteins similar to E. coli mutL, a postreplicative DNA mismatch repair (MMR) component. In mammalian cells, members of this family act as heterodimers (MLH1-PMS2, MLH1-PMS1, MLH1- MLH3). Biochemical and genetic evidence indicates that the principal mutL-like activity is provided by the MLH1-PMS2 dimer (mutLa). Loss of MLH1 or PMS2 activity results in a severe defect of MMR, manifested typically as somatic instability of simple tandem repeat sequences (microsatellite instability [MSI]). In addition to the 15-exon PMS2 gene on 7p22, some 14 pseudogenes, each containing pseudocopies of some or all of exons 1–5, are present at several loci on 7q [Horii et al., 1994; Nicolaides et al., 1995; De Vos et al., 2004]. A further pseudogene, corresponding to exons 9 and 11–15, lies 700 kb centromeric to PMS2 on 7p22, where it forms part of a 100-kb inverted duplication (inv dup). We originally referred to this latter pseudogene as c0; its official name is now PMS2CL. We showed previously that c0 interferes with mutation analysis, so that pathogenic mutations in the C-terminal region of PMS2 may be overlooked [De Vos et al., 2004]. Also, some published studies have misinterpreted paralogous sequence variants (PSVs) within c0 as being pathogenic [Basil et al., 1999; Hayward et al., 2004; Thompson et al., 2004]. Partly because of technical issues related to the interfering pseudogenes, PMS2 mutations have rather infrequently been shown to underlie cancer predisposition. Homozygous or com- pound heterozygous germline mutations cause a childhood cancer syndrome in which various tumor types can occur, notably lymphoma or supratentorial primitive neuroectodermal tumor, with colorectal cancer in late childhood or adolescence [Miyaki et al., 1997; De Rosa et al., 2000; Trimbath et al., 2001; De Vos et al., 2004, 2006]. In these families, heterozygous parents of affected children were generally healthy, the inheritance pattern thus appearing to be recessive. Nonetheless, several adult color- ectal cancer cases have been shown to carry apparently heterozygous germline PMS2 mutations [Nicolaides et al., 1994; Nakagawa et al., 2004; Truninger et al., 2005; Worthley et al., 2005; Hendriks et al., 2006]. Most such cases have not been familial, again suggesting that heterozygous PMS2 mutations are incompletely penetrant; the true magnitude of the cancer risk they confer is not known. In a previous study [De Vos et al., 2004], we used reference genomic sequences to allow design of PCR-based mutation screening methods that we hoped were specific for the PMS2 gene. Here, however, we show that asymmetrical sequence exchange between PMS2 and c0 is a source of frequent Published online 25 January 2007 in Wiley InterScience (www. interscience.wiley.com). DOI 10.1002/humu.20457 The Supplementary Material referred to in this article can be accessed at http://www.interscience.wiley.com/jpages/1059-7794/suppmat. Received 24 September 2006; accepted revised manuscript 1 November 2006. à Correspondence to: DavidT. Bonthron, Leeds Institute of Molecu- lar Medicine,WellcomeTrust Brenner Building, St James’s University Hospital, Leeds LS97TF,United Kingdom. E-mail: d.t.bonthron@leeds.ac.uk r r 2007 WILEY-LISS, INC.