title: Improved multiplex ligation-dependent probe amplification analysis identifies a deleterious PMS2 allele generated by recombination with crossover between PMS2 and PMS2CL.
abstract: Heterozygous PMS2 germline mutations are associated with Lynch syndrome. Up to one third of these mutations are genomic deletions. Their detection is complicated by a pseudogene (PMS2CL), which--owing to extensive interparalog sequence exchange--closely resembles PMS2 downstream of exon 12. A recently redesigned multiplex ligation-dependent probe amplification (MLPA) assay identifies PMS2 copy number alterations with improved reliability when used with reference DNAs containing equal numbers of PMS2- and PMS2CL-specific sequences. We selected eight such reference samples--all publicly available--and used them with this assay to study 13 patients with PMS2-defective colorectal tumors. Three presented deleterious alterations: an Alu-mediated exon deletion; a 125-kb deletion encompassing PMS2 and four additional genes (two with tumor-suppressing functions); and a novel deleterious hybrid PMS2 allele produced by recombination with crossover between PMS2 and PMS2CL, with the breakpoint in intron 10 (the most 5' breakpoint of its kind reported thus far). We discuss mechanisms that might generate this allele in different chromosomal configurations (and their diagnostic implications) and describe an allele-specific PCR assay that facilitates its detection. Our data indicate that the redesigned PMS2 MLPA assay is a valid first-line option. In our series, it identified roughly a quarter of all PMS2 mutations.
authors.affiliation: Division of Human Genetics, Medical University Innsbruck, Innsbruck, Austria.
authors.forename: Annekatrin
authors.initials: A
authors.lastname: Wernstedt
authors.forename: Emanuele
authors.initials: E
authors.lastname: Valtorta
authors.forename: Franco
authors.initials: F
authors.lastname: Armelao
authors.forename: Roberto
authors.initials: R
authors.lastname: Togni
authors.forename: Salvatore
authors.initials: S
authors.lastname: Girlando
authors.forename: Michael
authors.initials: M
authors.lastname: Baudis
authors.forename: Karl
authors.initials: K
authors.lastname: Heinimann
authors.forename: Ludwine
authors.initials: L
authors.lastname: Messiaen
authors.forename: Noemie
authors.initials: N
authors.lastname: Staehli
authors.forename: Johannes
authors.initials: J
authors.lastname: Zschocke
authors.forename: Giancarlo
authors.initials: G
authors.lastname: Marra
authors.forename: Katharina
authors.initials: K
authors.lastname: Wimmer
mesh_terms: D000251:Adenosine Triphosphatases / Q000235:genetics*; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D000483:Alleles; D015179:Colorectal Neoplasms / Q000235:genetics*; D045643:DNA Repair Enzymes / Q000235:genetics*; D004273:DNA, Neoplasm / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics*; D005260:Female; D017353:Gene Deletion; D006801:Humans; D008297:Male; D008875:Middle Aged; D000070976:Mismatch Repair Endonuclease PMS2; D009154:Mutation / Q000235:genetics*; D009367:Neoplasm Staging; D021141:Nucleic Acid Amplification Techniques; D016133:Polymerase Chain Reaction; D011544:Pseudogenes; D011995:Recombination, Genetic
chemical_list: D004273:DNA, Neoplasm; D004268:DNA-Binding Proteins; D000251:Adenosine Triphosphatases; C094934:PMS2 protein, human; D000070976:Mismatch Repair Endonuclease PMS2; D045643:DNA Repair Enzymes