Identification and characterization of genomic rearrangements of MSH2 and MLH1 in Lynch syndrome (HNPCC) by novel techniques

Hum Mutat. 2003 Sep;22(3):258. doi: 10.1002/humu.9171.


It has recently been suggested that large genomic rearrangements account for 10-20% of all MSH2 mutations, and a lower proportion of all MLH1 mutations, among individuals with Lynch syndrome (hereditary non-polyposis colorectal cancer, HNPCC). These rearrangements are notoriously difficult to detect; moreover, for clinical purposes, simple tests must be devised to screen family members at risk. Here we used the multiplex ligation-dependent probe amplification (MLPA) method to screen for MSH2 and MLH1 deletions in 70 patients whose colorectal or endometrial tumors were MSI positive, yet no mutation had been found by genomic exon-by-exon sequencing of MSH2, MLH1, and MSH6. We identified five candidates with four different MSH2 deletions (exons 1-2, exons 1-6, exons 1-7 and exon 8) and one candidate with an MLH1 deletion (exons 3-6). To confirm the screening results and to characterize the breakpoints of these genomic deletions precisely, we used diploid-to-haploid conversion and inverse PCR as well as long-range PCR. In each case, we were able to pinpoint the breakpoint and design a simple diagnostic PCR. The procedures we used appear to be sensitive, specific, and simple enough for clinical use.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Adaptor Proteins, Signal Transducing
  • Carrier Proteins
  • Chromosome Breakage / genetics
  • Chromosome Deletion
  • Cohort Studies
  • Colorectal Neoplasms, Hereditary Nonpolyposis / genetics*
  • DNA Mutational Analysis / methods
  • DNA, Neoplasm / analysis
  • DNA-Binding Proteins*
  • Female
  • Gene Rearrangement / genetics*
  • Humans
  • Mass Screening / methods
  • MutL Protein Homolog 1
  • MutS Homolog 2 Protein
  • Neoplasm Proteins / genetics*
  • Nuclear Proteins
  • Oligonucleotide Probes / genetics
  • Polymerase Chain Reaction / methods
  • Proto-Oncogene Proteins / genetics*
  • Reagent Kits, Diagnostic
  • Sensitivity and Specificity


  • Adaptor Proteins, Signal Transducing
  • Carrier Proteins
  • DNA, Neoplasm
  • DNA-Binding Proteins
  • MLH1 protein, human
  • Neoplasm Proteins
  • Nuclear Proteins
  • Oligonucleotide Probes
  • Proto-Oncogene Proteins
  • Reagent Kits, Diagnostic
  • MSH2 protein, human
  • MutL Protein Homolog 1
  • MutS Homolog 2 Protein