A complex rearrangement in the APC gene uncovered by multiplex ligation-dependent probe amplification

J Mol Diagn. 2007 Feb;9(1):122-6. doi: 10.2353/jmoldx.2007.060096.


Germline mutations in the tumor suppressor gene APC are the underlying cause of familial adenomatous polyposis, an autosomal-dominant cancer predisposition syndrome of the colorectum. Here, we describe a complex pathogenic rearrangement in the APC gene that was detected during deletion screening and transmitted throughout at least three generations. The rearrangement consists of a deletion of 604 bp in intron 4 that impairs the binding site of the reverse primer for exon 4 and of an insertion of 119 bp in exon 4 that interferes with the binding site of the multiplex ligation-dependent probe amplification (MLPA) probes for exon 4. The insertion is composed of three duplicated sequences derived from exon 4, intron 3, and intron 4, all in inverse direction. By transcript analysis, we found that the mutation results in complete skipping of exon 4 and that it leads to a frameshift. The rearrangement would not have been identified had it occurred outside the MLPA hybridization site. Our findings demonstrate that part of the pathogenic mutations remain undetected by routine methods. Moreover, MLPA and RNA analysis alone would have led to an incorrect interpretation of a genomic deletion of exon 4.

Publication types

  • Case Reports
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenomatous Polyposis Coli / genetics*
  • Adult
  • Base Sequence
  • DNA Mutational Analysis
  • DNA Primers
  • DNA Probes / genetics*
  • Female
  • Gene Rearrangement / genetics*
  • Genes, APC*
  • Humans
  • Molecular Diagnostic Techniques / methods*
  • Molecular Sequence Data
  • Nucleic Acid Amplification Techniques / methods*
  • Polymerase Chain Reaction / methods*


  • DNA Primers
  • DNA Probes