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Assessment of allele dosage at polymorphic microsatellite loci displaying allelic imbalance in tumors by means of quantitative competitive-polymerase chain reaction.

Abstract
Analysis of allelic imbalance at polymorphic marker loci is usually employed to identify chromosomal regions affected by recurrent aberrations in tumor genomes. Such regions are likely to harbor genes involved in the onset and/or progression of cancer. Although often used to identify regions of loss of heterozygosity caused by deletions/rearrangements near tumor suppressor gene loci, allelic imbalance can also reflect regional amplification, indicating the presence of oncogenes. It is difficult to tell these two situations apart after ordinary polymerase chain reaction (PCR), but here we describe a method that distinguishes allelic loss from allelic gain. The level of allelic imbalance was determined by quantitative PCR (QPCR) in the presence of an internal control DNA that displayed a third allele at the locus studied. To validate the efficiency of allele quantitation, we analyzed an amplified region in a set of rat fibrosarcomas. In four tumor samples with amplification of the Met oncogene, we could show with QPCR that there was amplification of one of the alleles at a microsatellite marker located close to Met. QPCR may be useful for cancer studies because experiments may be predesigned for using either suitable microsatellite markers or the abundant and polymorphic poly-A tails of rodent identifier sequences.
AuthorsAsa Sjöling, Anna Walentinsson, Carola Nordlander, Asa Karlsson, Afrouz Behboudi, Emma Samuelson, Göran Levan, Dan Röhme
JournalCancer genetics and cytogenetics (Cancer Genet Cytogenet) Vol. 157 Issue 2 Pg. 97-103 (Mar 2005) ISSN: 0165-4608 [Print] United States
PMID15721629 (Publication Type: Evaluation Study, Journal Article, Research Support, Non-U.S. Gov't)
Topics
  • Allelic Imbalance
  • Animals
  • Fibrosarcoma (genetics)
  • Gene Dosage
  • Microsatellite Repeats
  • Polymerase Chain Reaction (methods)
  • Polymorphism, Restriction Fragment Length
  • Rats
  • Rats, Inbred Strains

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