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JMD 2007, Vol. 9, No. 2
Copyright © 2007 American Society for Investigative Pathology & Association for Molecular Pathology

Assessment of the Frequency of Allelic Imbalance in Human Tissue Using a Multiplex Polymerase Chain Reaction System

Christopher M. Heaphy*, William C. Hines*, Kimberly S. Butler*, Christina M. Haaland*, Glenroy Heywood{dagger}{ddagger}, Edgar G. Fischer§, Marco Bisoffi*{ddagger} and Jeffrey K. Griffith*{ddagger}

From the Departments of Biochemistry and Molecular Biology, * Surgery, {dagger} and Pathology, § and the Cancer Research and Treatment Center, {ddagger} University of New Mexico School of Medicine, Albuquerque, New Mexico

Genomic instability can generate chromosome breakage and fusion randomly throughout the genome, frequently resulting in allelic imbalance, a deviation from the normal 1:1 ratio of maternal and paternal alleles. Allelic imbalance reflects the karyotypic complexity of the cancer genome. Therefore, it is reasonable to speculate that tissues with more sites of allelic imbalance have a greater likelihood of having disruption of any of the numerous critical genes that cause a cancerous phenotype and thus may have diagnostic or prognostic significance. For this reason, it is desirable to develop a robust method to assess the frequency of allelic imbalance in any tissue. To address this need, we designed an economical and high-throughput method, based on the Applied Biosystems AmpFlSTR Identifiler multiplex polymerase chain reaction system, to evaluate allelic imbalance at 16 unlinked, microsatellite loci located throughout the genome. This method provides a quantitative comparison of the extent of allelic imbalance between samples that can be applied to a variety of frozen and archival tissues. The method does not require matched normal tissue, requires little DNA (the equivalent of ~150 cells) and uses commercially available reagents, instrumentation, and analysis software. Greater than 99% of tissue specimens with ≥2 unbalanced loci were cancerous.






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Copyright © 2007 by the American Society for Investigative Pathology and the Association for Molecular Pathology.