TY - JOUR
T1 - Assessment of the frequency of allelic imbalance in human tissue using a multiplex polymerase chain reaction system
AU - Heaphy, Christopher M.
AU - Hines, William C.
AU - Butler, Kimberly S.
AU - Haaland, Christina M.
AU - Heywood, Glenroy
AU - Fischer, Edgar G.
AU - Bisoffi, Marco
AU - Griffith, Jeffrey K.
N1 - Funding Information:
Supported by the Department of Defense (Breast Cancer Research Program: DAMD17-02-1-0514, W81XWH-05-1-0273, and W81XWH-04-1-0370 ; Prostate Cancer Research Program: W81XWH-04-1-0831 and W81XWH-06-1-0120 ) and the National Institutes of Health (grant RR0164880 ).
PY - 2007/4
Y1 - 2007/4
N2 - 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.
AB - 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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U2 - 10.2353/jmoldx.2007.060115
DO - 10.2353/jmoldx.2007.060115
M3 - Article
C2 - 17384220
AN - SCOPUS:34247851055
SN - 1525-1578
VL - 9
SP - 266
EP - 271
JO - Journal of Molecular Diagnostics
JF - Journal of Molecular Diagnostics
IS - 2
ER -