Estimating mutant microsatellite allele frequencies in somatic cells by small-pool PCR

Coolbaugh-Murphy, M., Maleki, A., Ramagli, L., Frazier, M., Lichtiger, B., Monckton, D.G. , Siciliano, M.J. and Brown, B.W. (2004) Estimating mutant microsatellite allele frequencies in somatic cells by small-pool PCR. Genomics, 84(2), 419 -430. (doi: 10.1016/j.ygeno.2004.03.007)

Abstract

Identifying microsatellite instability (MSI) by partitioning DNA into multiple small pools containing only single genome amounts of DNA results in trapping both progenitor and low-frequency mutant alleles into pools where they can be identified and counted following PCR. Statistical approaches determining both the frequencies and the significant differences between frequencies of these Poisson-distributed alleles are presented. Results indicate a level of sensitivity and quantification not possible by standard PCR methods. Using material from colon cancer patients with high levels of MSI in their tumors, we also present the molecular and robotic methods for carrying out such studies. Validation experiments indicated mutants detectable at frequencies greater than 0.03 above background. Frequencies obtained in tumor tissue (greater than 0.25) met the expectations of the approach. Significant levels of MSI were detected in the constitutive tissue of the patient carrying a germ-line mutation for mismatch repair, suggesting both mechanistic and clinical applications of the procedure.

• Item Type: Articles
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Monckton, Professor Darren
• Authors: Coolbaugh-Murphy, M., Maleki, A., Ramagli, L., Frazier, M., Lichtiger, B., Monckton, D.G., Siciliano, M.J., and Brown, B.W.
• Subjects: R Medicine > RC Internal medicine > RC0254 Neoplasms. Tumors. Oncology (including Cancer); R Medicine > RB Pathology; Q Science > QH Natural history > QH426 Genetics
• College/School: College of Medical Veterinary and Life Sciences > School of Molecular Biosciences
• Journal Name: Genomics
• ISSN: 0888-7543