Copy-number variation genotyping of GSTT1 and GSTM1 gene deletions by real-time PCR


Rose-Zerilli, M.J., Barton, S.J., Henderson, A.J., Shaheen, S.O. and Holloway, J.W. (2009) Copy-number variation genotyping of GSTT1 and GSTM1 gene deletions by real-time PCR. Clinical Chemistry, 55, (9), 1680-1685. (doi:10.1373/clinchem.2008.120105).

Download

Full text not available from this repository.

Description/Abstract

Background: Structural variation in the human genome is increasingly recognized as being highly prevalent and having relevance to common human diseases. Array-based comparative genome-hybridization technology can be used to determine copy-number variation (CNV) across entire genomes, and quantitative PCR (qPCR) can be used to validate de novo variation or assays of common CNV in disease-association studies. Analysis of large qPCR data sets can be complicated and time-consuming, however.

Methods: We describe qPCR assays for GSTM1 (glutathione S-transferase mu 1) and GSTT1 (glutathione S-transferase theta 1) gene deletions that can genotype up to 192 samples in duplicate 5-µL reaction volumes in <2 h on the ABI Prism 7900HT Sequence Detection System. To streamline data handling and analysis of these CNVs by qPCR, we developed a novel interactive, macro-driven Microsoft Excel® spreadsheet. As proof of principle, we used our software to analyze CNV data for 1478 DNA samples from a family-based cohort.

Results: With only 8 ng of DNA template, we assigned CNV genotypes (i.e., 2, 1, or 0 copies) to either 96% (GSTM1) or 91% (GSTT1) of all DNA samples in a single round of PCR amplification. Genotyping accuracy, as ascertained by familial inheritance, was >99.5%, and independent genotype assignments with replicate real-time PCR runs were 100% concordant.

Conclusions: The genotyping assay for GSTM1 and GSTT1 gene deletion is suitable for large genetic epidemiologic studies and is a highly effective analysis system that is readily adaptable to analysis of other CNVs

Item Type: Article
Related URLs:
Subjects: Q Science > QH Natural history > QH426 Genetics
Divisions: University Structure - Pre August 2011 > School of Medicine > Infection, Inflammation and Repair
University Structure - Pre August 2011 > School of Medicine > Community Clinical Sciences
University Structure - Pre August 2011 > School of Medicine > Human Genetics
ePrint ID: 69838
Date Deposited: 08 Dec 2009
Last Modified: 27 Mar 2014 18:49
URI: http://eprints.soton.ac.uk/id/eprint/69838

Actions (login required)

View Item View Item