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http://purl.uniprot.org/citations/19589847http://www.w3.org/1999/02/22-rdf-syntax-ns#typehttp://purl.uniprot.org/core/Journal_Citation
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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-microL 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(R) 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. ."xsd:string
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http://purl.uniprot.org/citations/19589847http://purl.uniprot.org/core/author"Holloway J.W."xsd:string
http://purl.uniprot.org/citations/19589847http://purl.uniprot.org/core/author"Henderson A.J."xsd:string
http://purl.uniprot.org/citations/19589847http://purl.uniprot.org/core/author"Barton S.J."xsd:string
http://purl.uniprot.org/citations/19589847http://purl.uniprot.org/core/author"Rose-Zerilli M.J."xsd:string
http://purl.uniprot.org/citations/19589847http://purl.uniprot.org/core/author"Shaheen S.O."xsd:string
http://purl.uniprot.org/citations/19589847http://purl.uniprot.org/core/date"2009"xsd:gYear
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http://purl.uniprot.org/citations/19589847http://purl.uniprot.org/core/pages"1680-1685"xsd:string
http://purl.uniprot.org/citations/19589847http://purl.uniprot.org/core/title"Copy-number variation genotyping of GSTT1 and GSTM1 gene deletions by real-time PCR."xsd:string
http://purl.uniprot.org/citations/19589847http://purl.uniprot.org/core/volume"55"xsd:string
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