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Nucleic Acids Research Advance Access originally published online on October 21, 2008
Nucleic Acids Research 2008 36(22):e145; doi:10.1093/nar/gkn736
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Nucleic Acids Research, 2008, Vol. 36, No. 22 e145
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Methods Online

A novel procedure for genotyping of single nucleotide polymorphisms in trisomy with genomic DNA and the invader assay

Kelly J. Duffy1, Jack Littrell1, Adam Locke2, Stephanie L. Sherman2 and Michael Olivier1,*

1Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI and 2Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA

*To whom correspondence should be addressed. Tel: +1 414 955 4968; Fax: +1 414 955 6568; Email: molivier{at}mcw.edu

Received September 4, 2008. Revised October 1, 2008. Accepted October 1, 2008.

Individuals with trisomy 21 display complex phenotypes with differing degrees of severity. Numerous reliable methods have been established to diagnose the initial trisomy in these patients, but the identification and characterization of the genetic basis of the phenotypic variation in individuals with trisomy remains challenging. To date, methods that can accurately determine genotypes in trisomic DNA samples are expensive, require specialized equipment and complicated analyses. Here we report proof-of-concept results for an Invader® assay-based genotyping procedure that can determine SNP genotypes in trisomic genomic DNA samples in a simple and cost-effective manner. The procedure requires only two experimental steps: a real-time measurement of the fluorescent Invader® signal and analysis with a specifically designed clustering algorithm. The approach was tested using genomic DNA samples from 23 individuals with trisomy 21, and results were compared to genotypes previously determined with pyrosequencing. Additional assays for 15 SNPs were tested in a set of 21 DNA samples to assess assay performance. Our method successfully identified the correct SNP genotypes for the trisomic genomic DNA samples tested, and thus provides an alternative to determine SNP genotypes in trisomic DNA samples for subsequent association studies in patients with Down syndrome and other trisomies.


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