Genotyping single nucleotide polymorphisms directly from genomic DNA by invasive cleavage reaction on microspheres.

Kakuturu V.N. Rao*, Priscilla Wilkins Stevens, Jeff G. Hall, Victor Lyamichev, Bruce P. Neri, David M. Kelso

*Corresponding author for this work

Research output: Contribution to journalArticle

24 Scopus citations

Abstract

Here we report proof-of-principle for a microsphere-based genotyping assay that detects single nucleotide polymorphisms (SNPs) directly from human genomic DNA samples. This assay is based on a structure-specific cleavage reaction that achieves single base discrimination with a 5'-nuclease which recognizes a tripartite substrate formed upon hybridization of target DNA with probe and upstream oligonucleotides. The assay is simple with two easy steps: a cleavage reaction, which generates fluorescent signal on microsphere surfaces, followed by flow cytometry analysis of the microspheres. Genomic DNA samples were genotyped for the SNP in the Apolipoprotein E gene at amino acid position 158. The assay successfully scored wild type, heterozygous and homozygous mutants. To our knowledge, this is the first report of a solid-support assay for detection of SNPs directly from genomic DNA without PCR amplification of the target.

Original languageEnglish (US)
Pages (from-to)e66
JournalNucleic acids research
Volume31
Issue number11
DOIs
StatePublished - Jun 1 2003

ASJC Scopus subject areas

  • Genetics

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