title: Accuracy of genotyping for single nucleotide polymorphisms by a microarray-based single nucleotide polymorphism typing method involving hybridization of short allele-specific oligonucleotides.
abstract: Advances in technologies for identifying genetic polymorphisms rapidly and accurately will dramatically accelerate the discovery of disease-related genes. Among a variety of newly described methods for rapid typing of single-nucleotide polymorphisms (SNPs), gene detection using DNA microarrays is gradually achieving widespread use. This method involves the use of short (11- to 13-mer) allele-specific oligonucleotides. This method allows simultaneous analysis of many SNPs in DNAs from a large number of individuals, in a single experiment. In this work, we evaluated the accuracy of a new microarray-based short allele-specific oligonucleotide (ASO) hybridization method. There is a 96-well formatted array on a single plate, in which up to 256 spots are included in each well. Fluorescent probes for our experiments were produced by multiplex PCR amplification often target SNP-containing regions. We genotyped 192 individuals across a panel of ten single base variations, which included an insertion/deletion polymorphism. For comparison, we genotyped the same individuals for the same SNPs by the method of single-base extension with fluorescence detection. The typing accuracies of the microarray-based PCR-ASO and single-base extension methods were calculated as 99.9% and 99.1%, respectively, on the basis of genotyping results determined by direct sequencing. We conclude that the microarray-based hybridization method using short ASO probes represents a potential breakthrough technology for typing large numbers of SNPs rapidly and efficiently.
authors.affiliation: Department of Molecular Biology, Institute of Gerontology, Nippon Medical School, Kawasaki, Japan.
authors.forename: Hironori
authors.initials: H
authors.lastname: Iwasaki
authors.forename: Yoichi
authors.initials: Y
authors.lastname: Ezura
authors.forename: Ryota
authors.initials: R
authors.lastname: Ishida
authors.forename: Mitsuko
authors.initials: M
authors.lastname: Kajita
authors.forename: Mina
authors.initials: M
authors.lastname: Kodaira
authors.forename: Jim
authors.initials: J
authors.lastname: Knight
authors.forename: Steve
authors.initials: S
authors.lastname: Daniel
authors.forename: Michael
authors.initials: M
authors.lastname: Shi
authors.forename: Mitsuru
authors.initials: M
authors.lastname: Emi
mesh_terms: D000483:Alleles; D005838:Genotype; D006801:Humans; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D016133:Polymerase Chain Reaction / Q000379:methods; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results