title: Accessing single nucleotide polymorphisms in genomic DNA by direct multiplex polymerase chain reaction amplification on oligonucleotide microarrays.
abstract: This study introduces a DNA microarray-based genotyping system for accessing single nucleotide polymorphisms (SNPs) directly from a genomic DNA sample. The described one-step approach combines multiplex amplification and allele-specific solid-phase PCR into an on-chip reaction platform. The multiplex amplification of genomic DNA and the genotyping reaction are both performed directly on the microarray in a single reaction. Oligonucleotides that interrogate single nucleotide positions within multiple genomic regions of interest are covalently tethered to a glass chip, allowing quick analysis of reaction products by fluorescence scanning. Due to a fourfold SNP detection approach employing simultaneous probing of sense and antisense strand information, genotypes can be automatically assigned and validated using a simple computer algorithm. We used the described procedure for parallel genotyping of 10 different polymorphisms in a single reaction and successfully analyzed more than 100 human DNA samples. More than 99% of genotype data were in agreement with data obtained in control experiments with allele-specific oligonucleotide hybridization and capillary sequencing. Our results suggest that this approach might constitute a powerful tool for the analysis of genetic variation.
authors.affiliation: VBC-GENOMICS Bioscience Research GmbH, Rennweg 95b/5, A-1030 Vienna, Austria.
authors.forename: Martin
authors.initials: M
authors.lastname: Huber
authors.forename: Axel
authors.initials: A
authors.lastname: Mündlein
authors.forename: Eva
authors.initials: E
authors.lastname: Dornstauder
authors.forename: Christian
authors.initials: C
authors.lastname: Schneeberger
authors.forename: Clemens B
authors.initials: CB
authors.lastname: Tempfer
authors.forename: Manfred W
authors.initials: MW
authors.lastname: Mueller
authors.forename: Wolfgang M
authors.initials: WM
authors.lastname: Schmidt
mesh_terms: D000465:Algorithms; D004247:DNA / Q000032:analysis*; D016678:Genome; D005838:Genotype; D006801:Humans; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*
chemical_list: D004247:DNA