title: A genome-wide scalable SNP genotyping assay using microarray technology.
abstract: Oligonucleotide probe arrays have enabled massively parallel analysis of gene expression levels from a single cDNA sample. Application of microarray technology to analyzing genomic DNA has been stymied by the sequence complexity of the entire human genome. A robust, single base-resolution direct genomic assay would extend the reach of microarray technology. We developed an array-based whole-genome genotyping assay that does not require PCR and enables effectively unlimited multiplexing. The assay achieves a high signal-to-noise ratio by combining specific hybridization of picomolar concentrations of whole genome-amplified DNA to arrayed probes with allele-specific primer extension and signal amplification. As proof of principle, we genotyped several hundred previously characterized SNPs. The conversion rate, call rate and accuracy were comparable to those of high-performance PCR-based genotyping assays.
authors.affiliation: Illumina, Inc., 9885 Towne Centre Dr., San Diego, California 92121, USA. kgunderson@illumina.com
authors.forename: Kevin L
authors.initials: KL
authors.lastname: Gunderson
authors.forename: Frank J
authors.initials: FJ
authors.lastname: Steemers
authors.forename: Grace
authors.initials: G
authors.lastname: Lee
authors.forename: Leo G
authors.initials: LG
authors.lastname: Mendoza
authors.forename: Mark S
authors.initials: MS
authors.lastname: Chee
mesh_terms: D019295:Computational Biology; D015894:Genome, Human; D005838:Genotype; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020641:Polymorphism, Single Nucleotide