A genome-wide scalable SNP genotyping assay using microarray technology

Nat Genet. 2005 May;37(5):549-54. doi: 10.1038/ng1547. Epub 2005 Apr 17.

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.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Computational Biology
  • Genome, Human
  • Genotype
  • Humans
  • Oligonucleotide Array Sequence Analysis / methods*
  • Polymorphism, Single Nucleotide*