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Vol. 10, Issue 6, 853-860, June 2000

LETTER
Parallel Genotyping of Human SNPs Using Generic High-density Oligonucleotide Tag Arrays

Jian-Bing Fan,1,3 Xiaoqiong Chen,1 Marc K. Halushka,2 Anthony Berno,1 Xiaohua Huang,1,4 Thomas Ryder,1 Robert J. Lipshutz,1,6 David J. Lockhart,1,5 and Aravinda Chakravarti2

1 Affymetrix, Inc., California 95051 USA; 2 Department of Genetics and Center for Human Genetics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, Ohio 44106 USA

Large scale human genetic studies require technologies for generating millions of genotypes with relative ease but also at a reasonable cost and with high accuracy. We describe a highly parallel method for genotyping single nucleotide polymorphisms (SNPs), using generic high-density oligonucleotide arrays that contain thousands of preselected 20-mer oligonucleotide tags. First, marker-specific primers are used in PCR amplifications of genomic regions containing SNPs. Second, the amplification products are used as templates in single base extension (SBE) reactions using chimeric primers with 3' complementarity to the specific SNP loci and 5' complementarity to specific probes, or tags, synthesized on the array. The SBE primers, terminating one base before the polymorphic site, are extended in the presence of labeled dideoxy NTPs, using a different label for each of the two SNP alleles, and hybridized to the tag array. Third, genotypes are deduced from the fluorescence intensity ratio of the two colors. This approach takes advantage of multiplexed sample preparation, hybridization, and analysis at each stage. We illustrate and test this method by genotyping 44 individuals for 142 human SNPs identified previously in 62 candidate hypertension genes. Because the hybridization results are quantitative, this method can also be used for allele-frequency estimation in pooled DNA samples.

Present addresses: 3Illumina, Inc., San Diego, California 92121 USA; 4Kiva Genetics, Inc., Mountain View, California 94043 USA; 5Genomics Institute of the Novartis Research Foundation (GNF), San Diego, California 92121 USA.

6 Corresponding author.

10:853-860 ©2000 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/00 $5.00
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