RT Journal
A1 Fan, Jian-Bing
A1 Chen, Xiaoqiong
A1 Halushka, Marc K.
A1 Berno, Anthony
A1 Huang, Xiaohua
A1 Ryder, Thomas
A1 Lipshutz, Robert J.
A1 Lockhart, David J.
A1 Chakravarti, Aravinda
T1 Parallel Genotyping of Human SNPs Using Generic High-density Oligonucleotide Tag Arrays
JF Genome Research 
JO Genome Research 
YR 2000 
FD June 01 
VO 10 
IS 6 
SP 853 
OP 860 
DO 10.1101/gr.10.6.853 
UL http://genome.cshlp.org/content/10/6/853.abstract 
AB 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.