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Published online before print July 12, 2001, 10.1101/gr.171101
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Vol. 11, Issue 8, 1418-1424, August 2001

METHODS
Flexible Use of High-Density Oligonucleotide Arrays for Single-Nucleotide Polymorphism Discovery and Validation

Shoulian Dong,1 Eugene Wang, Linda Hsie, Yanxiang Cao, Xiaogiong Chen, and Thomas R. Gingeras

Affymetrix, Inc., Santa Clara, California 95051, USA

A method for identifying and validating single nucleotide polymorphisms (SNPs) with high-density oligonucleotide arrays without the need for locus-specific polymerase chain reactions (PCR) is described in this report. Genomic DNAs were divided into subsets with complexity of ~10 Mb by restriction enzyme digestion and gel-based fragment size resolution, ligated to a common adaptor, and amplified with one primer in a single PCR reaction. As a demonstration of this approach, a total of 124 SNPs were located in 190 kb of genomic sequences distributed across the entire human genome by hybridizing to high-density variant detection arrays (VDA). A set of independent validation experiments was conducted for these SNPs employing bead-based affinity selection followed by hybridization of the affinity-selected SNP-containing fragments to the same VDA that was used to identify the SNPs. A total of 98.7% (74/75) of these SNPs were confirmed using both DNA dideoxynucleotide sequencing and the VDA methodologies. With flexible sample preparation, high-density oligonucleotide arrays can be tailored for even larger scale genome-wide SNP discovery as well as validation.

1 Corresponding author.

11:1418-1424 ©2001 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/01 $5.00
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