TY  - JOUR
A1  - Dong, Shoulian
A1  - Wang, Eugene
A1  - Hsie, Linda
A1  - Cao, Yanxiang
A1  - Chen, Xiaogiong
A1  - Gingeras, Thomas R.
T1  - Flexible Use of High-Density Oligonucleotide Arrays for Single-Nucleotide Polymorphism Discovery and Validation
Y1  - 2001/08/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 1418 
EP  - 1424 
DO  - 10.1101/gr.171101 
VL  - 11 
IS  - 8 
UR  - http://genome.cshlp.org/content/11/8/1418.abstract 
N2  - 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. 
ER  -