A method for identifying and validating single nucleotide polymorphisms (SN
Ps) with high-density oligonucleotide arrays without the need for locus-spe
cific polymerase chain reactions (PCR) is described in this report.: Genomi
c DNAs were divided into subsets with complexity of similar to 10 Mb by res
triction enzyme digestion and gel-based fragment size resolution, ligated t
o 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 h
ybridizing to high-density variant detection arrays (VDA). A set of indepen
dent validation experiments was conducted for these SNPs employing bead-bas
ed affinity selection followed by hybridization of the affinity-selected SN
P-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 dideox
ynucleotide sequencing and the VDA methodologies. With flexible sample prep
aration, high-density oligonucleotide arrays can be tailored for even large
r scale genome-wide SNP discovery as well as validation.