Flexible use of high-density oligonucleotide arrays for single-nucleotide polymorphism discovery and validation

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.