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

Schemes of (A) single nucleotide polymorphism (SNP) discovery and (B) validation. (A) Genomic DNA was digested withEcoRI and separated by size on agarose gel. A 250–350 bp fraction was cut from the gel, extracted, and ligated to an adaptor. The ligated DNA was amplified with one primer that interrogated the adaptor sequence. SNPs were screened by hybridizins to VDA. (B) Designated targets were enriched from total genomic DNA by oligonucleotides bound to magnetic beads that interrogated the SNP sites. The genomic DNA was digested with EcoRI and ligated with an adaptor. The enriched targets were amplified with the same primer and screened similarly as in A.