title: Flexible use of high-density oligonucleotide arrays for single-nucleotide polymorphism discovery and validation.
abstract: 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.
authors.affiliation: Affymetrix, Inc., Santa Clara, California 95051, USA. Shoulian_Dong@affymetrix.com
authors.forename: S
authors.initials: S
authors.lastname: Dong
authors.forename: E
authors.initials: E
authors.lastname: Wang
authors.forename: L
authors.initials: L
authors.lastname: Hsie
authors.forename: Y
authors.initials: Y
authors.lastname: Cao
authors.forename: X
authors.initials: X
authors.lastname: Chen
authors.forename: T R
authors.initials: TR
authors.lastname: Gingeras
mesh_terms: D002460:Cell Line; D004247:DNA / Q000235:genetics / Q000302:isolation & purification; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods; D015894:Genome, Human; D006801:Humans; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D009841:Oligonucleotides / Q000235:genetics / Q000302:isolation & purification; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000379:methods
chemical_list: D009841:Oligonucleotides; D004247:DNA