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

Citation
Sl. Dong et al., Flexible use of high-density oligonucleotide arrays for single-nucleotide polymorphism discovery and validation, GENOME RES, 11(8), 2001, pp. 1418-1424
Citations number
9
Language
INGLESE
art.tipo
Article
Categorie Soggetti
Molecular Biology & Genetics
Journal title
GENOME RESEARCH
ISSN journal
1088-9051 → ACNP
Volume
11
Issue
8
Year of publication
2001
Pages
1418 - 1424
Database
ISI
SICI code
1088-9051(200108)11:8<1418:FUOHOA>2.0.ZU;2-C
Abstract
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.