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

Dong, S. L., Wang, E., Hsie, L., Cao, Y. X., Chen, X. G., Gingeras, T. R. (August 2001) Flexible use of high-density oligonucleotide arrays for single-nucleotide polymorphism discovery and validation. Genome Research, 11 (8). pp. 1418-1424. ISSN 1088-9051

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URL: http://www.ncbi.nlm.nih.gov/pubmed/11483583
DOI: 10.1101/gr.171101

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 similar to 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.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics > analysis and processing > microarray gene expression processing
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > SNP
CSHL Authors:
Communities: CSHL labs > Gingeras lab
Depositing User: CSHL Librarian
Date: August 2001
Date Deposited: 13 Mar 2012 15:13
Last Modified: 15 Jul 2013 15:56
PMCID: PMC311102
Related URLs:
URI: http://repository.cshl.edu/id/eprint/25280

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