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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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: | https://repository.cshl.edu/id/eprint/25280 |
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