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rdf:type |
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lifeskim:mentions |
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pubmed:issue |
8
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pubmed:dateCreated |
2001-8-2
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pubmed:abstractText |
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.
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pubmed:commentsCorrections |
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pubmed:language |
eng
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pubmed:journal |
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pubmed:citationSubset |
IM
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pubmed:chemical |
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pubmed:status |
MEDLINE
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pubmed:month |
Aug
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pubmed:issn |
1088-9051
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pubmed:author |
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pubmed:issnType |
Print
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pubmed:volume |
11
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pubmed:owner |
NLM
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pubmed:authorsComplete |
Y
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pubmed:pagination |
1418-24
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pubmed:dateRevised |
2009-11-18
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pubmed:meshHeading |
pubmed-meshheading:11483583-Cell Line,
pubmed-meshheading:11483583-DNA,
pubmed-meshheading:11483583-Female,
pubmed-meshheading:11483583-Gene Expression Profiling,
pubmed-meshheading:11483583-Genome, Human,
pubmed-meshheading:11483583-Humans,
pubmed-meshheading:11483583-Male,
pubmed-meshheading:11483583-Oligonucleotide Array Sequence Analysis,
pubmed-meshheading:11483583-Oligonucleotides,
pubmed-meshheading:11483583-Polymorphism, Single Nucleotide,
pubmed-meshheading:11483583-Reproducibility of Results,
pubmed-meshheading:11483583-Sequence Analysis, DNA
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pubmed:year |
2001
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pubmed:articleTitle |
Flexible use of high-density oligonucleotide arrays for single-nucleotide polymorphism discovery and validation.
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pubmed:affiliation |
Affymetrix, Inc., Santa Clara, California 95051, USA. Shoulian_Dong@affymetrix.com
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pubmed:publicationType |
Journal Article,
Comparative Study
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