A strategy for detection of known and unknown SNP using a minimum number of oligonucleotides applicable in the clinical settings

Ena Wang, Sharon Adams, Yingdong Zhao, Monica Panelli, Richard Simon, Harvey Klein, Francesco M. Marincola

Research output: Contribution to journalArticle

22 Citations (Scopus)

Abstract

Detection of unknown single nucleotide polymorphism (SNP) relies on large scale sequencing expeditions of genomic fragments or complex high-throughput chip technology. We describe a simplified strategy for fluorimetric detection of known and unknown SNP by proportional hybridization to oligonucleotide arrays based on optimization of the established principle of signal loss or gain that requires a drastically reduced number of matched or mismatched probes. The array consists of two sets of 18-mer oligonucleotide probes. One set includes overlapping oligos with 4-nucleotide tiling representing an arbitrarily selected "consensus" sequence (consensus-oligos), the other includes oligos specific for known SNP within the same genomic region (variant-oligos). Fluorescence-labeled DNA amplified from a homozygous source identical to the consensus represents the reference target and is co-hybridized with a differentially-labeled test sample. Lack of hybridization of the test sample to consensus- with simultaneous hybridization to variant-oligos designates a known allele. Lack of hybridization to consensus- and variant-oligos indicates a new allele. Detection of unknown variants in heterozygous samples depends upon fluorimetric analysis of signal intensity based on the principle that homozygous samples generate twice the amount of signal. This method can identify unknown SNP in heterozygous conditions with a sensitivity of 82% and specificity of 90%. This strategy should dramatically increase the efficiency of SNP detection throughout the human genome and will decrease the cost and complexity of applying genomic wide analysis in the context of clinical trials.

Original languageEnglish
Article number4
JournalJournal of Translational Medicine
Volume1
DOIs
Publication statusPublished - 20 Aug 2003
Externally publishedYes

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Polymorphism
Oligonucleotides
Single Nucleotide Polymorphism
Nucleotides
Alleles
Expeditions
Oligonucleotide Probes
Consensus Sequence
Human Genome
Oligonucleotide Array Sequence Analysis
Fluorescence
Clinical Trials
Technology
Costs and Cost Analysis
Sensitivity and Specificity
Genes
Throughput
DNA
Costs

ASJC Scopus subject areas

  • Medicine(all)
  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

A strategy for detection of known and unknown SNP using a minimum number of oligonucleotides applicable in the clinical settings. / Wang, Ena; Adams, Sharon; Zhao, Yingdong; Panelli, Monica; Simon, Richard; Klein, Harvey; Marincola, Francesco M.

In: Journal of Translational Medicine, Vol. 1, 4, 20.08.2003.

Research output: Contribution to journalArticle

Wang, Ena ; Adams, Sharon ; Zhao, Yingdong ; Panelli, Monica ; Simon, Richard ; Klein, Harvey ; Marincola, Francesco M. / A strategy for detection of known and unknown SNP using a minimum number of oligonucleotides applicable in the clinical settings. In: Journal of Translational Medicine. 2003 ; Vol. 1.
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