Visualization of fine-scale genomic structure by oligonucleotide-based high-resolution FISH.
Identifieur interne : 001F18 ( PubMed/Corpus ); précédent : 001F17; suivant : 001F19Visualization of fine-scale genomic structure by oligonucleotide-based high-resolution FISH.
Auteurs : N A Yamada ; L S Rector ; P. Tsang ; E. Carr ; A. Scheffer ; M C Sederberg ; M E Aston ; R A Ach ; A. Tsalenko ; N. Sampas ; B. Peter ; L. Bruhn ; A R BrothmanSource :
- Cytogenetic and genome research [ 1424-859X ] ; 2011.
English descriptors
- KwdEn :
- Chromosome Duplication (genetics), Chromosomes, Human (genetics), Genome, Human, Humans, In Situ Hybridization, Fluorescence (methods), Male, Metaphase (genetics), Oligonucleotide Array Sequence Analysis (methods), Segmental Duplications, Genomic (genetics), Sequence Analysis, DNA (methods), Sequence Inversion.
- MESH :
Abstract
The discovery of complex structural variations that exist within individual genomes has prompted a need to visualize chromosomes at a higher resolution than previously possible. To address this concern, we established a robust, high-resolution fluorescence in situ hybridization (FISH) method that utilizes probes derived from high complexity libraries of long oligonucleotides (>150 mers) synthesized in massively parallel reactions. In silico selected oligonucleotides, targeted to only the most informative elements in 18 genomic regions of interest, eliminated the need for suppressive hybridization reagents. Because of the inherent flexibility in our probe design methods, we readily visualized regions as small as 6.7 kb with high specificity on human metaphase chromosomes, resulting in an overall success rate of 94%. Two-color FISH over a 479-kb duplication, initially reported as being identical in 2 individuals, revealed distinct 2-color patterns representing direct and inverted duplicons, demonstrating that visualization by high-resolution FISH provides further insight in the fine-scale complexity of genomic structures. The ability to design FISH probes for any sequenced genome along with the ease, reproducibility, and high level of accuracy of this technique suggests that it will be powerful for routine analysis of previously difficult genomic regions and structures.
DOI: 10.1159/000322717
PubMed: 21178330
Links to Exploration step
pubmed:21178330Le document en format XML
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<term>In Situ Hybridization, Fluorescence (methods)</term>
<term>Male</term>
<term>Metaphase (genetics)</term>
<term>Oligonucleotide Array Sequence Analysis (methods)</term>
<term>Segmental Duplications, Genomic (genetics)</term>
<term>Sequence Analysis, DNA (methods)</term>
<term>Sequence Inversion</term>
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<term>Oligonucleotide Array Sequence Analysis</term>
<term>Sequence Analysis, DNA</term>
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<term>Humans</term>
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<front><div type="abstract" xml:lang="en">The discovery of complex structural variations that exist within individual genomes has prompted a need to visualize chromosomes at a higher resolution than previously possible. To address this concern, we established a robust, high-resolution fluorescence in situ hybridization (FISH) method that utilizes probes derived from high complexity libraries of long oligonucleotides (>150 mers) synthesized in massively parallel reactions. In silico selected oligonucleotides, targeted to only the most informative elements in 18 genomic regions of interest, eliminated the need for suppressive hybridization reagents. Because of the inherent flexibility in our probe design methods, we readily visualized regions as small as 6.7 kb with high specificity on human metaphase chromosomes, resulting in an overall success rate of 94%. Two-color FISH over a 479-kb duplication, initially reported as being identical in 2 individuals, revealed distinct 2-color patterns representing direct and inverted duplicons, demonstrating that visualization by high-resolution FISH provides further insight in the fine-scale complexity of genomic structures. The ability to design FISH probes for any sequenced genome along with the ease, reproducibility, and high level of accuracy of this technique suggests that it will be powerful for routine analysis of previously difficult genomic regions and structures.</div>
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<Title>Cytogenetic and genome research</Title>
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<ArticleTitle>Visualization of fine-scale genomic structure by oligonucleotide-based high-resolution FISH.</ArticleTitle>
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<Abstract><AbstractText>The discovery of complex structural variations that exist within individual genomes has prompted a need to visualize chromosomes at a higher resolution than previously possible. To address this concern, we established a robust, high-resolution fluorescence in situ hybridization (FISH) method that utilizes probes derived from high complexity libraries of long oligonucleotides (>150 mers) synthesized in massively parallel reactions. In silico selected oligonucleotides, targeted to only the most informative elements in 18 genomic regions of interest, eliminated the need for suppressive hybridization reagents. Because of the inherent flexibility in our probe design methods, we readily visualized regions as small as 6.7 kb with high specificity on human metaphase chromosomes, resulting in an overall success rate of 94%. Two-color FISH over a 479-kb duplication, initially reported as being identical in 2 individuals, revealed distinct 2-color patterns representing direct and inverted duplicons, demonstrating that visualization by high-resolution FISH provides further insight in the fine-scale complexity of genomic structures. The ability to design FISH probes for any sequenced genome along with the ease, reproducibility, and high level of accuracy of this technique suggests that it will be powerful for routine analysis of previously difficult genomic regions and structures.</AbstractText>
<CopyrightInformation>Copyright © 2010 S. Karger AG, Basel.</CopyrightInformation>
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