Visualization of fine-scale genomic structure by oligonucleotide-based high-resolution FISH.
Identifieur interne : 001D26 ( PubMed/Checkpoint ); précédent : 001D25; suivant : 001D27Visualization of fine-scale genomic structure by oligonucleotide-based high-resolution FISH.
Auteurs : N A Yamada [États-Unis] ; 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.
Descripteurs français
- KwdFr :
- MESH :
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
Affiliations:
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Tsang</name></author><author><name sortKey="Carr, E" sort="Carr, E" uniqKey="Carr E" first="E" last="Carr">E. Carr</name></author><author><name sortKey="Scheffer, A" sort="Scheffer, A" uniqKey="Scheffer A" first="A" last="Scheffer">A. Scheffer</name></author><author><name sortKey="Sederberg, M C" sort="Sederberg, M C" uniqKey="Sederberg M" first="M C" last="Sederberg">M C Sederberg</name></author><author><name sortKey="Aston, M E" sort="Aston, M E" uniqKey="Aston M" first="M E" last="Aston">M E Aston</name></author><author><name sortKey="Ach, R A" sort="Ach, R A" uniqKey="Ach R" first="R A" last="Ach">R A Ach</name></author><author><name sortKey="Tsalenko, A" sort="Tsalenko, A" uniqKey="Tsalenko A" first="A" last="Tsalenko">A. Tsalenko</name></author><author><name sortKey="Sampas, N" sort="Sampas, N" uniqKey="Sampas N" first="N" last="Sampas">N. Sampas</name></author><author><name sortKey="Peter, B" sort="Peter, B" uniqKey="Peter B" first="B" last="Peter">B. Peter</name></author><author><name sortKey="Bruhn, L" sort="Bruhn, L" uniqKey="Bruhn L" first="L" last="Bruhn">L. Bruhn</name></author><author><name sortKey="Brothman, A R" sort="Brothman, A R" uniqKey="Brothman A" first="A R" last="Brothman">A R Brothman</name></author></analytic><series><title level="j">Cytogenetic and genome research</title><idno type="eISSN">1424-859X</idno><imprint><date when="2011" type="published">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Chromosome Duplication (genetics)</term><term>Chromosomes, Human (genetics)</term><term>Genome, Human</term><term>Humans</term><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></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ADN ()</term><term>Chromosomes humains (génétique)</term><term>Duplication chromosomique (génétique)</term><term>Duplications génomiques segmentaires (génétique)</term><term>Génome humain</term><term>Humains</term><term>Inversion de séquence</term><term>Mâle</term><term>Métaphase (génétique)</term><term>Séquençage par oligonucléotides en batterie ()</term><term>Technique FISH ()</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Chromosome Duplication</term><term>Chromosomes, Human</term><term>Metaphase</term><term>Segmental Duplications, Genomic</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Chromosomes humains</term><term>Duplication chromosomique</term><term>Duplications génomiques segmentaires</term><term>Métaphase</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>In Situ Hybridization, Fluorescence</term><term>Oligonucleotide Array Sequence Analysis</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Genome, Human</term><term>Humans</term><term>Male</term><term>Sequence Inversion</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Génome humain</term><term>Humains</term><term>Inversion de séquence</term><term>Mâle</term><term>Séquençage par oligonucléotides en batterie</term><term>Technique FISH</term></keywords></textClass></profileDesc></teiHeader><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></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">21178330</PMID><DateCompleted><Year>2011</Year><Month>04</Month><Day>06</Day></DateCompleted><DateRevised><Year>2011</Year><Month>02</Month><Day>10</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1424-859X</ISSN><JournalIssue CitedMedium="Internet"><Volume>132</Volume><Issue>4</Issue><PubDate><Year>2011</Year></PubDate></JournalIssue><Title>Cytogenetic and genome research</Title><ISOAbbreviation>Cytogenet. Genome Res.</ISOAbbreviation></Journal><ArticleTitle>Visualization of fine-scale genomic structure by oligonucleotide-based high-resolution FISH.</ArticleTitle><Pagination><MedlinePgn>248-54</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1159/000322717</ELocationID><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></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Yamada</LastName><ForeName>N A</ForeName><Initials>NA</Initials><AffiliationInfo><Affiliation>Agilent Laboratories, Agilent Technologies, Santa Clara, Calif., USA. alice_yamada@agilent.com</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Rector</LastName><ForeName>L S</ForeName><Initials>LS</Initials></Author><Author ValidYN="Y"><LastName>Tsang</LastName><ForeName>P</ForeName><Initials>P</Initials></Author><Author ValidYN="Y"><LastName>Carr</LastName><ForeName>E</ForeName><Initials>E</Initials></Author><Author ValidYN="Y"><LastName>Scheffer</LastName><ForeName>A</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Sederberg</LastName><ForeName>M C</ForeName><Initials>MC</Initials></Author><Author ValidYN="Y"><LastName>Aston</LastName><ForeName>M E</ForeName><Initials>ME</Initials></Author><Author ValidYN="Y"><LastName>Ach</LastName><ForeName>R A</ForeName><Initials>RA</Initials></Author><Author ValidYN="Y"><LastName>Tsalenko</LastName><ForeName>A</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Sampas</LastName><ForeName>N</ForeName><Initials>N</Initials></Author><Author ValidYN="Y"><LastName>Peter</LastName><ForeName>B</ForeName><Initials>B</Initials></Author><Author ValidYN="Y"><LastName>Bruhn</LastName><ForeName>L</ForeName><Initials>L</Initials></Author><Author ValidYN="Y"><LastName>Brothman</LastName><ForeName>A R</ForeName><Initials>AR</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2010</Year><Month>12</Month><Day>18</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Cytogenet Genome Res</MedlineTA><NlmUniqueID>101142708</NlmUniqueID><ISSNLinking>1424-8581</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D058674" MajorTopicYN="N">Chromosome Duplication</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D002877" MajorTopicYN="N">Chromosomes, Human</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D015894" MajorTopicYN="N">Genome, Human</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017404" MajorTopicYN="N">In Situ Hybridization, Fluorescence</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008297" MajorTopicYN="N">Male</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008677" MajorTopicYN="N">Metaphase</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020411" MajorTopicYN="N">Oligonucleotide Array Sequence Analysis</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D056916" MajorTopicYN="N">Segmental Duplications, Genomic</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D057345" MajorTopicYN="N">Sequence Inversion</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="accepted"><Year>2010</Year><Month>09</Month><Day>23</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2010</Year><Month>12</Month><Day>24</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2010</Year><Month>12</Month><Day>24</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2011</Year><Month>4</Month><Day>7</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">21178330</ArticleId><ArticleId IdType="pii">000322717</ArticleId><ArticleId IdType="doi">10.1159/000322717</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country></list><tree><noCountry><name sortKey="Ach, R A" sort="Ach, R A" uniqKey="Ach R" first="R A" last="Ach">R A Ach</name><name sortKey="Aston, M E" sort="Aston, M E" uniqKey="Aston M" first="M E" last="Aston">M E Aston</name><name sortKey="Brothman, A R" sort="Brothman, A R" uniqKey="Brothman A" first="A R" last="Brothman">A R Brothman</name><name sortKey="Bruhn, L" sort="Bruhn, L" uniqKey="Bruhn L" first="L" last="Bruhn">L. Bruhn</name><name sortKey="Carr, E" sort="Carr, E" uniqKey="Carr E" first="E" last="Carr">E. Carr</name><name sortKey="Peter, B" sort="Peter, B" uniqKey="Peter B" first="B" last="Peter">B. Peter</name><name sortKey="Rector, L S" sort="Rector, L S" uniqKey="Rector L" first="L S" last="Rector">L S Rector</name><name sortKey="Sampas, N" sort="Sampas, N" uniqKey="Sampas N" first="N" last="Sampas">N. Sampas</name><name sortKey="Scheffer, A" sort="Scheffer, A" uniqKey="Scheffer A" first="A" last="Scheffer">A. Scheffer</name><name sortKey="Sederberg, M C" sort="Sederberg, M C" uniqKey="Sederberg M" first="M C" last="Sederberg">M C Sederberg</name><name sortKey="Tsalenko, A" sort="Tsalenko, A" uniqKey="Tsalenko A" first="A" last="Tsalenko">A. Tsalenko</name><name sortKey="Tsang, P" sort="Tsang, P" uniqKey="Tsang P" first="P" last="Tsang">P. Tsang</name></noCountry><country name="États-Unis"><noRegion><name sortKey="Yamada, N A" sort="Yamada, N A" uniqKey="Yamada N" first="N A" last="Yamada">N A Yamada</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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