High fidelity copy number analysis of formalin-fixed and paraffin-embedded tissues using Affymetrix Cytoscan HD chip.
Identifieur interne : 003384 ( PubMed/Corpus ); précédent : 003383; suivant : 003385High fidelity copy number analysis of formalin-fixed and paraffin-embedded tissues using Affymetrix Cytoscan HD chip.
Auteurs : Yan P. Yu ; Amantha Michalopoulos ; Ying Ding ; George Tseng ; Jian-Hua LuoSource :
- PloS one [ 1932-6203 ] ; 2014.
English descriptors
- KwdEn :
- Chromosome Aberrations, DNA Copy Number Variations (genetics), DNA, Neoplasm (genetics), Formaldehyde (chemistry), Gene Expression Profiling, Genome, Human, Humans, In Situ Hybridization, Fluorescence, Lymphoma (genetics), Oligonucleotide Array Sequence Analysis, Paraffin Embedding (methods), Proto-Oncogene Proteins B-raf (genetics), Repressor Proteins (genetics), Tissue Fixation, Trans-Activators (genetics).
- MESH :
- chemical , chemistry : Formaldehyde.
- chemical , genetics : DNA, Neoplasm, Proto-Oncogene Proteins B-raf, Repressor Proteins, Trans-Activators.
- genetics : DNA Copy Number Variations, Lymphoma.
- methods : Paraffin Embedding.
- Chromosome Aberrations, Gene Expression Profiling, Genome, Human, Humans, In Situ Hybridization, Fluorescence, Oligonucleotide Array Sequence Analysis, Tissue Fixation.
Abstract
Detection of human genome copy number variation (CNV) is one of the most important analyses in diagnosing human malignancies. Genome CNV detection in formalin-fixed and paraffin-embedded (FFPE) tissues remains challenging due to suboptimal DNA quality and failure to use appropriate baseline controls for such tissues. Here, we report a modified method in analyzing CNV in FFPE tissues using microarray with Affymetrix Cytoscan HD chips. Gel purification was applied to select DNA with good quality and data of fresh frozen and FFPE tissues from healthy individuals were included as baseline controls in our data analysis. Our analysis showed a 91% overlap between CNV detection by microarray with FFPE tissues and chromosomal abnormality detection by karyotyping with fresh tissues on 8 cases of lymphoma samples. The CNV overlap between matched frozen and FFPE tissues reached 93.8%. When the analyses were restricted to regions containing genes, 87.1% concordance between FFPE and fresh frozen tissues was found. The analysis was further validated by Fluorescence In Situ Hybridization on these samples using probes specific for BRAF and CITED2. The results suggested that the modified method using Affymetrix Cytoscan HD chip gave rise to a significant improvement over most of the previous methods in terms of accuracy in detecting CNV in FFPE tissues. This FFPE microarray methodology may hold promise for broad application of CNV analysis on clinical samples.
DOI: 10.1371/journal.pone.0092820
PubMed: 24699316
Links to Exploration step
pubmed:24699316Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">High fidelity copy number analysis of formalin-fixed and paraffin-embedded tissues using Affymetrix Cytoscan HD chip.</title><author><name sortKey="Yu, Yan P" sort="Yu, Yan P" uniqKey="Yu Y" first="Yan P" last="Yu">Yan P. Yu</name><affiliation><nlm:affiliation>Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America.</nlm:affiliation></affiliation></author><author><name sortKey="Michalopoulos, Amantha" sort="Michalopoulos, Amantha" uniqKey="Michalopoulos A" first="Amantha" last="Michalopoulos">Amantha Michalopoulos</name><affiliation><nlm:affiliation>Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America.</nlm:affiliation></affiliation></author><author><name sortKey="Ding, Ying" sort="Ding, Ying" uniqKey="Ding Y" first="Ying" last="Ding">Ying Ding</name><affiliation><nlm:affiliation>Department of Statistics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America.</nlm:affiliation></affiliation></author><author><name sortKey="Tseng, George" sort="Tseng, George" uniqKey="Tseng G" first="George" last="Tseng">George Tseng</name><affiliation><nlm:affiliation>Department of Statistics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America.</nlm:affiliation></affiliation></author><author><name sortKey="Luo, Jian Hua" sort="Luo, Jian Hua" uniqKey="Luo J" first="Jian-Hua" last="Luo">Jian-Hua Luo</name><affiliation><nlm:affiliation>Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2014">2014</date><idno type="RBID">pubmed:24699316</idno><idno type="pmid">24699316</idno><idno type="doi">10.1371/journal.pone.0092820</idno><idno type="wicri:Area/PubMed/Corpus">003384</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">003384</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">High fidelity copy number analysis of formalin-fixed and paraffin-embedded tissues using Affymetrix Cytoscan HD chip.</title><author><name sortKey="Yu, Yan P" sort="Yu, Yan P" uniqKey="Yu Y" first="Yan P" last="Yu">Yan P. Yu</name><affiliation><nlm:affiliation>Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America.</nlm:affiliation></affiliation></author><author><name sortKey="Michalopoulos, Amantha" sort="Michalopoulos, Amantha" uniqKey="Michalopoulos A" first="Amantha" last="Michalopoulos">Amantha Michalopoulos</name><affiliation><nlm:affiliation>Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America.</nlm:affiliation></affiliation></author><author><name sortKey="Ding, Ying" sort="Ding, Ying" uniqKey="Ding Y" first="Ying" last="Ding">Ying Ding</name><affiliation><nlm:affiliation>Department of Statistics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America.</nlm:affiliation></affiliation></author><author><name sortKey="Tseng, George" sort="Tseng, George" uniqKey="Tseng G" first="George" last="Tseng">George Tseng</name><affiliation><nlm:affiliation>Department of Statistics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America.</nlm:affiliation></affiliation></author><author><name sortKey="Luo, Jian Hua" sort="Luo, Jian Hua" uniqKey="Luo J" first="Jian-Hua" last="Luo">Jian-Hua Luo</name><affiliation><nlm:affiliation>Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America.</nlm:affiliation></affiliation></author></analytic><series><title level="j">PloS one</title><idno type="eISSN">1932-6203</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Chromosome Aberrations</term><term>DNA Copy Number Variations (genetics)</term><term>DNA, Neoplasm (genetics)</term><term>Formaldehyde (chemistry)</term><term>Gene Expression Profiling</term><term>Genome, Human</term><term>Humans</term><term>In Situ Hybridization, Fluorescence</term><term>Lymphoma (genetics)</term><term>Oligonucleotide Array Sequence Analysis</term><term>Paraffin Embedding (methods)</term><term>Proto-Oncogene Proteins B-raf (genetics)</term><term>Repressor Proteins (genetics)</term><term>Tissue Fixation</term><term>Trans-Activators (genetics)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Formaldehyde</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Neoplasm</term><term>Proto-Oncogene Proteins B-raf</term><term>Repressor Proteins</term><term>Trans-Activators</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>DNA Copy Number Variations</term><term>Lymphoma</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Paraffin Embedding</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Chromosome Aberrations</term><term>Gene Expression Profiling</term><term>Genome, Human</term><term>Humans</term><term>In Situ Hybridization, Fluorescence</term><term>Oligonucleotide Array Sequence Analysis</term><term>Tissue Fixation</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Detection of human genome copy number variation (CNV) is one of the most important analyses in diagnosing human malignancies. Genome CNV detection in formalin-fixed and paraffin-embedded (FFPE) tissues remains challenging due to suboptimal DNA quality and failure to use appropriate baseline controls for such tissues. Here, we report a modified method in analyzing CNV in FFPE tissues using microarray with Affymetrix Cytoscan HD chips. Gel purification was applied to select DNA with good quality and data of fresh frozen and FFPE tissues from healthy individuals were included as baseline controls in our data analysis. Our analysis showed a 91% overlap between CNV detection by microarray with FFPE tissues and chromosomal abnormality detection by karyotyping with fresh tissues on 8 cases of lymphoma samples. The CNV overlap between matched frozen and FFPE tissues reached 93.8%. When the analyses were restricted to regions containing genes, 87.1% concordance between FFPE and fresh frozen tissues was found. The analysis was further validated by Fluorescence In Situ Hybridization on these samples using probes specific for BRAF and CITED2. The results suggested that the modified method using Affymetrix Cytoscan HD chip gave rise to a significant improvement over most of the previous methods in terms of accuracy in detecting CNV in FFPE tissues. This FFPE microarray methodology may hold promise for broad application of CNV analysis on clinical samples.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">24699316</PMID><DateCreated><Year>2014</Year><Month>04</Month><Day>04</Day></DateCreated><DateCompleted><Year>2015</Year><Month>01</Month><Day>27</Day></DateCompleted><DateRevised><Year>2016</Year><Month>10</Month><Day>25</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">1932-6203</ISSN><JournalIssue CitedMedium="Internet"><Volume>9</Volume><Issue>4</Issue><PubDate><Year>2014</Year></PubDate></JournalIssue><Title>PloS one</Title><ISOAbbreviation>PLoS ONE</ISOAbbreviation></Journal><ArticleTitle>High fidelity copy number analysis of formalin-fixed and paraffin-embedded tissues using Affymetrix Cytoscan HD chip.</ArticleTitle><Pagination><MedlinePgn>e92820</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pone.0092820</ELocationID><Abstract><AbstractText>Detection of human genome copy number variation (CNV) is one of the most important analyses in diagnosing human malignancies. Genome CNV detection in formalin-fixed and paraffin-embedded (FFPE) tissues remains challenging due to suboptimal DNA quality and failure to use appropriate baseline controls for such tissues. Here, we report a modified method in analyzing CNV in FFPE tissues using microarray with Affymetrix Cytoscan HD chips. Gel purification was applied to select DNA with good quality and data of fresh frozen and FFPE tissues from healthy individuals were included as baseline controls in our data analysis. Our analysis showed a 91% overlap between CNV detection by microarray with FFPE tissues and chromosomal abnormality detection by karyotyping with fresh tissues on 8 cases of lymphoma samples. The CNV overlap between matched frozen and FFPE tissues reached 93.8%. When the analyses were restricted to regions containing genes, 87.1% concordance between FFPE and fresh frozen tissues was found. The analysis was further validated by Fluorescence In Situ Hybridization on these samples using probes specific for BRAF and CITED2. The results suggested that the modified method using Affymetrix Cytoscan HD chip gave rise to a significant improvement over most of the previous methods in terms of accuracy in detecting CNV in FFPE tissues. This FFPE microarray methodology may hold promise for broad application of CNV analysis on clinical samples.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Yu</LastName><ForeName>Yan P</ForeName><Initials>YP</Initials><AffiliationInfo><Affiliation>Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Michalopoulos</LastName><ForeName>Amantha</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ding</LastName><ForeName>Ying</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Department of Statistics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tseng</LastName><ForeName>George</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Department of Statistics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Luo</LastName><ForeName>Jian-Hua</ForeName><Initials>JH</Initials><AffiliationInfo><Affiliation>Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>R01 CA098249</GrantID><Acronym>CA</Acronym><Agency>NCI NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>UL1 TR000005</GrantID><Acronym>TR</Acronym><Agency>NCATS NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D003160">Comparative Study</PublicationType><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D052061">Research Support, N.I.H., Extramural</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2014</Year><Month>04</Month><Day>03</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>PLoS One</MedlineTA><NlmUniqueID>101285081</NlmUniqueID><ISSNLinking>1932-6203</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="C486381">CITED2 protein, human</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D004273">DNA, Neoplasm</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012097">Repressor Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D015534">Trans-Activators</NameOfSubstance></Chemical><Chemical><RegistryNumber>1HG84L3525</RegistryNumber><NameOfSubstance UI="D005557">Formaldehyde</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 2.7.11.1</RegistryNumber><NameOfSubstance UI="C482119">BRAF protein, human</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 2.7.11.1</RegistryNumber><NameOfSubstance UI="D048493">Proto-Oncogene Proteins B-raf</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><CommentsCorrectionsList><CommentsCorrections RefType="Cites"><RefSource>Am J Pathol. 2012 Apr;180(4):1495-508</RefSource><PMID Version="1">22326833</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Genes Chromosomes Cancer. 2012 Apr;51(4):344-52</RefSource><PMID Version="1">22162309</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Cancer 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Jun;180(6):2240-8</RefSource><PMID Version="1">22569189</PMID></CommentsCorrections></CommentsCorrectionsList><MeshHeadingList><MeshHeading><DescriptorName UI="D002869" MajorTopicYN="N">Chromosome Aberrations</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D056915" MajorTopicYN="N">DNA Copy Number Variations</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004273" MajorTopicYN="N">DNA, Neoplasm</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005557" MajorTopicYN="N">Formaldehyde</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="Y">Gene Expression Profiling</DescriptorName></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></MeshHeading><MeshHeading><DescriptorName UI="D008223" MajorTopicYN="N">Lymphoma</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020411" MajorTopicYN="Y">Oligonucleotide Array Sequence Analysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016612" MajorTopicYN="N">Paraffin Embedding</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D048493" MajorTopicYN="N">Proto-Oncogene Proteins B-raf</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012097" MajorTopicYN="N">Repressor Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016707" MajorTopicYN="N">Tissue Fixation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015534" MajorTopicYN="N">Trans-Activators</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading></MeshHeadingList><OtherID Source="NLM">PMC3974686</OtherID></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2013</Year><Month>12</Month><Day>04</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2014</Year><Month>02</Month><Day>26</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2014</Year><Month>4</Month><Day>5</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2014</Year><Month>4</Month><Day>5</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2015</Year><Month>1</Month><Day>28</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">24699316</ArticleId><ArticleId IdType="doi">10.1371/journal.pone.0092820</ArticleId><ArticleId IdType="pii">PONE-D-13-51000</ArticleId><ArticleId IdType="pmc">PMC3974686</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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