High Fidelity Copy Number Analysis of Formalin-Fixed and Paraffin-Embedded Tissues Using Affymetrix Cytoscan HD Chip
Identifieur interne : 001120 ( Pmc/Checkpoint ); précédent : 001119; suivant : 001121High Fidelity Copy Number Analysis of Formalin-Fixed and Paraffin-Embedded Tissues Using Affymetrix Cytoscan HD Chip
Auteurs : Yan P. Yu [États-Unis] ; Amantha Michalopoulos [États-Unis] ; Ying Ding [États-Unis] ; George Tseng [États-Unis] ; Jian-Hua Luo [États-Unis]Source :
- PLoS ONE [ 1932-6203 ] ; 2014.
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.
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DOI: 10.1371/journal.pone.0092820
PubMed: 24699316
PubMed Central: 3974686
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Yu</name><affiliation wicri:level="2"><nlm:aff id="aff1"><addr-line>Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania</wicri:regionArea><placeName><region type="state">Pennsylvanie</region></placeName></affiliation></author><author><name sortKey="Michalopoulos, Amantha" sort="Michalopoulos, Amantha" uniqKey="Michalopoulos A" first="Amantha" last="Michalopoulos">Amantha Michalopoulos</name><affiliation wicri:level="2"><nlm:aff id="aff1"><addr-line>Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania</wicri:regionArea><placeName><region type="state">Pennsylvanie</region></placeName></affiliation></author><author><name sortKey="Ding, Ying" sort="Ding, Ying" uniqKey="Ding Y" first="Ying" last="Ding">Ying Ding</name><affiliation wicri:level="2"><nlm:aff id="aff2"><addr-line>Department of Statistics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Statistics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania</wicri:regionArea><placeName><region type="state">Pennsylvanie</region></placeName></affiliation></author><author><name sortKey="Tseng, George" sort="Tseng, George" uniqKey="Tseng G" first="George" last="Tseng">George Tseng</name><affiliation wicri:level="2"><nlm:aff id="aff2"><addr-line>Department of Statistics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Statistics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania</wicri:regionArea><placeName><region type="state">Pennsylvanie</region></placeName></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 wicri:level="2"><nlm:aff id="aff1"><addr-line>Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania</wicri:regionArea><placeName><region type="state">Pennsylvanie</region></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">24699316</idno><idno type="pmc">3974686</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3974686</idno><idno type="RBID">PMC:3974686</idno><idno type="doi">10.1371/journal.pone.0092820</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">001D12</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">001D12</idno><idno type="wicri:Area/Pmc/Curation">001C87</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">001C87</idno><idno type="wicri:Area/Pmc/Checkpoint">001120</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">001120</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">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 wicri:level="2"><nlm:aff id="aff1"><addr-line>Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania</wicri:regionArea><placeName><region type="state">Pennsylvanie</region></placeName></affiliation></author><author><name sortKey="Michalopoulos, Amantha" sort="Michalopoulos, Amantha" uniqKey="Michalopoulos A" first="Amantha" last="Michalopoulos">Amantha Michalopoulos</name><affiliation wicri:level="2"><nlm:aff id="aff1"><addr-line>Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania</wicri:regionArea><placeName><region type="state">Pennsylvanie</region></placeName></affiliation></author><author><name sortKey="Ding, Ying" sort="Ding, Ying" uniqKey="Ding Y" first="Ying" last="Ding">Ying Ding</name><affiliation wicri:level="2"><nlm:aff id="aff2"><addr-line>Department of Statistics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Statistics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania</wicri:regionArea><placeName><region type="state">Pennsylvanie</region></placeName></affiliation></author><author><name sortKey="Tseng, George" sort="Tseng, George" uniqKey="Tseng G" first="George" last="Tseng">George Tseng</name><affiliation wicri:level="2"><nlm:aff id="aff2"><addr-line>Department of Statistics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Statistics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania</wicri:regionArea><placeName><region type="state">Pennsylvanie</region></placeName></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 wicri:level="2"><nlm:aff id="aff1"><addr-line>Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania</wicri:regionArea><placeName><region type="state">Pennsylvanie</region></placeName></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>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.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Barigozzi, C" uniqKey="Barigozzi C">C Barigozzi</name></author><author><name sortKey="Cusmano, L" uniqKey="Cusmano L">L Cusmano</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ren, B" uniqKey="Ren B">B Ren</name></author><author><name sortKey="Yu, G" uniqKey="Yu G">G Yu</name></author><author><name sortKey="Tseng, Gc" uniqKey="Tseng G">GC Tseng</name></author><author><name sortKey="Cieply, K" uniqKey="Cieply K">K Cieply</name></author><author><name sortKey="Gavel, T" uniqKey="Gavel T">T Gavel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yu, G" uniqKey="Yu G">G Yu</name></author><author><name sortKey="Tseng, Gc" uniqKey="Tseng G">GC Tseng</name></author><author><name sortKey="Yu, Yp" uniqKey="Yu Y">YP Yu</name></author><author><name sortKey="Gavel, T" uniqKey="Gavel T">T Gavel</name></author><author><name sortKey="Nelson, J" uniqKey="Nelson J">J Nelson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Luo, Jh" uniqKey="Luo J">JH Luo</name></author><author><name sortKey="Ren, B" uniqKey="Ren B">B Ren</name></author><author><name sortKey="Keryanov, S" uniqKey="Keryanov S">S Keryanov</name></author><author><name sortKey="Tseng, Gc" uniqKey="Tseng G">GC Tseng</name></author><author><name sortKey="Rao, Un" uniqKey="Rao U">UN Rao</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yu, Yp" uniqKey="Yu Y">YP Yu</name></author><author><name sortKey="Luo, Jh" uniqKey="Luo J">JH Luo</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Liu, W" uniqKey="Liu W">W Liu</name></author><author><name sortKey="Laitinen, S" uniqKey="Laitinen S">S Laitinen</name></author><author><name sortKey="Khan, S" uniqKey="Khan S">S Khan</name></author><author><name sortKey="Vihinen, M" uniqKey="Vihinen M">M Vihinen</name></author><author><name sortKey="Kowalski, J" uniqKey="Kowalski J">J Kowalski</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yu, Yp" uniqKey="Yu Y">YP Yu</name></author><author><name sortKey="Song, C" uniqKey="Song C">C Song</name></author><author><name sortKey="Tseng, G" uniqKey="Tseng G">G Tseng</name></author><author><name sortKey="Ren, Bg" uniqKey="Ren B">BG Ren</name></author><author><name sortKey="Laframboise, W" uniqKey="Laframboise W">W Laframboise</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nalesnik, Ma" uniqKey="Nalesnik M">MA Nalesnik</name></author><author><name sortKey="Tseng, G" uniqKey="Tseng G">G Tseng</name></author><author><name sortKey="Ding, Y" uniqKey="Ding Y">Y Ding</name></author><author><name sortKey="Xiang, Gs" uniqKey="Xiang G">GS Xiang</name></author><author><name sortKey="Zheng, Zl" uniqKey="Zheng Z">ZL Zheng</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Strassburger, K" uniqKey="Strassburger K">K Strassburger</name></author><author><name sortKey="Bretz, F" uniqKey="Bretz F">F Bretz</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hu, J" uniqKey="Hu J">J Hu</name></author><author><name sortKey="Surti, U" uniqKey="Surti U">U Surti</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Du, J" uniqKey="Du J">J Du</name></author><author><name sortKey="Li, Q" uniqKey="Li Q">Q Li</name></author><author><name sortKey="Tang, F" uniqKey="Tang F">F Tang</name></author><author><name sortKey="Puchowitz, Ma" uniqKey="Puchowitz M">MA Puchowitz</name></author><author><name sortKey="Fujioka, H" uniqKey="Fujioka H">H Fujioka</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cheung, Kf" uniqKey="Cheung K">KF Cheung</name></author><author><name sortKey="Zhao, J" uniqKey="Zhao J">J Zhao</name></author><author><name sortKey="Hao, Y" uniqKey="Hao Y">Y Hao</name></author><author><name sortKey="Li, X" uniqKey="Li X">X Li</name></author><author><name sortKey="Lowe, Aw" uniqKey="Lowe A">AW Lowe</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Thompson, Er" uniqKey="Thompson E">ER Thompson</name></author><author><name sortKey="Herbert, Sc" uniqKey="Herbert S">SC Herbert</name></author><author><name sortKey="Forrest, Sm" uniqKey="Forrest S">SM Forrest</name></author><author><name sortKey="Campbell, Ig" uniqKey="Campbell I">IG Campbell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wang, L" uniqKey="Wang L">L Wang</name></author><author><name sortKey="Rao, M" uniqKey="Rao M">M Rao</name></author><author><name sortKey="Fang, Y" uniqKey="Fang Y">Y Fang</name></author><author><name sortKey="Hameed, M" uniqKey="Hameed M">M Hameed</name></author><author><name sortKey="Viale, A" uniqKey="Viale A">A Viale</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tuefferd, M" uniqKey="Tuefferd M">M Tuefferd</name></author><author><name sortKey="De Bondt, A" uniqKey="De Bondt A">A De Bondt</name></author><author><name sortKey="Van Den Wyngaert, I" uniqKey="Van Den Wyngaert I">I Van Den Wyngaert</name></author><author><name sortKey="Talloen, W" uniqKey="Talloen W">W Talloen</name></author><author><name sortKey="Verbeke, T" uniqKey="Verbeke T">T Verbeke</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Little, Se" uniqKey="Little S">SE Little</name></author><author><name sortKey="Vuononvirta, R" uniqKey="Vuononvirta R">R Vuononvirta</name></author><author><name sortKey="Reis Filho, Js" uniqKey="Reis Filho J">JS Reis-Filho</name></author><author><name sortKey="Natrajan, R" uniqKey="Natrajan R">R Natrajan</name></author><author><name sortKey="Iravani, M" uniqKey="Iravani M">M Iravani</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nasri, S" uniqKey="Nasri S">S Nasri</name></author><author><name sortKey="Anjomshoaa, A" uniqKey="Anjomshoaa A">A Anjomshoaa</name></author><author><name sortKey="Song, S" uniqKey="Song S">S Song</name></author><author><name sortKey="Guilford, P" uniqKey="Guilford P">P Guilford</name></author><author><name sortKey="Mcnoe, L" uniqKey="Mcnoe L">L McNoe</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Oosting, J" uniqKey="Oosting J">J Oosting</name></author><author><name sortKey="Lips, Eh" uniqKey="Lips E">EH Lips</name></author><author><name sortKey="Van Eijk, R" uniqKey="Van Eijk R">R van Eijk</name></author><author><name sortKey="Eilers, Ph" uniqKey="Eilers P">PH Eilers</name></author><author><name sortKey="Szuhai, K" uniqKey="Szuhai K">K Szuhai</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lips, Eh" uniqKey="Lips E">EH Lips</name></author><author><name sortKey="Dierssen, Jw" uniqKey="Dierssen J">JW Dierssen</name></author><author><name sortKey="Van Eijk, R" uniqKey="Van Eijk R">R van Eijk</name></author><author><name sortKey="Oosting, J" uniqKey="Oosting J">J Oosting</name></author><author><name sortKey="Eilers, Ph" uniqKey="Eilers P">PH Eilers</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Krijgsman, O" uniqKey="Krijgsman O">O Krijgsman</name></author><author><name sortKey="Israeli, D" uniqKey="Israeli D">D Israeli</name></author><author><name sortKey="Haan, Jc" uniqKey="Haan J">JC Haan</name></author><author><name sortKey="Van Essen, Hf" uniqKey="Van Essen H">HF van Essen</name></author><author><name sortKey="Smeets, Sj" uniqKey="Smeets S">SJ Smeets</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wang, Y" uniqKey="Wang Y">Y Wang</name></author><author><name sortKey="Cottman, M" uniqKey="Cottman M">M Cottman</name></author><author><name sortKey="Schiffman, Jd" uniqKey="Schiffman J">JD Schiffman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Salawu, A" uniqKey="Salawu A">A Salawu</name></author><author><name sortKey="Ul Hassan, A" uniqKey="Ul Hassan A">A Ul-Hassan</name></author><author><name sortKey="Hammond, D" uniqKey="Hammond D">D Hammond</name></author><author><name sortKey="Fernando, M" uniqKey="Fernando M">M Fernando</name></author><author><name sortKey="Reed, M" uniqKey="Reed M">M Reed</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id><journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id><journal-id journal-id-type="publisher-id">plos</journal-id><journal-id journal-id-type="pmc">plosone</journal-id><journal-title-group><journal-title>PLoS ONE</journal-title></journal-title-group><issn pub-type="epub">1932-6203</issn><publisher><publisher-name>Public Library of Science</publisher-name><publisher-loc>San Francisco, USA</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">24699316</article-id><article-id pub-id-type="pmc">3974686</article-id><article-id pub-id-type="publisher-id">PONE-D-13-51000</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0092820</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="Discipline-v2"><subject>Biology and Life Sciences</subject><subj-group><subject>Genetics</subject><subj-group><subject>Genomics</subject><subj-group><subject>Genomic Medicine</subject><subj-group><subject>Genetic Testing</subject></subj-group></subj-group></subj-group><subj-group><subject>Human Genetics</subject></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v2"><subject>Medicine and Health Sciences</subject><subj-group><subject>Clinical Genetics</subject></subj-group><subj-group><subject>Diagnostic Medicine</subject></subj-group><subj-group><subject>Oncology</subject><subj-group><subject>Cancer Detection and Diagnosis</subject></subj-group></subj-group><subj-group><subject>Pathology and Laboratory Medicine</subject><subj-group><subject>Anatomical Pathology</subject><subject>Clinical Pathology</subject></subj-group></subj-group></subj-group></article-categories><title-group><article-title>High Fidelity Copy Number Analysis of Formalin-Fixed and Paraffin-Embedded Tissues Using Affymetrix Cytoscan HD Chip</article-title><alt-title alt-title-type="running-head">High Fidelity CNV Callings in FFPE</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Yu</surname><given-names>Yan P.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Michalopoulos</surname><given-names>Amantha</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Ding</surname><given-names>Ying</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Tseng</surname><given-names>George</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Luo</surname><given-names>Jian-Hua</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib></contrib-group><aff id="aff1"><label>1</label><addr-line>Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America</addr-line></aff><aff id="aff2"><label>2</label><addr-line>Department of Statistics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Franco</surname><given-names>Renato</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1"><addr-line>Istituto dei tumori Fondazione Pascale, Italy</addr-line></aff><author-notes><corresp id="cor1">* E-mail: <email>luoj@msx.upmc.edu</email></corresp><fn fn-type="conflict"><p><bold>Competing Interests: </bold>The authors have declared that no competing interests exist.</p></fn><fn fn-type="con"><p>Conceived and designed the experiments: JHL. Performed the experiments: YPY AM YD GT. Analyzed the data: YPY YD GT. Contributed reagents/materials/analysis tools: YD GT. Wrote the paper: JHL.</p></fn></author-notes><pub-date pub-type="collection"><year>2014</year></pub-date><pub-date pub-type="epub"><day>3</day><month>4</month><year>2014</year></pub-date><volume>9</volume><issue>4</issue><elocation-id>e92820</elocation-id><history><date date-type="received"><day>4</day><month>12</month><year>2013</year></date><date date-type="accepted"><day>26</day><month>2</month><year>2014</year></date></history><permissions><copyright-year>2014</copyright-year><copyright-holder>Yu et al</copyright-holder><license><license-p>This is an open-access article distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</ext-link>, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</license-p></license></permissions><abstract><p>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.</p></abstract><funding-group><funding-statement>This work was funded by the National Cancer Institute, Amercain Cancer Society and University of Pittsburgh Cancer Institute. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.</funding-statement></funding-group><counts><page-count count="9"></page-count></counts></article-meta></front></pmc><affiliations><list><country><li>États-Unis</li></country><region><li>Pennsylvanie</li></region></list><tree><country name="États-Unis"><region name="Pennsylvanie"><name sortKey="Yu, Yan P" sort="Yu, Yan P" uniqKey="Yu Y" first="Yan P." last="Yu">Yan P. Yu</name></region><name sortKey="Ding, Ying" sort="Ding, Ying" uniqKey="Ding Y" first="Ying" last="Ding">Ying Ding</name><name sortKey="Luo, Jian Hua" sort="Luo, Jian Hua" uniqKey="Luo J" first="Jian-Hua" last="Luo">Jian-Hua Luo</name><name sortKey="Michalopoulos, Amantha" sort="Michalopoulos, Amantha" uniqKey="Michalopoulos A" first="Amantha" last="Michalopoulos">Amantha Michalopoulos</name><name sortKey="Tseng, George" sort="Tseng, George" uniqKey="Tseng G" first="George" last="Tseng">George Tseng</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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