Protocol for qRT-PCR analysis from formalin fixed paraffin embedded tissue sections from diffuse large b-cell lymphoma: Validation of the six-gene predictor score
As a part of an international study on the molecular analysis of Diffuse Large B-cell Lymphoma (DLBCL), a robust protocol for gene expression analysis from RNA extraction to qRT-PCR using Formalin Fixed Paraffin Embedded tissues was developed. Here a study was conducted to define a strategy to valid...
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| Veröffentlicht in: | Oncotarget 2016-12, Vol.7 (50), p.83319-83329 |
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| creator | Tekin, Nilgun Omidvar, Nader Morris, Tim Peter Conget, Paulette Bruna, Flavia Timar, Botond Gagyi, Eva Basak, Ranjan Naik, Omkar Auewarakul, Chirayu Sritana, Narongrit Levy, Debora Cerci, Juliano Julio Bydlowski, Sergio Paulo Pereira, Juliana Dimamay, Mark Pierre Natividad, Filipinas Chung, June-Key Belder, Nevin Kuzu, Isinsu Paez, Diana Dondi, Maurizio Carr, Robert Ozdag, Hilal Padua, Rose Ann |
| description | As a part of an international study on the molecular analysis of Diffuse Large B-cell Lymphoma (DLBCL), a robust protocol for gene expression analysis from RNA extraction to qRT-PCR using Formalin Fixed Paraffin Embedded tissues was developed. Here a study was conducted to define a strategy to validate the previously reported 6-gene (LMO2, BCL6, FN1, CCND2, SCYA3 and BCL2) model as predictor of prognosis in DLBCL. To avoid variation, all samples were tested in a single centre and single platform. This study comprised 8 countries (Brazil, Chile, Hungary, India, Philippines, S. Korea, Thailand and Turkey). Using the Kaplan-Meier and log rank test on patients (n=162) and two mortality risk groups (with those above and below the mean representing high and low risk groups) confirmed that the 6-gene predictor score correlates significantly with overall survival (OS, p |
| doi_str_mv | 10.18632/oncotarget.13066 |
| format | Article |
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Here a study was conducted to define a strategy to validate the previously reported 6-gene (LMO2, BCL6, FN1, CCND2, SCYA3 and BCL2) model as predictor of prognosis in DLBCL. To avoid variation, all samples were tested in a single centre and single platform. This study comprised 8 countries (Brazil, Chile, Hungary, India, Philippines, S. Korea, Thailand and Turkey). Using the Kaplan-Meier and log rank test on patients (n=162) and two mortality risk groups (with those above and below the mean representing high and low risk groups) confirmed that the 6-gene predictor score correlates significantly with overall survival (OS, p<0.01) but not with event free survival (EFS, p=0.18). Adding the International Prognostic Index (IPI) shows that the 6-gene predictor score correlates significantly with high IPI scores for OS (p<0.05), whereas those with low IPI scores show a trend not reaching significance (p=0.08). This study defined an effective and economical qRT-PCR strategy and validated the 6-gene score as a predictor of OS in an international setting.</description><identifier>ISSN: 1949-2553</identifier><identifier>EISSN: 1949-2553</identifier><identifier>DOI: 10.18632/oncotarget.13066</identifier><identifier>PMID: 27825111</identifier><language>eng</language><publisher>United States: Impact Journals LLC</publisher><subject>Aged ; Asia ; Biomarkers, Tumor - genetics ; Biopsy ; Disease-Free Survival ; Europe ; Female ; Fixatives - chemistry ; Formaldehyde - chemistry ; Gene Expression Profiling - methods ; Gene Expression Profiling - standards ; Genetic Predisposition to Disease ; Humans ; Kaplan-Meier Estimate ; Lymphoma, Large B-Cell, Diffuse - drug therapy ; Lymphoma, Large B-Cell, Diffuse - genetics ; Lymphoma, Large B-Cell, Diffuse - mortality ; Lymphoma, Large B-Cell, Diffuse - pathology ; Male ; Middle Aged ; Paraffin Embedding ; Phenotype ; Predictive Value of Tests ; Proportional Hazards Models ; Real-Time Polymerase Chain Reaction - standards ; Reproducibility of Results ; Research Paper ; Reverse Transcriptase Polymerase Chain Reaction - standards ; South America ; Time Factors ; Tissue Fixation - methods ; Transcriptome</subject><ispartof>Oncotarget, 2016-12, Vol.7 (50), p.83319-83329</ispartof><rights>Copyright: © 2016 Tekin et al. 2016</rights><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c422t-512fd87d408a9efa2b7094249ccd245e90dac69c212d17e1ffb9a79c8d86850a3</citedby><cites>FETCH-LOGICAL-c422t-512fd87d408a9efa2b7094249ccd245e90dac69c212d17e1ffb9a79c8d86850a3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5347772/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5347772/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,27922,27923,53789,53791</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/27825111$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Tekin, Nilgun</creatorcontrib><creatorcontrib>Omidvar, Nader</creatorcontrib><creatorcontrib>Morris, Tim Peter</creatorcontrib><creatorcontrib>Conget, Paulette</creatorcontrib><creatorcontrib>Bruna, Flavia</creatorcontrib><creatorcontrib>Timar, Botond</creatorcontrib><creatorcontrib>Gagyi, Eva</creatorcontrib><creatorcontrib>Basak, Ranjan</creatorcontrib><creatorcontrib>Naik, Omkar</creatorcontrib><creatorcontrib>Auewarakul, Chirayu</creatorcontrib><creatorcontrib>Sritana, Narongrit</creatorcontrib><creatorcontrib>Levy, Debora</creatorcontrib><creatorcontrib>Cerci, Juliano Julio</creatorcontrib><creatorcontrib>Bydlowski, Sergio Paulo</creatorcontrib><creatorcontrib>Pereira, Juliana</creatorcontrib><creatorcontrib>Dimamay, Mark Pierre</creatorcontrib><creatorcontrib>Natividad, Filipinas</creatorcontrib><creatorcontrib>Chung, June-Key</creatorcontrib><creatorcontrib>Belder, Nevin</creatorcontrib><creatorcontrib>Kuzu, Isinsu</creatorcontrib><creatorcontrib>Paez, Diana</creatorcontrib><creatorcontrib>Dondi, Maurizio</creatorcontrib><creatorcontrib>Carr, Robert</creatorcontrib><creatorcontrib>Ozdag, Hilal</creatorcontrib><creatorcontrib>Padua, Rose Ann</creatorcontrib><title>Protocol for qRT-PCR analysis from formalin fixed paraffin embedded tissue sections from diffuse large b-cell lymphoma: Validation of the six-gene predictor score</title><title>Oncotarget</title><addtitle>Oncotarget</addtitle><description>As a part of an international study on the molecular analysis of Diffuse Large B-cell Lymphoma (DLBCL), a robust protocol for gene expression analysis from RNA extraction to qRT-PCR using Formalin Fixed Paraffin Embedded tissues was developed. 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This study defined an effective and economical qRT-PCR strategy and validated the 6-gene score as a predictor of OS in an international setting.</description><subject>Aged</subject><subject>Asia</subject><subject>Biomarkers, Tumor - genetics</subject><subject>Biopsy</subject><subject>Disease-Free Survival</subject><subject>Europe</subject><subject>Female</subject><subject>Fixatives - chemistry</subject><subject>Formaldehyde - chemistry</subject><subject>Gene Expression Profiling - methods</subject><subject>Gene Expression Profiling - standards</subject><subject>Genetic Predisposition to Disease</subject><subject>Humans</subject><subject>Kaplan-Meier Estimate</subject><subject>Lymphoma, Large B-Cell, Diffuse - drug therapy</subject><subject>Lymphoma, Large B-Cell, Diffuse - genetics</subject><subject>Lymphoma, Large B-Cell, Diffuse - mortality</subject><subject>Lymphoma, Large B-Cell, Diffuse - pathology</subject><subject>Male</subject><subject>Middle Aged</subject><subject>Paraffin Embedding</subject><subject>Phenotype</subject><subject>Predictive Value of Tests</subject><subject>Proportional Hazards Models</subject><subject>Real-Time Polymerase Chain Reaction - standards</subject><subject>Reproducibility of Results</subject><subject>Research Paper</subject><subject>Reverse Transcriptase Polymerase Chain Reaction - standards</subject><subject>South America</subject><subject>Time Factors</subject><subject>Tissue Fixation - methods</subject><subject>Transcriptome</subject><issn>1949-2553</issn><issn>1949-2553</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpVUU1P3DAQtaqigig_oJfKx15CY8f5cA-VqlULlZCKEPRqTezxrqskDraD2L_DL8ULW0p9GXvmvec3eoR8YOUp65qKf_aT9gnCGtMpq8qmeUOOmBSy4HVdvX11PyQnMf4p86lF23H5jhzyXGvG2BF5uAw-ee0Han2gt1fXxeXqisIEwza6SG3w424ywuAmat09GjpDAGvzE8cejcmd5GJckEbUyflpzzLO2iUiHXYWaV9oHAY6bMd540f4Qn9nRQM7PPWWpk2mu_tijRPSOaBxOmU_UfuA78mBhSHiyb4ek5sf369X58XFr7Ofq28XhRacp6Jm3JquNaLsQKIF3relFFxIrQ0XNcrSgG6k5owb1iKztpfQSt2ZrunqEqpj8vVZd176EY3GKQUY1BzcCGGrPDj1_2RyG7X2d6quRNu2PAt82gsEf7tgTGp0cbc2TOiXqFhXScaEbGSGsmeoDj7GgPblG1aqp3jVv3jVU7yZ8_G1vxfG3zCrRxBnqGo</recordid><startdate>20161213</startdate><enddate>20161213</enddate><creator>Tekin, Nilgun</creator><creator>Omidvar, Nader</creator><creator>Morris, Tim Peter</creator><creator>Conget, Paulette</creator><creator>Bruna, Flavia</creator><creator>Timar, Botond</creator><creator>Gagyi, Eva</creator><creator>Basak, Ranjan</creator><creator>Naik, Omkar</creator><creator>Auewarakul, Chirayu</creator><creator>Sritana, Narongrit</creator><creator>Levy, Debora</creator><creator>Cerci, Juliano Julio</creator><creator>Bydlowski, Sergio Paulo</creator><creator>Pereira, Juliana</creator><creator>Dimamay, Mark Pierre</creator><creator>Natividad, Filipinas</creator><creator>Chung, June-Key</creator><creator>Belder, Nevin</creator><creator>Kuzu, Isinsu</creator><creator>Paez, Diana</creator><creator>Dondi, Maurizio</creator><creator>Carr, Robert</creator><creator>Ozdag, Hilal</creator><creator>Padua, Rose Ann</creator><general>Impact Journals LLC</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20161213</creationdate><title>Protocol for qRT-PCR analysis from formalin fixed paraffin embedded tissue sections from diffuse large b-cell lymphoma: Validation of the six-gene predictor score</title><author>Tekin, Nilgun ; Omidvar, Nader ; Morris, Tim Peter ; Conget, Paulette ; Bruna, Flavia ; Timar, Botond ; Gagyi, Eva ; Basak, Ranjan ; Naik, Omkar ; Auewarakul, Chirayu ; Sritana, Narongrit ; Levy, Debora ; Cerci, Juliano Julio ; Bydlowski, Sergio Paulo ; Pereira, Juliana ; Dimamay, Mark Pierre ; Natividad, Filipinas ; Chung, June-Key ; Belder, Nevin ; Kuzu, Isinsu ; Paez, Diana ; Dondi, Maurizio ; Carr, Robert ; Ozdag, Hilal ; Padua, Rose Ann</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c422t-512fd87d408a9efa2b7094249ccd245e90dac69c212d17e1ffb9a79c8d86850a3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2016</creationdate><topic>Aged</topic><topic>Asia</topic><topic>Biomarkers, Tumor - genetics</topic><topic>Biopsy</topic><topic>Disease-Free Survival</topic><topic>Europe</topic><topic>Female</topic><topic>Fixatives - chemistry</topic><topic>Formaldehyde - chemistry</topic><topic>Gene Expression Profiling - methods</topic><topic>Gene Expression Profiling - standards</topic><topic>Genetic Predisposition to Disease</topic><topic>Humans</topic><topic>Kaplan-Meier Estimate</topic><topic>Lymphoma, Large B-Cell, Diffuse - drug therapy</topic><topic>Lymphoma, Large B-Cell, Diffuse - genetics</topic><topic>Lymphoma, Large B-Cell, Diffuse - mortality</topic><topic>Lymphoma, Large B-Cell, Diffuse - pathology</topic><topic>Male</topic><topic>Middle Aged</topic><topic>Paraffin Embedding</topic><topic>Phenotype</topic><topic>Predictive Value of Tests</topic><topic>Proportional Hazards Models</topic><topic>Real-Time Polymerase Chain Reaction - standards</topic><topic>Reproducibility of Results</topic><topic>Research Paper</topic><topic>Reverse Transcriptase Polymerase Chain Reaction - standards</topic><topic>South America</topic><topic>Time Factors</topic><topic>Tissue Fixation - methods</topic><topic>Transcriptome</topic><toplevel>online_resources</toplevel><creatorcontrib>Tekin, Nilgun</creatorcontrib><creatorcontrib>Omidvar, Nader</creatorcontrib><creatorcontrib>Morris, Tim Peter</creatorcontrib><creatorcontrib>Conget, Paulette</creatorcontrib><creatorcontrib>Bruna, Flavia</creatorcontrib><creatorcontrib>Timar, Botond</creatorcontrib><creatorcontrib>Gagyi, Eva</creatorcontrib><creatorcontrib>Basak, Ranjan</creatorcontrib><creatorcontrib>Naik, Omkar</creatorcontrib><creatorcontrib>Auewarakul, Chirayu</creatorcontrib><creatorcontrib>Sritana, Narongrit</creatorcontrib><creatorcontrib>Levy, Debora</creatorcontrib><creatorcontrib>Cerci, Juliano Julio</creatorcontrib><creatorcontrib>Bydlowski, Sergio Paulo</creatorcontrib><creatorcontrib>Pereira, Juliana</creatorcontrib><creatorcontrib>Dimamay, Mark Pierre</creatorcontrib><creatorcontrib>Natividad, Filipinas</creatorcontrib><creatorcontrib>Chung, June-Key</creatorcontrib><creatorcontrib>Belder, Nevin</creatorcontrib><creatorcontrib>Kuzu, Isinsu</creatorcontrib><creatorcontrib>Paez, Diana</creatorcontrib><creatorcontrib>Dondi, Maurizio</creatorcontrib><creatorcontrib>Carr, Robert</creatorcontrib><creatorcontrib>Ozdag, Hilal</creatorcontrib><creatorcontrib>Padua, Rose Ann</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Oncotarget</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Tekin, Nilgun</au><au>Omidvar, Nader</au><au>Morris, Tim Peter</au><au>Conget, Paulette</au><au>Bruna, Flavia</au><au>Timar, Botond</au><au>Gagyi, Eva</au><au>Basak, Ranjan</au><au>Naik, Omkar</au><au>Auewarakul, Chirayu</au><au>Sritana, Narongrit</au><au>Levy, Debora</au><au>Cerci, Juliano Julio</au><au>Bydlowski, Sergio Paulo</au><au>Pereira, Juliana</au><au>Dimamay, Mark Pierre</au><au>Natividad, Filipinas</au><au>Chung, June-Key</au><au>Belder, Nevin</au><au>Kuzu, Isinsu</au><au>Paez, Diana</au><au>Dondi, Maurizio</au><au>Carr, Robert</au><au>Ozdag, Hilal</au><au>Padua, Rose Ann</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Protocol for qRT-PCR analysis from formalin fixed paraffin embedded tissue sections from diffuse large b-cell lymphoma: Validation of the six-gene predictor score</atitle><jtitle>Oncotarget</jtitle><addtitle>Oncotarget</addtitle><date>2016-12-13</date><risdate>2016</risdate><volume>7</volume><issue>50</issue><spage>83319</spage><epage>83329</epage><pages>83319-83329</pages><issn>1949-2553</issn><eissn>1949-2553</eissn><abstract>As a part of an international study on the molecular analysis of Diffuse Large B-cell Lymphoma (DLBCL), a robust protocol for gene expression analysis from RNA extraction to qRT-PCR using Formalin Fixed Paraffin Embedded tissues was developed. 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This study defined an effective and economical qRT-PCR strategy and validated the 6-gene score as a predictor of OS in an international setting.</abstract><cop>United States</cop><pub>Impact Journals LLC</pub><pmid>27825111</pmid><doi>10.18632/oncotarget.13066</doi><tpages>11</tpages><oa>free_for_read</oa></addata></record> |
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| ispartof | Oncotarget, 2016-12, Vol.7 (50), p.83319-83329 |
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| source | MEDLINE; PubMed Central Open Access; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free E- Journals |
| subjects | Aged Asia Biomarkers, Tumor - genetics Biopsy Disease-Free Survival Europe Female Fixatives - chemistry Formaldehyde - chemistry Gene Expression Profiling - methods Gene Expression Profiling - standards Genetic Predisposition to Disease Humans Kaplan-Meier Estimate Lymphoma, Large B-Cell, Diffuse - drug therapy Lymphoma, Large B-Cell, Diffuse - genetics Lymphoma, Large B-Cell, Diffuse - mortality Lymphoma, Large B-Cell, Diffuse - pathology Male Middle Aged Paraffin Embedding Phenotype Predictive Value of Tests Proportional Hazards Models Real-Time Polymerase Chain Reaction - standards Reproducibility of Results Research Paper Reverse Transcriptase Polymerase Chain Reaction - standards South America Time Factors Tissue Fixation - methods Transcriptome |
| title | Protocol for qRT-PCR analysis from formalin fixed paraffin embedded tissue sections from diffuse large b-cell lymphoma: Validation of the six-gene predictor score |
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