Identification of methods for use of formalin-fixed, paraffin-embedded tissue samples in RNA expression profiling
Formalin-fixed paraffin-embedded (FFPE) tissue samples are a potentially valuable resource of expression information for medical research, but are under-utilized due to degradation and modification of the RNA. Using a random primer-based RNA amplification strategy, we have evaluated multiple protoco...
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| Veröffentlicht in: | Genomics (San Diego, Calif.) Calif.), 2009-11, Vol.94 (5), p.341-348 |
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| description | Formalin-fixed paraffin-embedded (FFPE) tissue samples are a potentially valuable resource of expression information for medical research, but are under-utilized due to degradation and modification of the RNA. Using a random primer-based RNA amplification strategy, we have evaluated multiple protocols for the extraction and isolation of RNA from FFPE samples. We found that the RecoverAll RNA isolation procedure with three or four slices (ten-microns in thickness), supplemented with additional DNAse, gave optimal results. RNA integrity as assessed by Agilent Bioanalyzer, and amplification of the 28S ribosomal RNA, were predictive for the number of genes detected on Affymetrix arrays. We obtained expression data for colon and lung tumor and normal FFPE samples and matched frozen samples and found a high correlation between frozen and matched FFPE samples (
R
2 between 0.82 and 0.89), while the signature sets in tumor versus normal comparisons were also quite similar. QPCR confirmed all 16 of the differential expression results from the microarrays that we tested. Differentially expressed signature genes from tumor versus matched normal FFPE tissue from colon and lung were identified as cancer-related, with 95 colon tumor and 67 lung tumor genes identified, respectively. |
| doi_str_mv | 10.1016/j.ygeno.2009.07.007 |
| format | Article |
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R
2 between 0.82 and 0.89), while the signature sets in tumor versus normal comparisons were also quite similar. QPCR confirmed all 16 of the differential expression results from the microarrays that we tested. Differentially expressed signature genes from tumor versus matched normal FFPE tissue from colon and lung were identified as cancer-related, with 95 colon tumor and 67 lung tumor genes identified, respectively.</description><identifier>ISSN: 0888-7543</identifier><identifier>EISSN: 1089-8646</identifier><identifier>DOI: 10.1016/j.ygeno.2009.07.007</identifier><identifier>PMID: 19660539</identifier><language>eng</language><publisher>Amsterdam: Elsevier Inc</publisher><subject>Biological and medical sciences ; Colon cancer ; Colonic Neoplasms - metabolism ; Expression profiling ; FFPE ; Formaldehyde ; Freezing ; Fundamental and applied biological sciences. Psychology ; Gastroenterology. Liver. Pancreas. Abdomen ; Gene Expression Profiling ; Genes. Genome ; Genetics of eukaryotes. Biological and molecular evolution ; Humans ; Lung cancer ; Lung Neoplasms - metabolism ; Medical sciences ; Microarrays ; Molecular and cellular biology ; Molecular genetics ; Oligonucleotide Array Sequence Analysis - methods ; Paraffin Embedding - methods ; RampUP ; Reverse Transcriptase Polymerase Chain Reaction ; RNA - analysis ; RNA - isolation & purification ; RNA extraction ; RNA, Neoplasm - analysis ; RNA, Neoplasm - isolation & purification ; RNA, Ribosomal, 28S - genetics ; Stomach. Duodenum. Small intestine. Colon. Rectum. Anus ; Tissue Fixation - methods ; Tumors</subject><ispartof>Genomics (San Diego, Calif.), 2009-11, Vol.94 (5), p.341-348</ispartof><rights>2009 Elsevier Inc.</rights><rights>2009 INIST-CNRS</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c485t-8cbe4f3438fc228d8ed151271cc3e8e7e579f57c4ed2bc1da2c531476b1ae03</citedby><cites>FETCH-LOGICAL-c485t-8cbe4f3438fc228d8ed151271cc3e8e7e579f57c4ed2bc1da2c531476b1ae03</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.ygeno.2009.07.007$$EHTML$$P50$$Gelsevier$$Hfree_for_read</linktohtml><link.rule.ids>314,780,784,3550,27924,27925,45995</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=22081070$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/19660539$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Roberts, Lisa</creatorcontrib><creatorcontrib>Bowers, Jessica</creatorcontrib><creatorcontrib>Sensinger, Kelly</creatorcontrib><creatorcontrib>Lisowski, Andrew</creatorcontrib><creatorcontrib>Getts, Robert</creatorcontrib><creatorcontrib>Anderson, Mark G.</creatorcontrib><title>Identification of methods for use of formalin-fixed, paraffin-embedded tissue samples in RNA expression profiling</title><title>Genomics (San Diego, Calif.)</title><addtitle>Genomics</addtitle><description>Formalin-fixed paraffin-embedded (FFPE) tissue samples are a potentially valuable resource of expression information for medical research, but are under-utilized due to degradation and modification of the RNA. Using a random primer-based RNA amplification strategy, we have evaluated multiple protocols for the extraction and isolation of RNA from FFPE samples. We found that the RecoverAll RNA isolation procedure with three or four slices (ten-microns in thickness), supplemented with additional DNAse, gave optimal results. RNA integrity as assessed by Agilent Bioanalyzer, and amplification of the 28S ribosomal RNA, were predictive for the number of genes detected on Affymetrix arrays. We obtained expression data for colon and lung tumor and normal FFPE samples and matched frozen samples and found a high correlation between frozen and matched FFPE samples (
R
2 between 0.82 and 0.89), while the signature sets in tumor versus normal comparisons were also quite similar. QPCR confirmed all 16 of the differential expression results from the microarrays that we tested. Differentially expressed signature genes from tumor versus matched normal FFPE tissue from colon and lung were identified as cancer-related, with 95 colon tumor and 67 lung tumor genes identified, respectively.</description><subject>Biological and medical sciences</subject><subject>Colon cancer</subject><subject>Colonic Neoplasms - metabolism</subject><subject>Expression profiling</subject><subject>FFPE</subject><subject>Formaldehyde</subject><subject>Freezing</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Gastroenterology. Liver. Pancreas. Abdomen</subject><subject>Gene Expression Profiling</subject><subject>Genes. Genome</subject><subject>Genetics of eukaryotes. Biological and molecular evolution</subject><subject>Humans</subject><subject>Lung cancer</subject><subject>Lung Neoplasms - metabolism</subject><subject>Medical sciences</subject><subject>Microarrays</subject><subject>Molecular and cellular biology</subject><subject>Molecular genetics</subject><subject>Oligonucleotide Array Sequence Analysis - methods</subject><subject>Paraffin Embedding - methods</subject><subject>RampUP</subject><subject>Reverse Transcriptase Polymerase Chain Reaction</subject><subject>RNA - analysis</subject><subject>RNA - isolation & purification</subject><subject>RNA extraction</subject><subject>RNA, Neoplasm - analysis</subject><subject>RNA, Neoplasm - isolation & purification</subject><subject>RNA, Ribosomal, 28S - genetics</subject><subject>Stomach. Duodenum. Small intestine. Colon. Rectum. Anus</subject><subject>Tissue Fixation - methods</subject><subject>Tumors</subject><issn>0888-7543</issn><issn>1089-8646</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2009</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kUtv1TAQRi1ERS-FX4CEvAE2JPiRxM6CRVXxqFS1ErC3HHtcfJVXPQlq_30d7hXsurI9OvPZ40PIG85KznjzaV8-3MI4lYKxtmSqZEw9IzvOdFvopmqekx3TWheqruQpeYm4ZxmUWrwgp7xtGlbLdkfuLj2MSwzR2SVOI50CHWD5PXmkYUp0RdhKeTvYPo5FiPfgP9LZJhtCPsPQgffg6RIRV6Boh7kHpHGkP67PKdzPCRC34DlNIeaI21fkJNge4fVxPSM_v375dfG9uLr5dnlxflW4StdLoV0HVZCV1MEJob0Gz2suFHdOggYFtWpDrVwFXnSOeytcLXmlmo5bYPKMfDik5nvvVsDFDBEd9L0dYVrRKFmxljMpMvn-SVJw1jRCtBmUB9ClCTFBMHOKg00PhjOzGTF789eI2YwYpkw2krveHuPXbgD_v-eoIAPvjoBFZ_uQ7Ogi_uOEYJoztU30-cBB_rQ_EZJBF2F04GMCtxg_xScf8ghWhaxk</recordid><startdate>20091101</startdate><enddate>20091101</enddate><creator>Roberts, Lisa</creator><creator>Bowers, Jessica</creator><creator>Sensinger, Kelly</creator><creator>Lisowski, Andrew</creator><creator>Getts, Robert</creator><creator>Anderson, Mark G.</creator><general>Elsevier Inc</general><general>Elsevier</general><scope>6I.</scope><scope>AAFTH</scope><scope>IQODW</scope><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>7TM</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>20091101</creationdate><title>Identification of methods for use of formalin-fixed, paraffin-embedded tissue samples in RNA expression profiling</title><author>Roberts, Lisa ; Bowers, Jessica ; Sensinger, Kelly ; Lisowski, Andrew ; Getts, Robert ; Anderson, Mark G.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c485t-8cbe4f3438fc228d8ed151271cc3e8e7e579f57c4ed2bc1da2c531476b1ae03</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2009</creationdate><topic>Biological and medical sciences</topic><topic>Colon cancer</topic><topic>Colonic Neoplasms - metabolism</topic><topic>Expression profiling</topic><topic>FFPE</topic><topic>Formaldehyde</topic><topic>Freezing</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Gastroenterology. Liver. Pancreas. Abdomen</topic><topic>Gene Expression Profiling</topic><topic>Genes. Genome</topic><topic>Genetics of eukaryotes. Biological and molecular evolution</topic><topic>Humans</topic><topic>Lung cancer</topic><topic>Lung Neoplasms - metabolism</topic><topic>Medical sciences</topic><topic>Microarrays</topic><topic>Molecular and cellular biology</topic><topic>Molecular genetics</topic><topic>Oligonucleotide Array Sequence Analysis - methods</topic><topic>Paraffin Embedding - methods</topic><topic>RampUP</topic><topic>Reverse Transcriptase Polymerase Chain Reaction</topic><topic>RNA - analysis</topic><topic>RNA - isolation & purification</topic><topic>RNA extraction</topic><topic>RNA, Neoplasm - analysis</topic><topic>RNA, Neoplasm - isolation & purification</topic><topic>RNA, Ribosomal, 28S - genetics</topic><topic>Stomach. Duodenum. Small intestine. Colon. Rectum. Anus</topic><topic>Tissue Fixation - methods</topic><topic>Tumors</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Roberts, Lisa</creatorcontrib><creatorcontrib>Bowers, Jessica</creatorcontrib><creatorcontrib>Sensinger, Kelly</creatorcontrib><creatorcontrib>Lisowski, Andrew</creatorcontrib><creatorcontrib>Getts, Robert</creatorcontrib><creatorcontrib>Anderson, Mark G.</creatorcontrib><collection>ScienceDirect Open Access Titles</collection><collection>Elsevier:ScienceDirect:Open Access</collection><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Nucleic Acids Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Genomics (San Diego, Calif.)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Roberts, Lisa</au><au>Bowers, Jessica</au><au>Sensinger, Kelly</au><au>Lisowski, Andrew</au><au>Getts, Robert</au><au>Anderson, Mark G.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Identification of methods for use of formalin-fixed, paraffin-embedded tissue samples in RNA expression profiling</atitle><jtitle>Genomics (San Diego, Calif.)</jtitle><addtitle>Genomics</addtitle><date>2009-11-01</date><risdate>2009</risdate><volume>94</volume><issue>5</issue><spage>341</spage><epage>348</epage><pages>341-348</pages><issn>0888-7543</issn><eissn>1089-8646</eissn><abstract>Formalin-fixed paraffin-embedded (FFPE) tissue samples are a potentially valuable resource of expression information for medical research, but are under-utilized due to degradation and modification of the RNA. Using a random primer-based RNA amplification strategy, we have evaluated multiple protocols for the extraction and isolation of RNA from FFPE samples. We found that the RecoverAll RNA isolation procedure with three or four slices (ten-microns in thickness), supplemented with additional DNAse, gave optimal results. RNA integrity as assessed by Agilent Bioanalyzer, and amplification of the 28S ribosomal RNA, were predictive for the number of genes detected on Affymetrix arrays. We obtained expression data for colon and lung tumor and normal FFPE samples and matched frozen samples and found a high correlation between frozen and matched FFPE samples (
R
2 between 0.82 and 0.89), while the signature sets in tumor versus normal comparisons were also quite similar. QPCR confirmed all 16 of the differential expression results from the microarrays that we tested. Differentially expressed signature genes from tumor versus matched normal FFPE tissue from colon and lung were identified as cancer-related, with 95 colon tumor and 67 lung tumor genes identified, respectively.</abstract><cop>Amsterdam</cop><pub>Elsevier Inc</pub><pmid>19660539</pmid><doi>10.1016/j.ygeno.2009.07.007</doi><tpages>8</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Biological and medical sciences Colon cancer Colonic Neoplasms - metabolism Expression profiling FFPE Formaldehyde Freezing Fundamental and applied biological sciences. Psychology Gastroenterology. Liver. Pancreas. Abdomen Gene Expression Profiling Genes. Genome Genetics of eukaryotes. Biological and molecular evolution Humans Lung cancer Lung Neoplasms - metabolism Medical sciences Microarrays Molecular and cellular biology Molecular genetics Oligonucleotide Array Sequence Analysis - methods Paraffin Embedding - methods RampUP Reverse Transcriptase Polymerase Chain Reaction RNA - analysis RNA - isolation & purification RNA extraction RNA, Neoplasm - analysis RNA, Neoplasm - isolation & purification RNA, Ribosomal, 28S - genetics Stomach. Duodenum. Small intestine. Colon. Rectum. Anus Tissue Fixation - methods Tumors |
| title | Identification of methods for use of formalin-fixed, paraffin-embedded tissue samples in RNA expression profiling |
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