Cross-laboratory validation of the OncoScan® FFPE Assay, a multiplex tool for whole genome tumour profiling
Adoption of new technology in both basic research and clinical settings requires rigorous validation of analytical performance. The OncoScan® FFPE Assay is a multiplexing tool that offers genome-wide copy number and loss of heterozygosity detection, as well as identification of frequently tested som...
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creator | Foster, Joseph M Oumie, Assa Togneri, Fiona S Vasques, Fabiana Ramos Hau, Debra Taylor, Morag Tinkler-Hundal, Emma Southward, Katie Medlow, Paul McGreeghan-Crosby, Keith Halfpenny, Iris McMullan, Dominic J Quirke, Phil Keating, Katherine E Griffiths, Mike Spink, Karen G Brew, Fiona |
description | Adoption of new technology in both basic research and clinical settings requires rigorous validation of analytical performance. The OncoScan® FFPE Assay is a multiplexing tool that offers genome-wide copy number and loss of heterozygosity detection, as well as identification of frequently tested somatic mutations.
In this study, 162 formalin fixed paraffin embedded samples, representing six different tumour types, were profiled in triplicate across three independent laboratories. OncoScan® formalin fixed paraffin embedded assay data was then analysed for reproducibility of genome-wide copy number, loss of heterozygosity and somatic mutations. Where available, somatic mutation data was compared to data from orthogonal technologies (pyro/sanger sequencing).
Cross site comparisons of genome-wide copy number and loss of heterozygosity profiles showed greater than 95% average agreement between sites. Somatic mutations pre-validated by orthogonal technologies showed greater than 90% agreement with OncoScan® somatic mutation calls and somatic mutation concordance between sites averaged 97%.
Reproducibility of whole-genome copy number, loss of heterozygosity and somatic mutation data using the OncoScan® assay has been demonstrated with comparatively low DNA inputs from a range of highly degraded formalin fixed paraffin embedded samples. In addition, our data shows examples of clinically-relevant aberrations that demonstrate the potential utility of the OncoScan® assay as a robust clinical tool for guiding tumour therapy. |
doi_str_mv | 10.1186/s12920-015-0079-z |
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In this study, 162 formalin fixed paraffin embedded samples, representing six different tumour types, were profiled in triplicate across three independent laboratories. OncoScan® formalin fixed paraffin embedded assay data was then analysed for reproducibility of genome-wide copy number, loss of heterozygosity and somatic mutations. Where available, somatic mutation data was compared to data from orthogonal technologies (pyro/sanger sequencing).
Cross site comparisons of genome-wide copy number and loss of heterozygosity profiles showed greater than 95% average agreement between sites. Somatic mutations pre-validated by orthogonal technologies showed greater than 90% agreement with OncoScan® somatic mutation calls and somatic mutation concordance between sites averaged 97%.
Reproducibility of whole-genome copy number, loss of heterozygosity and somatic mutation data using the OncoScan® assay has been demonstrated with comparatively low DNA inputs from a range of highly degraded formalin fixed paraffin embedded samples. In addition, our data shows examples of clinically-relevant aberrations that demonstrate the potential utility of the OncoScan® assay as a robust clinical tool for guiding tumour therapy.</description><identifier>ISSN: 1755-8794</identifier><identifier>EISSN: 1755-8794</identifier><identifier>DOI: 10.1186/s12920-015-0079-z</identifier><identifier>PMID: 25889064</identifier><language>eng</language><publisher>England: BioMed Central Ltd</publisher><subject>Analysis ; Biotechnology industry ; Clinical Laboratory Techniques - standards ; Comparative analysis ; DNA Mutational Analysis ; Female ; Gene Expression Profiling - methods ; Gene Expression Regulation, Neoplastic ; Genome, Human ; Health aspects ; Humans ; Innovations ; Loss of Heterozygosity ; Male ; Mutation ; Neoplasms - genetics ; Neoplasms - metabolism ; Oligonucleotide Array Sequence Analysis - methods ; Paraffin Embedding ; Quality Control ; Reproducibility of Results ; Sensitivity and Specificity ; Sequence Analysis, DNA ; Technical Advance ; Tissue Fixation - methods</subject><ispartof>BMC medical genomics, 2015-02, Vol.8 (1), p.5-5, Article 5</ispartof><rights>COPYRIGHT 2015 BioMed Central Ltd.</rights><rights>Foster et al.; licensee BioMed Central. 2015</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c500t-56611af6c7f373ab378811e77d4ce55cc87a157ce25e1218ab03a69fb83263923</citedby><cites>FETCH-LOGICAL-c500t-56611af6c7f373ab378811e77d4ce55cc87a157ce25e1218ab03a69fb83263923</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/PMC4342810/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4342810/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,724,777,781,861,882,27905,27906,53772,53774</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25889064$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Foster, Joseph M</creatorcontrib><creatorcontrib>Oumie, Assa</creatorcontrib><creatorcontrib>Togneri, Fiona S</creatorcontrib><creatorcontrib>Vasques, Fabiana Ramos</creatorcontrib><creatorcontrib>Hau, Debra</creatorcontrib><creatorcontrib>Taylor, Morag</creatorcontrib><creatorcontrib>Tinkler-Hundal, Emma</creatorcontrib><creatorcontrib>Southward, Katie</creatorcontrib><creatorcontrib>Medlow, Paul</creatorcontrib><creatorcontrib>McGreeghan-Crosby, Keith</creatorcontrib><creatorcontrib>Halfpenny, Iris</creatorcontrib><creatorcontrib>McMullan, Dominic J</creatorcontrib><creatorcontrib>Quirke, Phil</creatorcontrib><creatorcontrib>Keating, Katherine E</creatorcontrib><creatorcontrib>Griffiths, Mike</creatorcontrib><creatorcontrib>Spink, Karen G</creatorcontrib><creatorcontrib>Brew, Fiona</creatorcontrib><title>Cross-laboratory validation of the OncoScan® FFPE Assay, a multiplex tool for whole genome tumour profiling</title><title>BMC medical genomics</title><addtitle>BMC Med Genomics</addtitle><description>Adoption of new technology in both basic research and clinical settings requires rigorous validation of analytical performance. The OncoScan® FFPE Assay is a multiplexing tool that offers genome-wide copy number and loss of heterozygosity detection, as well as identification of frequently tested somatic mutations.
In this study, 162 formalin fixed paraffin embedded samples, representing six different tumour types, were profiled in triplicate across three independent laboratories. OncoScan® formalin fixed paraffin embedded assay data was then analysed for reproducibility of genome-wide copy number, loss of heterozygosity and somatic mutations. Where available, somatic mutation data was compared to data from orthogonal technologies (pyro/sanger sequencing).
Cross site comparisons of genome-wide copy number and loss of heterozygosity profiles showed greater than 95% average agreement between sites. Somatic mutations pre-validated by orthogonal technologies showed greater than 90% agreement with OncoScan® somatic mutation calls and somatic mutation concordance between sites averaged 97%.
Reproducibility of whole-genome copy number, loss of heterozygosity and somatic mutation data using the OncoScan® assay has been demonstrated with comparatively low DNA inputs from a range of highly degraded formalin fixed paraffin embedded samples. In addition, our data shows examples of clinically-relevant aberrations that demonstrate the potential utility of the OncoScan® assay as a robust clinical tool for guiding tumour therapy.</description><subject>Analysis</subject><subject>Biotechnology industry</subject><subject>Clinical Laboratory Techniques - standards</subject><subject>Comparative analysis</subject><subject>DNA Mutational Analysis</subject><subject>Female</subject><subject>Gene Expression Profiling - methods</subject><subject>Gene Expression Regulation, Neoplastic</subject><subject>Genome, Human</subject><subject>Health aspects</subject><subject>Humans</subject><subject>Innovations</subject><subject>Loss of Heterozygosity</subject><subject>Male</subject><subject>Mutation</subject><subject>Neoplasms - genetics</subject><subject>Neoplasms - metabolism</subject><subject>Oligonucleotide Array Sequence Analysis - methods</subject><subject>Paraffin Embedding</subject><subject>Quality Control</subject><subject>Reproducibility of Results</subject><subject>Sensitivity and Specificity</subject><subject>Sequence Analysis, DNA</subject><subject>Technical Advance</subject><subject>Tissue Fixation - methods</subject><issn>1755-8794</issn><issn>1755-8794</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNptkt1qFDEYhgex2Fq9AE8k4ImCU5PJ5GdOCsvSrYVCxepxyGS_mY1kkjXJ1G4vyovwyjrLtqULkoME8rwv5MtTFO8IPiFE8i-JVE2FS0xYibFoyrsXxRERjJVSNPXLZ-fD4nVKvzDmmDXkVXFYMSkbzOujws1jSKl0ug1R5xA36EY7u9TZBo9Ch_IK0JU34dpo_-8vWiy-naFZSnrzGWk0jC7btYNblENwqAsR_VkFB6gHHwZAeRzCGNE6hs466_s3xUGnXYK3D_tx8XNx9mP-tby8Or-Yzy5LwzDOJeOcEN1xIzoqqG6pkJIQEGJZG2DMGCk0YcJAxYBUROoWU82brpW04rSp6HFxuutdj-0ASwM-R-3UOtpBx40K2qr9G29Xqg83qqZ1JQmeCj4-FMTwe4SU1WCTAee0hzAmRbiouWS1oBP6YYf22oGyvgtTo9niasZqUnNBKzFRJ_-hprWEwZrgYRoQ7Ac-7QUmJsNt7vWYkrq4_r7Pkh1rtn8ZoXt6KcFqK4raiaImUdRWFHU3Zd4_H9FT4tEMeg9K-7ls</recordid><startdate>20150218</startdate><enddate>20150218</enddate><creator>Foster, Joseph M</creator><creator>Oumie, Assa</creator><creator>Togneri, Fiona S</creator><creator>Vasques, Fabiana Ramos</creator><creator>Hau, Debra</creator><creator>Taylor, Morag</creator><creator>Tinkler-Hundal, Emma</creator><creator>Southward, Katie</creator><creator>Medlow, Paul</creator><creator>McGreeghan-Crosby, Keith</creator><creator>Halfpenny, Iris</creator><creator>McMullan, Dominic J</creator><creator>Quirke, Phil</creator><creator>Keating, Katherine E</creator><creator>Griffiths, Mike</creator><creator>Spink, Karen G</creator><creator>Brew, Fiona</creator><general>BioMed Central Ltd</general><general>BioMed Central</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>ISR</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20150218</creationdate><title>Cross-laboratory validation of the OncoScan® FFPE Assay, a multiplex tool for whole genome tumour profiling</title><author>Foster, Joseph M ; Oumie, Assa ; Togneri, Fiona S ; Vasques, Fabiana Ramos ; Hau, Debra ; Taylor, Morag ; Tinkler-Hundal, Emma ; Southward, Katie ; Medlow, Paul ; McGreeghan-Crosby, Keith ; Halfpenny, Iris ; McMullan, Dominic J ; Quirke, Phil ; Keating, Katherine E ; Griffiths, Mike ; Spink, Karen G ; Brew, Fiona</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c500t-56611af6c7f373ab378811e77d4ce55cc87a157ce25e1218ab03a69fb83263923</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Analysis</topic><topic>Biotechnology industry</topic><topic>Clinical Laboratory Techniques - standards</topic><topic>Comparative analysis</topic><topic>DNA Mutational Analysis</topic><topic>Female</topic><topic>Gene Expression Profiling - methods</topic><topic>Gene Expression Regulation, Neoplastic</topic><topic>Genome, Human</topic><topic>Health aspects</topic><topic>Humans</topic><topic>Innovations</topic><topic>Loss of Heterozygosity</topic><topic>Male</topic><topic>Mutation</topic><topic>Neoplasms - genetics</topic><topic>Neoplasms - metabolism</topic><topic>Oligonucleotide Array Sequence Analysis - methods</topic><topic>Paraffin Embedding</topic><topic>Quality Control</topic><topic>Reproducibility of Results</topic><topic>Sensitivity and Specificity</topic><topic>Sequence Analysis, DNA</topic><topic>Technical Advance</topic><topic>Tissue Fixation - methods</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Foster, Joseph M</creatorcontrib><creatorcontrib>Oumie, Assa</creatorcontrib><creatorcontrib>Togneri, Fiona S</creatorcontrib><creatorcontrib>Vasques, Fabiana Ramos</creatorcontrib><creatorcontrib>Hau, Debra</creatorcontrib><creatorcontrib>Taylor, Morag</creatorcontrib><creatorcontrib>Tinkler-Hundal, Emma</creatorcontrib><creatorcontrib>Southward, Katie</creatorcontrib><creatorcontrib>Medlow, Paul</creatorcontrib><creatorcontrib>McGreeghan-Crosby, Keith</creatorcontrib><creatorcontrib>Halfpenny, Iris</creatorcontrib><creatorcontrib>McMullan, Dominic J</creatorcontrib><creatorcontrib>Quirke, Phil</creatorcontrib><creatorcontrib>Keating, Katherine E</creatorcontrib><creatorcontrib>Griffiths, Mike</creatorcontrib><creatorcontrib>Spink, Karen G</creatorcontrib><creatorcontrib>Brew, Fiona</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Science</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>BMC medical genomics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Foster, Joseph M</au><au>Oumie, Assa</au><au>Togneri, Fiona S</au><au>Vasques, Fabiana Ramos</au><au>Hau, Debra</au><au>Taylor, Morag</au><au>Tinkler-Hundal, Emma</au><au>Southward, Katie</au><au>Medlow, Paul</au><au>McGreeghan-Crosby, Keith</au><au>Halfpenny, Iris</au><au>McMullan, Dominic J</au><au>Quirke, Phil</au><au>Keating, Katherine E</au><au>Griffiths, Mike</au><au>Spink, Karen G</au><au>Brew, Fiona</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Cross-laboratory validation of the OncoScan® FFPE Assay, a multiplex tool for whole genome tumour profiling</atitle><jtitle>BMC medical genomics</jtitle><addtitle>BMC Med Genomics</addtitle><date>2015-02-18</date><risdate>2015</risdate><volume>8</volume><issue>1</issue><spage>5</spage><epage>5</epage><pages>5-5</pages><artnum>5</artnum><issn>1755-8794</issn><eissn>1755-8794</eissn><abstract>Adoption of new technology in both basic research and clinical settings requires rigorous validation of analytical performance. The OncoScan® FFPE Assay is a multiplexing tool that offers genome-wide copy number and loss of heterozygosity detection, as well as identification of frequently tested somatic mutations.
In this study, 162 formalin fixed paraffin embedded samples, representing six different tumour types, were profiled in triplicate across three independent laboratories. OncoScan® formalin fixed paraffin embedded assay data was then analysed for reproducibility of genome-wide copy number, loss of heterozygosity and somatic mutations. Where available, somatic mutation data was compared to data from orthogonal technologies (pyro/sanger sequencing).
Cross site comparisons of genome-wide copy number and loss of heterozygosity profiles showed greater than 95% average agreement between sites. Somatic mutations pre-validated by orthogonal technologies showed greater than 90% agreement with OncoScan® somatic mutation calls and somatic mutation concordance between sites averaged 97%.
Reproducibility of whole-genome copy number, loss of heterozygosity and somatic mutation data using the OncoScan® assay has been demonstrated with comparatively low DNA inputs from a range of highly degraded formalin fixed paraffin embedded samples. In addition, our data shows examples of clinically-relevant aberrations that demonstrate the potential utility of the OncoScan® assay as a robust clinical tool for guiding tumour therapy.</abstract><cop>England</cop><pub>BioMed Central Ltd</pub><pmid>25889064</pmid><doi>10.1186/s12920-015-0079-z</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
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subjects | Analysis Biotechnology industry Clinical Laboratory Techniques - standards Comparative analysis DNA Mutational Analysis Female Gene Expression Profiling - methods Gene Expression Regulation, Neoplastic Genome, Human Health aspects Humans Innovations Loss of Heterozygosity Male Mutation Neoplasms - genetics Neoplasms - metabolism Oligonucleotide Array Sequence Analysis - methods Paraffin Embedding Quality Control Reproducibility of Results Sensitivity and Specificity Sequence Analysis, DNA Technical Advance Tissue Fixation - methods |
title | Cross-laboratory validation of the OncoScan® FFPE Assay, a multiplex tool for whole genome tumour profiling |
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