ProteinSeq: high-performance proteomic analyses by proximity ligation and next generation sequencing
Despite intense interest, methods that provide enhanced sensitivity and specificity in parallel measurements of candidate protein biomarkers in numerous samples have been lacking. We present herein a multiplex proximity ligation assay with readout via realtime PCR or DNA sequencing (ProteinSeq). We...
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| Veröffentlicht in: | PloS one 2011-09, Vol.6 (9), p.e25583-e25583 |
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| creator | Darmanis, Spyros Nong, Rachel Yuan Vänelid, Johan Siegbahn, Agneta Ericsson, Olle Fredriksson, Simon Bäcklin, Christofer Gut, Marta Heath, Simon Gut, Ivo Glynne Wallentin, Lars Gustafsson, Mats G Kamali-Moghaddam, Masood Landegren, Ulf |
| description | Despite intense interest, methods that provide enhanced sensitivity and specificity in parallel measurements of candidate protein biomarkers in numerous samples have been lacking. We present herein a multiplex proximity ligation assay with readout via realtime PCR or DNA sequencing (ProteinSeq). We demonstrate improved sensitivity over conventional sandwich assays for simultaneous analysis of sets of 35 proteins in 5 µl of blood plasma. Importantly, we observe a minimal tendency to increased background with multiplexing, compared to a sandwich assay, suggesting that higher levels of multiplexing are possible. We used ProteinSeq to analyze proteins in plasma samples from cardiovascular disease (CVD) patient cohorts and matched controls. Three proteins, namely P-selectin, Cystatin-B and Kallikrein-6, were identified as putative diagnostic biomarkers for CVD. The latter two have not been previously reported in the literature and their potential roles must be validated in larger patient cohorts. We conclude that ProteinSeq is promising for screening large numbers of proteins and samples while the technology can provide a much-needed platform for validation of diagnostic markers in biobank samples and in clinical use. |
| doi_str_mv | 10.1371/journal.pone.0025583 |
| format | Article |
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We present herein a multiplex proximity ligation assay with readout via realtime PCR or DNA sequencing (ProteinSeq). We demonstrate improved sensitivity over conventional sandwich assays for simultaneous analysis of sets of 35 proteins in 5 µl of blood plasma. Importantly, we observe a minimal tendency to increased background with multiplexing, compared to a sandwich assay, suggesting that higher levels of multiplexing are possible. We used ProteinSeq to analyze proteins in plasma samples from cardiovascular disease (CVD) patient cohorts and matched controls. Three proteins, namely P-selectin, Cystatin-B and Kallikrein-6, were identified as putative diagnostic biomarkers for CVD. The latter two have not been previously reported in the literature and their potential roles must be validated in larger patient cohorts. We conclude that ProteinSeq is promising for screening large numbers of proteins and samples while the technology can provide a much-needed platform for validation of diagnostic markers in biobank samples and in clinical use.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0025583</identifier><identifier>PMID: 21980495</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Antigens ; Assaying ; Bioindicators ; Biology ; biomarker ; Biomarkers ; Biomarkers - blood ; Blood plasma ; Blood Proteins - analysis ; Blood Proteins - genetics ; Cardiovascular disease ; Cardiovascular diseases ; Comparative analysis ; Coronary vessels ; Cystatin ; Cystatins ; Deoxyribonucleic acid ; Diagnostic systems ; Disease control ; DNA ; DNA sequencing ; Gene sequencing ; Growth factors ; Heart attacks ; Humans ; Immunoassay - economics ; Immunoassay - methods ; Immunoglobulins ; Immunology ; Informatics ; Kallikrein ; Laboratories ; Medicine ; Methods ; Molecular Medicine ; Molecular weight ; Molekylär medicin ; Multiplexing ; Multivariate Analysis ; next generation sequencing ; P-selectin ; Pathology ; Physics ; Prostate cancer ; Proteins ; Proteomics ; Proteomics - economics ; Proteomics - methods ; proximity ligation assay ; Science ; Sensitivity ; Sensitivity analysis ; Sensitivity enhancement ; Sequence Analysis, DNA - economics ; Sequence Analysis, DNA - methods ; Studies ; Time Factors</subject><ispartof>PloS one, 2011-09, Vol.6 (9), p.e25583-e25583</ispartof><rights>COPYRIGHT 2011 Public Library of Science</rights><rights>2011 Darmanis et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>Darmanis et al. 2011</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c728t-bac6c1eb016bb3d06352f9c75769fd152417fad100da42f87e0d3cde9901190b3</citedby><cites>FETCH-LOGICAL-c728t-bac6c1eb016bb3d06352f9c75769fd152417fad100da42f87e0d3cde9901190b3</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/PMC3183061/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3183061/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2102,2928,23866,27924,27925,53791,53793,79600,79601</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/21980495$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-158802$$DView record from Swedish Publication Index$$Hfree_for_read</backlink></links><search><contributor>Rao, Jianghong</contributor><creatorcontrib>Darmanis, Spyros</creatorcontrib><creatorcontrib>Nong, Rachel Yuan</creatorcontrib><creatorcontrib>Vänelid, Johan</creatorcontrib><creatorcontrib>Siegbahn, Agneta</creatorcontrib><creatorcontrib>Ericsson, Olle</creatorcontrib><creatorcontrib>Fredriksson, Simon</creatorcontrib><creatorcontrib>Bäcklin, Christofer</creatorcontrib><creatorcontrib>Gut, Marta</creatorcontrib><creatorcontrib>Heath, Simon</creatorcontrib><creatorcontrib>Gut, Ivo Glynne</creatorcontrib><creatorcontrib>Wallentin, Lars</creatorcontrib><creatorcontrib>Gustafsson, Mats G</creatorcontrib><creatorcontrib>Kamali-Moghaddam, Masood</creatorcontrib><creatorcontrib>Landegren, Ulf</creatorcontrib><title>ProteinSeq: high-performance proteomic analyses by proximity ligation and next generation sequencing</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Despite intense interest, methods that provide enhanced sensitivity and specificity in parallel measurements of candidate protein biomarkers in numerous samples have been lacking. We present herein a multiplex proximity ligation assay with readout via realtime PCR or DNA sequencing (ProteinSeq). We demonstrate improved sensitivity over conventional sandwich assays for simultaneous analysis of sets of 35 proteins in 5 µl of blood plasma. Importantly, we observe a minimal tendency to increased background with multiplexing, compared to a sandwich assay, suggesting that higher levels of multiplexing are possible. We used ProteinSeq to analyze proteins in plasma samples from cardiovascular disease (CVD) patient cohorts and matched controls. Three proteins, namely P-selectin, Cystatin-B and Kallikrein-6, were identified as putative diagnostic biomarkers for CVD. The latter two have not been previously reported in the literature and their potential roles must be validated in larger patient cohorts. We conclude that ProteinSeq is promising for screening large numbers of proteins and samples while the technology can provide a much-needed platform for validation of diagnostic markers in biobank samples and in clinical use.</description><subject>Antigens</subject><subject>Assaying</subject><subject>Bioindicators</subject><subject>Biology</subject><subject>biomarker</subject><subject>Biomarkers</subject><subject>Biomarkers - blood</subject><subject>Blood plasma</subject><subject>Blood Proteins - analysis</subject><subject>Blood Proteins - genetics</subject><subject>Cardiovascular disease</subject><subject>Cardiovascular diseases</subject><subject>Comparative analysis</subject><subject>Coronary vessels</subject><subject>Cystatin</subject><subject>Cystatins</subject><subject>Deoxyribonucleic acid</subject><subject>Diagnostic systems</subject><subject>Disease control</subject><subject>DNA</subject><subject>DNA sequencing</subject><subject>Gene sequencing</subject><subject>Growth factors</subject><subject>Heart attacks</subject><subject>Humans</subject><subject>Immunoassay - 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We present herein a multiplex proximity ligation assay with readout via realtime PCR or DNA sequencing (ProteinSeq). We demonstrate improved sensitivity over conventional sandwich assays for simultaneous analysis of sets of 35 proteins in 5 µl of blood plasma. Importantly, we observe a minimal tendency to increased background with multiplexing, compared to a sandwich assay, suggesting that higher levels of multiplexing are possible. We used ProteinSeq to analyze proteins in plasma samples from cardiovascular disease (CVD) patient cohorts and matched controls. Three proteins, namely P-selectin, Cystatin-B and Kallikrein-6, were identified as putative diagnostic biomarkers for CVD. The latter two have not been previously reported in the literature and their potential roles must be validated in larger patient cohorts. We conclude that ProteinSeq is promising for screening large numbers of proteins and samples while the technology can provide a much-needed platform for validation of diagnostic markers in biobank samples and in clinical use.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>21980495</pmid><doi>10.1371/journal.pone.0025583</doi><tpages>e25583</tpages><oa>free_for_read</oa></addata></record> |
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| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2011-09, Vol.6 (9), p.e25583-e25583 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_1308929561 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Public Library of Science (PLoS) Journals Open Access; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Antigens Assaying Bioindicators Biology biomarker Biomarkers Biomarkers - blood Blood plasma Blood Proteins - analysis Blood Proteins - genetics Cardiovascular disease Cardiovascular diseases Comparative analysis Coronary vessels Cystatin Cystatins Deoxyribonucleic acid Diagnostic systems Disease control DNA DNA sequencing Gene sequencing Growth factors Heart attacks Humans Immunoassay - economics Immunoassay - methods Immunoglobulins Immunology Informatics Kallikrein Laboratories Medicine Methods Molecular Medicine Molecular weight Molekylär medicin Multiplexing Multivariate Analysis next generation sequencing P-selectin Pathology Physics Prostate cancer Proteins Proteomics Proteomics - economics Proteomics - methods proximity ligation assay Science Sensitivity Sensitivity analysis Sensitivity enhancement Sequence Analysis, DNA - economics Sequence Analysis, DNA - methods Studies Time Factors |
| title | ProteinSeq: high-performance proteomic analyses by proximity ligation and next generation sequencing |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-24T20%3A23%3A57IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=ProteinSeq:%20high-performance%20proteomic%20analyses%20by%20proximity%20ligation%20and%20next%20generation%20sequencing&rft.jtitle=PloS%20one&rft.au=Darmanis,%20Spyros&rft.date=2011-09-29&rft.volume=6&rft.issue=9&rft.spage=e25583&rft.epage=e25583&rft.pages=e25583-e25583&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0025583&rft_dat=%3Cgale_plos_%3EA476877807%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1308929561&rft_id=info:pmid/21980495&rft_galeid=A476877807&rft_doaj_id=oai_doaj_org_article_27f06ed15582440eb5de5170a0c956b1&rfr_iscdi=true |