Exhaustive expansion: A novel technique for analyzing complex data generated by higher-order polychromatic flow cytometry experiments
<p>Abstract</p> <p>Background</p> <p>The complex data sets generated by higher-order polychromatic flow cytometry experiments are a challenge to analyze. Here we describe Exhaustive Expansion, a data analysis approach for deriving hundreds to thousands of cell phenotype...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2010-10-01
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| Series: | Journal of Translational Medicine |
| Online Access: | http://www.translational-medicine.com/content/8/1/106 |
| _version_ | 1818497695101222912 |
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| author | Munsil Wes Zheng Bo Romer Ann Haley Daniel P Wang Lian Siebert Janet C Gregory Kenton W Walker Edwin B |
| author_facet | Munsil Wes Zheng Bo Romer Ann Haley Daniel P Wang Lian Siebert Janet C Gregory Kenton W Walker Edwin B |
| author_sort | Munsil Wes |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>The complex data sets generated by higher-order polychromatic flow cytometry experiments are a challenge to analyze. Here we describe Exhaustive Expansion, a data analysis approach for deriving hundreds to thousands of cell phenotypes from raw data, and for interrogating these phenotypes to identify populations of biological interest given the experimental context.</p> <p>Methods</p> <p>We apply this approach to two studies, illustrating its broad applicability. The first examines the longitudinal changes in circulating human memory T cell populations within individual patients in response to a melanoma peptide (gp100<sub>209-2M</sub>) cancer vaccine, using 5 monoclonal antibodies (mAbs) to delineate subpopulations of viable, gp100-specific, CD8+ T cells. The second study measures the mobilization of stem cells in porcine bone marrow that may be associated with wound healing, and uses 5 different staining panels consisting of 8 mAbs each.</p> <p>Results</p> <p>In the first study, our analysis suggests that the cell surface markers CD45RA, CD27 and CD28, commonly used in historical lower order (2-4 color) flow cytometry analysis to distinguish memory from naïve and effector T cells, may not be obligate parameters in defining central memory T cells (T<sub>CM</sub>). In the second study, we identify novel phenotypes such as CD29+CD31+CD56+CXCR4+CD90+Sca1-CD44+, which may characterize progenitor cells that are significantly increased in wounded animals as compared to controls.</p> <p>Conclusions</p> <p>Taken together, these results demonstrate that Exhaustive Expansion supports thorough interrogation of complex higher-order flow cytometry data sets and aids in the identification of potentially clinically relevant findings.</p> |
| first_indexed | 2024-12-10T18:48:27Z |
| format | Article |
| id | doaj.art-8c0f57a158e0488a81b187b005cd2e5e |
| institution | Directory Open Access Journal |
| issn | 1479-5876 |
| language | English |
| last_indexed | 2024-12-10T18:48:27Z |
| publishDate | 2010-10-01 |
| publisher | BMC |
| record_format | Article |
| series | Journal of Translational Medicine |
| spelling | doaj.art-8c0f57a158e0488a81b187b005cd2e5e2022-12-22T01:37:25ZengBMCJournal of Translational Medicine1479-58762010-10-018110610.1186/1479-5876-8-106Exhaustive expansion: A novel technique for analyzing complex data generated by higher-order polychromatic flow cytometry experimentsMunsil WesZheng BoRomer AnnHaley Daniel PWang LianSiebert Janet CGregory Kenton WWalker Edwin B<p>Abstract</p> <p>Background</p> <p>The complex data sets generated by higher-order polychromatic flow cytometry experiments are a challenge to analyze. Here we describe Exhaustive Expansion, a data analysis approach for deriving hundreds to thousands of cell phenotypes from raw data, and for interrogating these phenotypes to identify populations of biological interest given the experimental context.</p> <p>Methods</p> <p>We apply this approach to two studies, illustrating its broad applicability. The first examines the longitudinal changes in circulating human memory T cell populations within individual patients in response to a melanoma peptide (gp100<sub>209-2M</sub>) cancer vaccine, using 5 monoclonal antibodies (mAbs) to delineate subpopulations of viable, gp100-specific, CD8+ T cells. The second study measures the mobilization of stem cells in porcine bone marrow that may be associated with wound healing, and uses 5 different staining panels consisting of 8 mAbs each.</p> <p>Results</p> <p>In the first study, our analysis suggests that the cell surface markers CD45RA, CD27 and CD28, commonly used in historical lower order (2-4 color) flow cytometry analysis to distinguish memory from naïve and effector T cells, may not be obligate parameters in defining central memory T cells (T<sub>CM</sub>). In the second study, we identify novel phenotypes such as CD29+CD31+CD56+CXCR4+CD90+Sca1-CD44+, which may characterize progenitor cells that are significantly increased in wounded animals as compared to controls.</p> <p>Conclusions</p> <p>Taken together, these results demonstrate that Exhaustive Expansion supports thorough interrogation of complex higher-order flow cytometry data sets and aids in the identification of potentially clinically relevant findings.</p>http://www.translational-medicine.com/content/8/1/106 |
| spellingShingle | Munsil Wes Zheng Bo Romer Ann Haley Daniel P Wang Lian Siebert Janet C Gregory Kenton W Walker Edwin B Exhaustive expansion: A novel technique for analyzing complex data generated by higher-order polychromatic flow cytometry experiments Journal of Translational Medicine |
| title | Exhaustive expansion: A novel technique for analyzing complex data generated by higher-order polychromatic flow cytometry experiments |
| title_full | Exhaustive expansion: A novel technique for analyzing complex data generated by higher-order polychromatic flow cytometry experiments |
| title_fullStr | Exhaustive expansion: A novel technique for analyzing complex data generated by higher-order polychromatic flow cytometry experiments |
| title_full_unstemmed | Exhaustive expansion: A novel technique for analyzing complex data generated by higher-order polychromatic flow cytometry experiments |
| title_short | Exhaustive expansion: A novel technique for analyzing complex data generated by higher-order polychromatic flow cytometry experiments |
| title_sort | exhaustive expansion a novel technique for analyzing complex data generated by higher order polychromatic flow cytometry experiments |
| url | http://www.translational-medicine.com/content/8/1/106 |
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