Joint Modeling and Registration of Cell Populations in Cohorts of High-Dimensional Flow Cytometric Data
Identifieur interne : 003768 ( Main/Exploration ); précédent : 003767; suivant : 003769Joint Modeling and Registration of Cell Populations in Cohorts of High-Dimensional Flow Cytometric Data
Auteurs : Saumyadipta Pyne [Inde] ; Sharon X. Lee [Australie] ; Kui Wang [Australie] ; Jonathan Irish [États-Unis] ; Pablo Tamayo [États-Unis] ; Marc-Danie Nazaire [États-Unis] ; Tarn Duong [France] ; Shu-Kay Ng [Australie] ; David Hafler [États-Unis] ; Ronald Levy [États-Unis] ; Garry P. Nolan [États-Unis] ; Jill Mesirov [États-Unis] ; Geoffrey J. Mclachlan [Australie]Source :
- PLoS ONE [ 1932-6203 ] ; 2014.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
Abstract
In biomedical applications, an experimenter encounters different potential sources of variation in data such as individual samples, multiple experimental conditions, and multivariate responses of a panel of markers such as from a signaling network. In multiparametric cytometry, which is often used for analyzing patient samples, such issues are critical. While computational methods can identify cell populations in individual samples, without the ability to automatically match them across samples, it is difficult to compare and characterize the populations in typical experiments, such as those responding to various stimulations or distinctive of particular patients or time-points, especially when there are many samples. Joint Clustering and Matching (JCM) is a multi-level framework for simultaneous modeling and registration of populations across a cohort. JCM models every population with a robust multivariate probability distribution. Simultaneously, JCM fits a random-effects model to construct an overall batch template – used for registering populations across samples, and classifying new samples. By tackling systems-level variation, JCM supports practical biomedical applications involving large cohorts. Software for fitting the JCM models have been implemented in an R package EMMIX-JCM, available from
Url:
DOI: 10.1371/journal.pone.0100334
PubMed: 24983991
PubMed Central: 4077578
Affiliations:
- Australie, France, Inde, États-Unis
- Californie, Connecticut, Massachusetts, Tennessee, Île-de-France
- Paris
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Lee</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Department of Mathematics, University of Queensland, St. Lucia, Queensland, Australia</addr-line></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Department of Mathematics, University of Queensland, St. Lucia, Queensland</wicri:regionArea><wicri:noRegion>Queensland</wicri:noRegion></affiliation></author><author><name sortKey="Wang, Kui" sort="Wang, Kui" uniqKey="Wang K" first="Kui" last="Wang">Kui Wang</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Department of Mathematics, University of Queensland, St. Lucia, Queensland, Australia</addr-line></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Department of Mathematics, University of Queensland, St. Lucia, Queensland</wicri:regionArea><wicri:noRegion>Queensland</wicri:noRegion></affiliation></author><author><name sortKey="Irish, Jonathan" sort="Irish, Jonathan" uniqKey="Irish J" first="Jonathan" last="Irish">Jonathan Irish</name><affiliation wicri:level="2"><nlm:aff id="aff3"><addr-line>Division of Oncology, Stanford Medical School, Stanford, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Division of Oncology, Stanford Medical School, Stanford, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="aff4"><addr-line>Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford School of Medicine, Stanford, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford School of Medicine, Stanford, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="aff5"><addr-line>Department of Cancer Biology, Vanderbilt University, Nashville, Tennessee, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Cancer Biology, Vanderbilt University, Nashville, Tennessee</wicri:regionArea><placeName><region type="state">Tennessee</region></placeName></affiliation></author><author><name sortKey="Tamayo, Pablo" sort="Tamayo, Pablo" uniqKey="Tamayo P" first="Pablo" last="Tamayo">Pablo Tamayo</name><affiliation wicri:level="2"><nlm:aff id="aff6"><addr-line>Broad Institute of MIT and Harvard University, Cambridge, Massachusetts, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Broad Institute of MIT and Harvard University, Cambridge, Massachusetts</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation></author><author><name sortKey="Nazaire, Marc Danie" sort="Nazaire, Marc Danie" uniqKey="Nazaire M" first="Marc-Danie" last="Nazaire">Marc-Danie Nazaire</name><affiliation wicri:level="2"><nlm:aff id="aff6"><addr-line>Broad Institute of MIT and Harvard University, Cambridge, Massachusetts, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Broad Institute of MIT and Harvard University, Cambridge, Massachusetts</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation></author><author><name sortKey="Duong, Tarn" sort="Duong, Tarn" uniqKey="Duong T" first="Tarn" last="Duong">Tarn Duong</name><affiliation wicri:level="3"><nlm:aff id="aff7"><addr-line>Molecular Mechanisms of Intracellular Transport, Unit Mixte de Recherche 144 Centre National de la Recherche Scientifique/Institut Curie, Paris, France</addr-line></nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Molecular Mechanisms of Intracellular Transport, Unit Mixte de Recherche 144 Centre National de la Recherche Scientifique/Institut Curie, Paris</wicri:regionArea><placeName><region type="region">Île-de-France</region><region type="old region">Île-de-France</region><settlement type="city">Paris</settlement></placeName></affiliation></author><author><name sortKey="Ng, Shu Kay" sort="Ng, Shu Kay" uniqKey="Ng S" first="Shu-Kay" last="Ng">Shu-Kay Ng</name><affiliation wicri:level="1"><nlm:aff id="aff8"><addr-line>School of Medicine, Griffith University, Meadowbrook, Queensland, Australia</addr-line></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>School of Medicine, Griffith University, Meadowbrook, Queensland</wicri:regionArea><wicri:noRegion>Queensland</wicri:noRegion></affiliation></author><author><name sortKey="Hafler, David" sort="Hafler, David" uniqKey="Hafler D" first="David" last="Hafler">David Hafler</name><affiliation wicri:level="2"><nlm:aff id="aff9"><addr-line>Department of Neurology, Yale School of Medicine, New Haven, Connecticut, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Neurology, Yale School of Medicine, New Haven, Connecticut</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation></author><author><name sortKey="Levy, Ronald" sort="Levy, Ronald" uniqKey="Levy R" first="Ronald" last="Levy">Ronald Levy</name><affiliation wicri:level="2"><nlm:aff id="aff3"><addr-line>Division of Oncology, Stanford Medical School, Stanford, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Division of Oncology, Stanford Medical School, Stanford, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Nolan, Garry P" sort="Nolan, Garry P" uniqKey="Nolan G" first="Garry P." last="Nolan">Garry P. Nolan</name><affiliation wicri:level="2"><nlm:aff id="aff4"><addr-line>Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford School of Medicine, Stanford, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford School of Medicine, Stanford, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Mesirov, Jill" sort="Mesirov, Jill" uniqKey="Mesirov J" first="Jill" last="Mesirov">Jill Mesirov</name><affiliation wicri:level="2"><nlm:aff id="aff6"><addr-line>Broad Institute of MIT and Harvard University, Cambridge, Massachusetts, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Broad Institute of MIT and Harvard University, Cambridge, Massachusetts</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation></author><author><name sortKey="Mclachlan, Geoffrey J" sort="Mclachlan, Geoffrey J" uniqKey="Mclachlan G" first="Geoffrey J." last="Mclachlan">Geoffrey J. Mclachlan</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Department of Mathematics, University of Queensland, St. Lucia, Queensland, Australia</addr-line></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Department of Mathematics, University of Queensland, St. Lucia, Queensland</wicri:regionArea><wicri:noRegion>Queensland</wicri:noRegion></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Cluster Analysis</term><term>Computational Biology (methods)</term><term>Computer Simulation</term><term>Flow Cytometry</term><term>Humans</term><term>Software</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term><term>Analyse de regroupements</term><term>Biologie informatique ()</term><term>Cytométrie en flux</term><term>Humains</term><term>Logiciel</term><term>Simulation numérique</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Cluster Analysis</term><term>Computer Simulation</term><term>Flow Cytometry</term><term>Humans</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Analyse de regroupements</term><term>Biologie informatique</term><term>Cytométrie en flux</term><term>Humains</term><term>Logiciel</term><term>Simulation numérique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>In biomedical applications, an experimenter encounters different potential sources of variation in data such as individual samples, multiple experimental conditions, and multivariate responses of a panel of markers such as from a signaling network. In multiparametric cytometry, which is often used for analyzing patient samples, such issues are critical. While computational methods can identify cell populations in individual samples, without the ability to automatically match them across samples, it is difficult to compare and characterize the populations in typical experiments, such as those responding to various stimulations or distinctive of particular patients or time-points, especially when there are many samples. Joint Clustering and Matching (JCM) is a multi-level framework for simultaneous modeling and registration of populations across a cohort. JCM models every population with a robust multivariate probability distribution. Simultaneously, JCM fits a random-effects model to construct an overall batch template – used for registering populations across samples, and classifying new samples. By tackling systems-level variation, JCM supports practical biomedical applications involving large cohorts. Software for fitting the JCM models have been implemented in an R package EMMIX-JCM, available from <ext-link ext-link-type="uri" xlink:href="http://www.maths.uq.edu.au/~gjm/mix_soft/EMMIX-JCM/">http://www.maths.uq.edu.au/~gjm/mix_soft/EMMIX-JCM/</ext-link>.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Irish, Jm" uniqKey="Irish J">JM Irish</name></author><author><name sortKey="Kotecha, N" uniqKey="Kotecha N">N Kotecha</name></author><author><name sortKey="Nolan, Gp" uniqKey="Nolan G">GP Nolan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Perfetto, Sp" uniqKey="Perfetto S">SP Perfetto</name></author><author><name sortKey="Chattopadhyay, Pk" uniqKey="Chattopadhyay P">PK Chattopadhyay</name></author><author><name sortKey="Roederer, M" uniqKey="Roederer M">M Roederer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lugli, E" uniqKey="Lugli E">E 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Celeux</name></author><author><name sortKey="Lo, K" uniqKey="Lo K">K Lo</name></author><author><name sortKey="Gottardo, R" uniqKey="Gottardo R">R Gottardo</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Liu, X" uniqKey="Liu X">X Liu</name></author><author><name sortKey="Yang, M" uniqKey="Yang M">M Yang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gaffney, Sj" uniqKey="Gaffney S">SJ Gaffney</name></author><author><name sortKey="Robertson, Aw" uniqKey="Robertson A">AW Robertson</name></author><author><name sortKey="Smyth, P" uniqKey="Smyth P">P Smyth</name></author><author><name sortKey="Camargo, Sj" uniqKey="Camargo S">SJ Camargo</name></author><author><name sortKey="Ghil, M" uniqKey="Ghil M">M Ghil</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Ng, Sk" uniqKey="Ng S">SK Ng</name></author><author><name sortKey="Mclachlan, Gj" uniqKey="Mclachlan G">GJ McLachlan</name></author><author><name sortKey="Wang, K" uniqKey="Wang K">K Wang</name></author><author><name sortKey="Ben Tovim, L" uniqKey="Ben Tovim L">L Ben-Tovim</name></author><author><name sortKey="Ng, Sw" uniqKey="Ng S">SW Ng</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hahne, F" uniqKey="Hahne F">F Hahne</name></author><author><name sortKey="Khodabakhshi, Ah" uniqKey="Khodabakhshi A">AH Khodabakhshi</name></author><author><name sortKey="Bashashati, A" uniqKey="Bashashati A">A Bashashati</name></author><author><name sortKey="Wong, Cj" uniqKey="Wong C">CJ Wong</name></author><author><name sortKey="Gascoyne, Rd" uniqKey="Gascoyne R">RD Gascoyne</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Sahu, Sk" uniqKey="Sahu S">SK Sahu</name></author><author><name sortKey="Dey, Dk" uniqKey="Dey D">DK Dey</name></author><author><name sortKey="Branco, Md" uniqKey="Branco M">MD Branco</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Australie</li><li>France</li><li>Inde</li><li>États-Unis</li></country><region><li>Californie</li><li>Connecticut</li><li>Massachusetts</li><li>Tennessee</li><li>Île-de-France</li></region><settlement><li>Paris</li></settlement></list><tree><country name="Inde"><noRegion><name sortKey="Pyne, Saumyadipta" sort="Pyne, Saumyadipta" uniqKey="Pyne S" first="Saumyadipta" last="Pyne">Saumyadipta Pyne</name></noRegion></country><country name="Australie"><noRegion><name sortKey="Lee, Sharon X" sort="Lee, Sharon X" uniqKey="Lee S" first="Sharon X." last="Lee">Sharon X. Lee</name></noRegion><name sortKey="Mclachlan, Geoffrey J" sort="Mclachlan, Geoffrey J" uniqKey="Mclachlan G" first="Geoffrey J." last="Mclachlan">Geoffrey J. Mclachlan</name><name sortKey="Ng, Shu Kay" sort="Ng, Shu Kay" uniqKey="Ng S" first="Shu-Kay" last="Ng">Shu-Kay Ng</name><name sortKey="Wang, Kui" sort="Wang, Kui" uniqKey="Wang K" first="Kui" last="Wang">Kui Wang</name></country><country name="États-Unis"><region name="Californie"><name sortKey="Irish, Jonathan" sort="Irish, Jonathan" uniqKey="Irish J" first="Jonathan" last="Irish">Jonathan Irish</name></region><name sortKey="Hafler, David" sort="Hafler, David" uniqKey="Hafler D" first="David" last="Hafler">David Hafler</name><name sortKey="Irish, Jonathan" sort="Irish, Jonathan" uniqKey="Irish J" first="Jonathan" last="Irish">Jonathan Irish</name><name sortKey="Irish, Jonathan" sort="Irish, Jonathan" uniqKey="Irish J" first="Jonathan" last="Irish">Jonathan Irish</name><name sortKey="Levy, Ronald" sort="Levy, Ronald" uniqKey="Levy R" first="Ronald" last="Levy">Ronald Levy</name><name sortKey="Mesirov, Jill" sort="Mesirov, Jill" uniqKey="Mesirov J" first="Jill" last="Mesirov">Jill Mesirov</name><name sortKey="Nazaire, Marc Danie" sort="Nazaire, Marc Danie" uniqKey="Nazaire M" first="Marc-Danie" last="Nazaire">Marc-Danie Nazaire</name><name sortKey="Nolan, Garry P" sort="Nolan, Garry P" uniqKey="Nolan G" first="Garry P." last="Nolan">Garry P. Nolan</name><name sortKey="Tamayo, Pablo" sort="Tamayo, Pablo" uniqKey="Tamayo P" first="Pablo" last="Tamayo">Pablo Tamayo</name></country><country name="France"><region name="Île-de-France"><name sortKey="Duong, Tarn" sort="Duong, Tarn" uniqKey="Duong T" first="Tarn" last="Duong">Tarn Duong</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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