{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T02:09:24Z","timestamp":1789524564667,"version":"build-2803163510"},"reference-count":19,"publisher":"Wiley","issue":"11","license":[{"start":{"date-parts":[[2009,10,2]],"date-time":"2009-10-02T00:00:00Z","timestamp":1254441600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Cytometry Pt A"],"published-print":{"date-parts":[[2009,11]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>The aim of this study was to find an objective computational approach for phenotype analysis of common variable immunodeficiency (CVID) patients that describes all differences in the six\u2010color space and to form groups of patients using computational methods. CVID is a heterogeneous primary immunodeficiency disorder where molecular defect is recognized in &lt;10% of the cases and is unknown in the majority of patients. The current CVID classification, EUROClass, is based on quantification of selected B\u2010cell subsets. Using six\u2010color polychromatic flow cytometry, we analyzed B\u2010cell phenotypes in a cohort of 48 CVID patients and 49 healthy donors. We used a \u201cprobability binning\u201d algorithm to create 1,024 bins (each bin is a six\u2010color gate) that covered the cells' distribution within the entire B\u2010cell compartment. A matrix file recording cellular content in all the bins was made. The hierarchical clustering of the individual samples was analyzed using a Pearson correlation of the bins' values. The Cut tree algorithm found 12 clusters. In six clusters, healthy individuals predominated; in one cluster, smB+CD21low (CVID patients by EUROClass) cells prevailed; in one cluster, smB\u2212CD21norm cells prevailed; in one cluster, smB+CD21low cells prevailed; the remaining cluster was mixed. The overall reproducibility of probability binning clustering was confirmed by matching of replicates to the original cohort using the similarity matrix of the Pearson correlation, 15 replicates matched the same individual, three replicates matched a different individual within the same cluster, and three replicates matched to a different cluster. We were able to define B\u2010cell subsets over\u2010 or under\u2010represented in a particular cluster and display them back in the flow cytometry software. We describe a new analytical approach that enables a search in an objective computational environment for patient cohorts that are defined by similar B\u2010cell profiles and thus contribute to the description of differences between CVID patient groups. \u00a9 2009 International Society for Advancement of Cytometry<\/jats:p>","DOI":"10.1002\/cyto.a.20801","type":"journal-article","created":{"date-parts":[[2009,10,3]],"date-time":"2009-10-03T04:10:12Z","timestamp":1254543012000},"page":"902-909","source":"Crossref","is-referenced-by-count":26,"title":["Profiling of polychromatic flow cytometry data on B\u2010cells reveals patients' clusters in common variable immunodeficiency"],"prefix":"10.1002","volume":"75A","author":[{"given":"Tom\u00e1\u0161","family":"Kalina","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jan","family":"Stuchl\u00fd","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ale\u0161","family":"Janda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ond\u0159ej","family":"Hru\u0161\u00e1k","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"\u0160\u00e1rka","family":"R\u016f\u017ei\u010dkov\u00e1","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna","family":"\u0160ediv\u00e1","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ji\u0159\u00ed","family":"Litzman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marcela","family":"Vlkov\u00e1","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2009,10,2]]},"reference":[{"key":"e_1_2_6_2_2","doi-asserted-by":"publisher","DOI":"10.1006\/clim.1999.4799"},{"key":"e_1_2_6_3_2","doi-asserted-by":"publisher","DOI":"10.1182\/blood.V99.5.1544"},{"key":"e_1_2_6_4_2","doi-asserted-by":"publisher","DOI":"10.1023\/A:1025373601374"},{"key":"e_1_2_6_5_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2249.2006.02999.x"},{"key":"e_1_2_6_6_2","doi-asserted-by":"publisher","DOI":"10.1182\/blood-2007-06-091744"},{"key":"e_1_2_6_7_2","doi-asserted-by":"publisher","DOI":"10.1002\/cyto.a.20333"},{"key":"e_1_2_6_8_2","doi-asserted-by":"publisher","DOI":"10.1002\/1097-0320(20010901)45:1<47::AID-CYTO1143>3.0.CO;2-A"},{"key":"e_1_2_6_9_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btm563"},{"key":"e_1_2_6_10_2","doi-asserted-by":"publisher","DOI":"10.18637\/jss.v025.i04"},{"key":"e_1_2_6_11_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-0-387-49317-6"},{"key":"e_1_2_6_12_2","doi-asserted-by":"publisher","DOI":"10.2144\/03342mt01"},{"key":"e_1_2_6_13_2","first-page":"455","article-title":"Principal components analysis to summarize microarray experiments: Application to sporulation time series","author":"Raychaudhuri S","year":"2000","journal-title":"Pac Symp Biocomput"},{"key":"e_1_2_6_14_2","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.174.7.4034"},{"key":"e_1_2_6_15_2","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.176.3.1506"},{"key":"e_1_2_6_16_2","doi-asserted-by":"publisher","DOI":"10.1084\/jem.188.9.1679"},{"key":"e_1_2_6_17_2","doi-asserted-by":"publisher","DOI":"10.1002\/cyto.b.20432"},{"key":"e_1_2_6_18_2","doi-asserted-by":"publisher","DOI":"10.1182\/blood-2004-01-0346"},{"key":"e_1_2_6_19_2","doi-asserted-by":"publisher","DOI":"10.1002\/cyto.a.20638"},{"key":"e_1_2_6_20_2","doi-asserted-by":"publisher","DOI":"10.1002\/cyto.a.20505"}],"container-title":["Cytometry Part A"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.wiley.com\/onlinelibrary\/tdm\/v1\/articles\/10.1002%2Fcyto.a.20801","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/cyto.a.20801","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,10,11]],"date-time":"2023-10-11T13:32:48Z","timestamp":1697031168000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/cyto.a.20801"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,10,2]]},"references-count":19,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2009,11]]}},"alternative-id":["10.1002\/cyto.a.20801"],"URL":"https:\/\/doi.org\/10.1002\/cyto.a.20801","archive":["Portico"],"relation":{},"ISSN":["1552-4922","1552-4930"],"issn-type":[{"value":"1552-4922","type":"print"},{"value":"1552-4930","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,10,2]]}}}