Generation of flow cytometry data files with a potentially infinite number of dimensions

2008 ◽  
Vol 73A (9) ◽  
pp. 834-846 ◽  
Author(s):  
Carlos E. Pedreira ◽  
Elaine S. Costa ◽  
Susana Barrena ◽  
Quentin Lecrevisse ◽  
Julia Almeida ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Infinite Number ◽  
Flow Cytometry Data ◽  
Data Files

scholarly journals Assessment of Protocol Impact on Subjectivity Uncertainty When Analyzing Peripheral Blood Mononuclear Cell Flow Cytometry Data Files

2021 ◽  
Vol 4 (2) ◽  
pp. 24
Author(s):  
Rebecca Grant ◽  
Karen Coopman ◽  
Sandro Silva-Gomes ◽  
Jonathan J. Campbell ◽  
Bo Kara ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Measurement Uncertainty ◽  
Target Cells ◽  
Peripheral Blood Mononuclear ◽  
Flow Cytometry Data ◽  
Uncertainty In Measurement ◽  
Cell Flow Cytometry ◽  
Data Files ◽  
Cell And Gene Therapy ◽  
Dying Cells

Measured variability of product within Cell and Gene Therapy (CGT) manufacturing arises from numerous sources across pre-analytical to post-analytical phases of testing. Operators are a function of the manufacturing process and are an important source of variability as a result of personal differences impacted by numerous factors. This research uses measurement uncertainty in comparison to Coefficient of Variation to quantify variation of participants when they complete Flow Cytometry data analysis through a 5-step gating sequence. Two study stages captured participants applying gates using their own judgement, and then following a diagrammatical protocol, respectively. Measurement uncertainty was quantified for each participant (and analysis phase) by following Guide to the Expression of Uncertainty in Measurement protocols, combining their standard deviations in quadrature from each gating step in the respective protocols. When participants followed a diagrammatical protocol, variation between participants reduced by 57%, increasing confidence in a more uniform reported cell count percentage. Measurement uncertainty provided greater resolution to the analysis processes, identifying that most variability contributed in the Flow Cytometry gating process is from the very first gate, where isolating target cells from dead or dying cells is required. This work has demonstrated the potential for greater usage of measurement uncertainty within CGT manufacturing scenarios, due to the resolution it provides for root cause analysis and continuous improvement.

scholarly journals An active, collaborative approach to learning skills in flow cytometry

2016 ◽  
Vol 40 (2) ◽  
pp. 176-185 ◽  
Author(s):  
Kathryn Fuller ◽  
Matthew D. Linden ◽  
Tracey Lee-Pullen ◽  
Clayton Fragall ◽  
Wendy N. Erber ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Data Analysis ◽  
Learning Outcomes ◽  
Undergraduate Students ◽  
Immune Cell ◽  
Complex Data ◽  
Collaborative Approach ◽  
Flow Cytometry Data ◽  
Antibody Staining ◽  
Data Files

Advances in science education research have the potential to improve the way students learn to perform scientific interpretations and understand science concepts. We developed active, collaborative activities to teach skills in manipulating flow cytometry data using FlowJo software. Undergraduate students were given compensated clinical flow cytometry listmode output (FCS) files and asked to design a gating strategy to diagnose patients with different hematological malignancies on the basis of their immunophenotype. A separate cohort of research trainees was given uncompensated data files on which they performed their own compensation, calculated the antibody staining index, designed a sequential gating strategy, and quantified rare immune cell subsets. Student engagement, confidence, and perceptions of flow cytometry were assessed using a survey. Competency against the learning outcomes was assessed by asking students to undertake tasks that required understanding of flow cytometry dot plot data and gating sequences. The active, collaborative approach allowed students to achieve learning outcomes not previously possible with traditional teaching formats, for example, having students design their own gating strategy, without forgoing essential outcomes such as the interpretation of dot plots. In undergraduate students, favorable perceptions of flow cytometry as a field and as a potential career choice were correlated with student confidence but not the ability to perform flow cytometry data analysis. We demonstrate that this new pedagogical approach to teaching flow cytometry is beneficial for student understanding and interpretation of complex concepts. It should be considered as a useful new method for incorporating complex data analysis tasks such as flow cytometry into curricula.

scholarly journals Recent Bioinformatics Advances in the Analysis of High Throughput Flow Cytometry Data

2009 ◽  
Vol 2009 ◽  
pp. 1-2
Author(s):  
Raphael Gottardo ◽  
Ryan R. Brinkman ◽  
George Luta ◽  
Matt P. Wand
Keyword(s):  
Flow Cytometry ◽  
High Throughput ◽  
Flow Cytometry Data

scholarly journals Automated gating of flow cytometry data via robust model-based clustering

2008 ◽  
Vol 73A (4) ◽  
pp. 321-332 ◽  
Author(s):  
Kenneth Lo ◽  
Ryan Remy Brinkman ◽  
Raphael Gottardo
Keyword(s):  
Flow Cytometry ◽  
Model Based Clustering ◽  
Flow Cytometry Data ◽  
Model Based ◽  
Robust Model

Natural polyploidy in Vanilla planifolia (Orchidaceae)

Genome ◽  
2008 ◽  
Vol 51 (10) ◽  
pp. 816-826 ◽  
Author(s):  
Séverine Bory ◽  
Olivier Catrice ◽  
Spencer Brown ◽  
Ilia J. Leitch ◽  
Rodolphe Gigant ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Phenotypic Variation ◽  
Chromosome Numbers ◽  
Reunion Island ◽  
Vanilla Planifolia ◽  
Root Cells ◽  
Flow Cytometry Data ◽  
Important Variation ◽  
Réunion Island ◽  
Stomatal Length

Vanilla planifolia accessions cultivated in Reunion Island display important phenotypic variation, but little genetic diversity is demonstrated by AFLP and SSR markers. This study, based on analyses of flow cytometry data, Feulgen microdensitometry data, chromosome counts, and stomatal length measurements, was performed to determine whether polyploidy could be responsible for some of the intraspecific phenotypic variation observed. Vanilla planifolia exhibited an important variation in somatic chromosome number in root cells, as well as endoreplication as revealed by flow cytometry. Nevertheless, the 2C-values of the 50 accessions studied segregated into three distinct groups averaging 5.03 pg (for most accessions), 7.67 pg (for the ‘Stérile’ phenotypes), and 10.00 pg (for the ‘Grosse Vanille’ phenotypes). For the three groups, chromosome numbers varied from 16 to 32, 16 to 38, and 22 to 54 chromosomes per cell, respectively. The stomatal length showed a significant variation from 37.75 µm to 48.25 µm. Given that 2C-values, mean chromosome numbers, and stomatal lengths were positively correlated and that ‘Stérile’ and ‘Grosse Vanille’ accessions were indistinguishable from ‘Classique’ accessions using molecular markers, the occurrence of recent autotriploid and autotetraploid types in Reunion Island is supported. This is the first report showing evidence of a recent autopolyploidy in V. planifolia contributing to the phenotypic variation observed in this species.

scholarly journals Normative data for flow cytometry immunophenotyping of benign lymph nodes sampled by surgical biopsy

2017 ◽  
Vol 71 (2) ◽  
pp. 174-179 ◽  
Author(s):  
Gregory David Scott ◽  
Susan K Atwater ◽  
Dita A Gratzinger
Keyword(s):  
Flow Cytometry ◽  
Lymph Node ◽  
T Cell ◽  
Lymph Nodes ◽  
Inflammatory Disease ◽  
Clinical History ◽  
Surgical Biopsy ◽  
Data Set ◽  
Flow Cytometry Data ◽  
Benign Lymph Node

AimsTo create clinically relevant normative flow cytometry data for understudied benign lymph nodes and characterise outliers.MethodsClinical, histological and flow cytometry data were collected and distributions summarised for 380 benign lymph node excisional biopsies. Outliers for kappa:lambda light chain ratio, CD10:CD19 coexpression, CD5:CD19 coexpression, CD4:CD8 ratios and CD7 loss were summarised for histological pattern, concomitant diseases and follow-up course.ResultsWe generated the largest data set of benign lymph node immunophenotypes by an order of magnitude. B and T cell antigen outliers often had background immunosuppression or inflammatory disease but did not subsequently develop lymphoma.ConclusionsDiagnostic immunophenotyping data from benign lymph nodes provide normative ranges for clinical use. Outliers raising suspicion for B or T cell lymphoma are not infrequent (26% of benign lymph nodes). Caution is indicated when interpreting outliers in the absence of excisional biopsy or clinical history, particularly in patients with concomitant immunosuppression or inflammatory disease.

Detection of microbial disturbances in a drinking water microbial community through continuous acquisition and advanced analysis of flow cytometry data

2018 ◽  
Vol 145 ◽  
pp. 73-82 ◽  
Author(s):  
Ruben Props ◽  
Peter Rubbens ◽  
Michael Besmer ◽  
Benjamin Buysschaert ◽  
Jurg Sigrist ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Drinking Water ◽  
Microbial Community ◽  
Flow Cytometry Data ◽  
Advanced Analysis

scholarly journals CD161 Is Expressed in a Subset of T-Cell Prolymphocytic Leukemia Cases and Is Useful for Disease Follow-up

2019 ◽  
Vol 152 (4) ◽  
pp. 471-478
Author(s):  
Scott R Gilles ◽  
Sophia L Yohe ◽  
Michael A Linden ◽  
Michelle Dolan ◽  
Betsy Hirsch ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
T Cell ◽  
Nk Cells ◽  
Retrospective Review ◽  
T Cell Subsets ◽  
Prolymphocytic Leukemia ◽  
Flow Cytometry Data ◽  
Flow Cytometric ◽  
Flow Cytometric Evaluation

AbstractObjectivesCD161 (NKRP1) is a lectin-like receptor present on NK cells and rare T-cell subsets. We have observed CD161 expression in some cases of T-cell prolymphocytic leukemia (T-PLL) and found it to be useful in follow-up and detection of disease after treatment.MethodsRetrospective review of T-PLL cases with complete flow cytometry data including CD161.ResultsWe identified 10 cases of T-PLL with flow cytometric evaluation of CD161 available. Six of these cases were positive for CD161 expression. All CD161-positive cases were positive for CD8 with variable CD4 expression, whereas all CD161-negative cases were negative for CD8. In a case with two neoplastic subsets positive and negative for CD8, only the former expressed CD161.ConclusionsThese novel results suggest that CD161 is often aberrantly expressed in a defined subset of T-PLL positive for CD8. We are showing the utility of this immunophenotype in diagnosis and follow-up.

Autogating in Flow Cytometry Data Using SVM Classifiers for Bacterioplankton Identification

2017 ◽  
Author(s):  
Elionai Moura Cordeiro ◽  
Bruno M. S. Wanderley ◽  
Daniel Sabino Amorim de Araujo ◽  
Adriao Duarte Doria Neto
Keyword(s):  
Flow Cytometry ◽  
Flow Cytometry Data
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