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Quantification of total T-cell receptor diversity by flow cytometry and spectratyping.

Ciupe SM, Devlin BH, Markert ML, Kepler TB - BMC Immunol. (2013)

Bottom Line: Spectratyping generates data about T-cell receptor CDR3 length distribution for each BV gene but is technically complex.We have shown that the sample size is a sensitive parameter in the predicted flow divergence values, but not in the spectratype divergence values.We have derived two ways to correct for the measurement bias using mathematical and statistical approaches and have predicted a lower bound in the number of lymphocytes needed when using the divergence as a substitute for diversity.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Mathematics, Virginia Tech, 460 McBryde Hall, Blacksburg, VA 24060, USA. stanca@vt.edu

ABSTRACT

Background: T-cell receptor diversity correlates with immune competency and is of particular interest in patients undergoing immune reconstitution. Spectratyping generates data about T-cell receptor CDR3 length distribution for each BV gene but is technically complex. Flow cytometry can also be used to generate data about T-cell receptor BV gene usage, but its utility has not been compared to or tested in combination with spectratyping.

Results: Using flow cytometry and spectratype data, we have defined a divergence metric that quantifies the deviation from normal of T-cell receptor repertoire. We have shown that the sample size is a sensitive parameter in the predicted flow divergence values, but not in the spectratype divergence values. We have derived two ways to correct for the measurement bias using mathematical and statistical approaches and have predicted a lower bound in the number of lymphocytes needed when using the divergence as a substitute for diversity.

Conclusions: Using both flow cytometry and spectratyping of T-cells, we have defined the divergence measure as an indirect measure of T-cell receptor diversity. We have shown the dependence of the divergence measure on the sample size before it can be used to make predictions regarding the diversity of the T-cell receptor repertoire.

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Flow divergence, Df, as a function of sample size n (∙), presented on a log-log scale.
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Figure 2: Flow divergence, Df, as a function of sample size n (∙), presented on a log-log scale.

Mentions: We specifically wanted to assess the performance of the divergences Df and Ds in predicting the diversity of the T-cell receptor repertoire under stressful, i.e. cell limited, circumstances. While Df and Ds account for deviations from normal of distributions of TCR BV family usage and CDR3 lengths within each TCR BV family, additional variability is added due to the dependence on the number of measured events, n, for every individual patient/control (see Figures 1 and 2). Knowing the sample size n and the dimensions of the measured space, Li, we derived the corrected divergence value, Di,corr (see section ‘Sampling bias - theoretical derivation’) to be given by


Quantification of total T-cell receptor diversity by flow cytometry and spectratyping.

Ciupe SM, Devlin BH, Markert ML, Kepler TB - BMC Immunol. (2013)

Flow divergence, Df, as a function of sample size n (∙), presented on a log-log scale.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3750526&req=5

Figure 2: Flow divergence, Df, as a function of sample size n (∙), presented on a log-log scale.
Mentions: We specifically wanted to assess the performance of the divergences Df and Ds in predicting the diversity of the T-cell receptor repertoire under stressful, i.e. cell limited, circumstances. While Df and Ds account for deviations from normal of distributions of TCR BV family usage and CDR3 lengths within each TCR BV family, additional variability is added due to the dependence on the number of measured events, n, for every individual patient/control (see Figures 1 and 2). Knowing the sample size n and the dimensions of the measured space, Li, we derived the corrected divergence value, Di,corr (see section ‘Sampling bias - theoretical derivation’) to be given by

Bottom Line: Spectratyping generates data about T-cell receptor CDR3 length distribution for each BV gene but is technically complex.We have shown that the sample size is a sensitive parameter in the predicted flow divergence values, but not in the spectratype divergence values.We have derived two ways to correct for the measurement bias using mathematical and statistical approaches and have predicted a lower bound in the number of lymphocytes needed when using the divergence as a substitute for diversity.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Mathematics, Virginia Tech, 460 McBryde Hall, Blacksburg, VA 24060, USA. stanca@vt.edu

ABSTRACT

Background: T-cell receptor diversity correlates with immune competency and is of particular interest in patients undergoing immune reconstitution. Spectratyping generates data about T-cell receptor CDR3 length distribution for each BV gene but is technically complex. Flow cytometry can also be used to generate data about T-cell receptor BV gene usage, but its utility has not been compared to or tested in combination with spectratyping.

Results: Using flow cytometry and spectratype data, we have defined a divergence metric that quantifies the deviation from normal of T-cell receptor repertoire. We have shown that the sample size is a sensitive parameter in the predicted flow divergence values, but not in the spectratype divergence values. We have derived two ways to correct for the measurement bias using mathematical and statistical approaches and have predicted a lower bound in the number of lymphocytes needed when using the divergence as a substitute for diversity.

Conclusions: Using both flow cytometry and spectratyping of T-cells, we have defined the divergence measure as an indirect measure of T-cell receptor diversity. We have shown the dependence of the divergence measure on the sample size before it can be used to make predictions regarding the diversity of the T-cell receptor repertoire.

Show MeSH
Related in: MedlinePlus