Measurement of absolute T cell receptor rearrangement diversity

Journal of Immunological Methods

Volumn 368, Issue 1-2, 2011, Pages 45-53

  Baum, Paul D ^a   Young, Jennifer J ^a   McCune, Joseph M ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

AmpliCot; Diversity; Rearrangement; Repertoire; Sequence; T cell receptor

Indexed keywords

T LYMPHOCYTE RECEPTOR; T LYMPHOCYTE RECEPTOR BETA CHAIN;

ADAPTIVE IMMUNITY; ARTICLE; CONTROLLED STUDY; DNA HYBRIDIZATION; FLOW CYTOMETRY; GENE REARRANGEMENT; GENE SEQUENCE; GENETIC VARIABILITY; HUMAN; HUMAN CELL; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; T LYMPHOCYTE; T LYMPHOCYTE RECEPTOR GENE;

ADAPTIVE IMMUNITY; FLOW CYTOMETRY; GENE REARRANGEMENT, BETA-CHAIN T-CELL ANTIGEN RECEPTOR; GENETIC VARIATION; HUMANS; IMMUNOGLOBULIN J-CHAINS; IMMUNOGLOBULIN VARIABLE REGION; RECEPTORS, ANTIGEN, T-CELL, ALPHA-BETA; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA; SEQUENCE ANALYSIS, DNA;

EID: 79955465886     PISSN: 00221759     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jim.2011.03.001     Document Type: Article

References (21)

1. Arstila T.P., Casrouge A., Baron V., Even J., Kanellopoulos J., Kourilsky P. Diversity of human alpha beta T cell receptors. Science 2000, 288:1135.
2. Baum P.D., McCune J.M. Direct measurement of T-cell receptor repertoire diversity with AmpliCot. Nat. Methods 2006, 3:895.
3. Baum P.D., Young J.J., Zhang Q., Kasakow Z., McCune J.M. Design, construction, and validation of a modular library of sequence diversity standards for polymerase chain reaction. Anal. Biochem. 2010.
4. Boyd S.D., Marshall E.L., Merker J.D., Maniar J.M., Zhang L.N., Sahaf B., Jones C.D., Simen B.B., Hanczaruk B., Nguyen K.D. Measurement and clinical monitoring of human lymphocyte clonality by massively parallel VDJ pyrosequencing. Sci. Transl. Med. 2009, 1. 12ra23.
5. Douek D.C., Betts M.R., Brenchley J.M., Hill B.J., Ambrozak D.R., Ngai K.L., Karandikar N.J., Casazza J.P., Koup R.A. A novel approach to the analysis of specificity, clonality, and frequency of HIV-specific T cell responses reveals a potential mechanism for control of viral escape. J. Immunol. 2002, 168:3099.
6. Freeman J.D., Warren R.L., Webb J.R., Nelson B.H., Holt R.A. Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing. Genome Res. 2009, 19:1817.
7. Gorski J., Yassai M., Zhu X., Kissela B., Kissella B., Keever C., Flomenberg N. Circulating T cell repertoire complexity in normal individuals and bone marrow recipients analyzed by CDR3 size spectratyping. Correlation with immune status. J. Immunol. 1994, 152:5109.
8. Hori S., Collette A., Demengeot J., Stewart J. A new statistical method for quantitative analyses: application to the precise quantification of T cell receptor repertoires. J. Immunol. Meth. 2002, 268:159.
9. Kepler T.B., He M., Tomfohr J.K., Devlin B.H., Sarzotti M., Markert M.L. Statistical analysis of antigen receptor spectratype data. Bioinformatics 2005, 21:3394.
10. Killian M.S., Matud J., Detels R., Giorgi J.V., Jamieson B.D. MaGiK method of T-cell receptor repertoire analysis. Clin. Vaccine Immunol. 2002, 9:858.
11. Long S.A., Khalili J., Ashe J., Berenson R., Ferrand C., Bonyhadi M. Standardized analysis for the quantification of Vbeta CDR3 T-cell receptor diversity. J. Immunol. Methods 2006, 317:100.
12. Melenhorst J.J., Lay M.D., Price D.A., Adams S.D., Zeilah J., Sosa E., Hensel N.F., Follmann D., Douek D.C., et al. Contribution of TCR-beta locus and HLA to the shape of the mature human Vbeta repertoire. J. Immunol. 2008, 180:6484.
13. Pannetier C., Even J., Kourilsky P. T-cell repertoire diversity and clonal expansions in normal and clinical samples. Immunol. Today 1995, 16:176.
14. Pfaffl M.W. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 2001, 29:e45.
15. Quigley M.F., Greenaway H.Y., Venturi V., Lindsay R., Quinn K.M., Seder R.A., Douek D.C., Davenport M.P., Price D.A. Convergent recombination shapes the clonotypic landscape of the naive T-cell repertoire. Proc. Natl Acad. Sci. U.S.A. 2010, 107:19414.
16. Robins H.S., Campregher P.V., Srivastava S.K., Wacher A., Turtle C.J., Kahsai O., Riddell S.R., Warren E.H., Carlson C.S. Comprehensive assessment of T-cell receptor beta-chain diversity in alphabeta T cells. Blood 2009, 114:4099.
17. Rowen L., Koop B.F., Hood L. The complete 685-kilobase DNA sequence of the human beta T cell receptor locus. Science 1996, 272:1755.
18. Sriram U., Wong M., Caillier S.J., Hecht F.M., Elkins M.K., Levy J.A., Oksenberg J.R., Baranzini S.E. Quantitative longitudinal analysis of T cell receptor repertoire expression in HIV-infected patients on antiretroviral and interleukin-2 therapy. AIDS Res. Hum. Retroviruses 2007, 23:741.
19. Venturi V., Kedzierska K., Turner S.J., Doherty P.C., Davenport M.P. Methods for comparing the diversity of samples of the T cell receptor repertoire. J. Immunol. Methods 2007, 321:182.
20. Wang C., Sanders C.M., Yang Q., Schroeder H.W., Wang E., Babrzadeh F., Gharizadeh B., Myers R.M., Hudson J.R., et al. High throughput sequencing reveals a complex pattern of dynamic interrelationships among human T cell subsets. Proc. Natl Acad. Sci. U.S.A. 2010, 107:1518.
21. Wettstein P., Strausbauch M., Therneau T., Borson N. The application of real-time PCR to the analysis of T cell repertoires. Nucleic Acids Res. 2008, 36:e140.