A Generalized Mathematical Model To Estimate T- and B-Cell Receptor Diversities Using AmpliCot

Biophysical Journal - Tập 103 - Trang 999-1010 - 2012
Irina Baltcheva1, Ellen Veel2, Thomas Volman2, Dan Koning2, Anja Brouwer2, Jean-Yves Le Boudec1, Kiki Tesselaar2, Rob J. de Boer3, José A.M. Borghans2
1Laboratory for Computer Communications and Applications, École Polytechnique Fédérale de Lausanne, Switzerland
2Department of Immunology, University Medical Center Utrecht
3Department of Theoretical Biology, Utrecht University, Utrecht, The Netherlands

Tài liệu tham khảo

Goldsby, 2003 Robins, 2009, Comprehensive assessment of T-cell receptor β-chain diversity in αβ T cells, Blood, 114, 4099, 10.1182/blood-2009-04-217604 Pannetier, 1993, The sizes of the CDR3 hypervariable regions of the murine T-cell receptor β-chains vary as a function of the recombined germ-line segments, Proc. Natl. Acad. Sci. USA, 90, 4319, 10.1073/pnas.90.9.4319 Currier, 2001, Spectratype/immunoscope analysis of the expressed TCR repertoire Shendure, 2008, Next-generation DNA sequencing, Nat. Biotechnol., 26, 1135, 10.1038/nbt1486 Mardis, 2008, Next-generation DNA sequencing methods, Annu. Rev. Genomics Hum. Genet., 9, 387, 10.1146/annurev.genom.9.081307.164359 Boyd, 2009, Measurement and clinical monitoring of human lymphocyte clonality by massively parallel V-D-J pyrosequencing, Sci. Transl. Med., 1, 12ra23, 10.1126/scitranslmed.3000540 Freeman, 2009, Profiling the T-cell receptor β-chain repertoire by massively parallel sequencing, Genome Res., 19, 1817, 10.1101/gr.092924.109 Wang, 2010, High throughput sequencing reveals a complex pattern of dynamic interrelationships among human T cell subsets, Proc. Natl. Acad. Sci. USA, 107, 1518, 10.1073/pnas.0913939107 Baum, 2006, Direct measurement of T-cell receptor repertoire diversity with AmpliCot, Nat. Methods, 3, 895, 10.1038/nmeth949 Baum, 2011, Measurement of absolute T cell receptor rearrangement diversity, J. Immunol. Methods, 368, 45, 10.1016/j.jim.2011.03.001 Britten, 1968, Repeated sequences in DNA. Hundreds of thousands of copies of DNA sequences have been incorporated into the genomes of higher organisms, Science, 161, 529, 10.1126/science.161.3841.529 Schütze, 2010, A calibrated diversity assay for nucleic acid libraries using DiStRO—a diversity standard of random oligonucleotides, Nucleic Acids Res., 38, e23, 10.1093/nar/gkp1108 Baum, 2011, Design, construction, and validation of a modular library of sequence diversity standards for polymerase chain reaction, Anal. Biochem., 411, 106, 10.1016/j.ab.2010.11.035 Ishii, 2001, Optimization of annealing temperature to reduce bias caused by a primer mismatch in multitemplate PCR, Appl. Environ. Microbiol., 67, 3753, 10.1128/AEM.67.8.3753-3755.2001 Sipos, 2007, Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene-targeting bacterial community analysis, FEMS Microbiol. Ecol., 60, 341, 10.1111/j.1574-6941.2007.00283.x Wetmur, 1968, Kinetics of renaturation of DNA, J. Mol. Biol., 31, 349, 10.1016/0022-2836(68)90414-2 Le Boudec, 2010 Schneeberger, 1995, Quantitative detection of reverse transcriptase-PCR products by means of a novel and sensitive DNA stain, PCR Methods Appl., 4, 234, 10.1101/gr.4.4.234 Colborn, 2008, Estimation of copy number using SYBR Green: confounding by AT-rich DNA and by variation in amplicon length, Am. J. Trop. Med. Hyg., 79, 887, 10.4269/ajtmh.2008.79.887