title: A generalized mathematical model to estimate T- and B-cell receptor diversities using AmpliCot.
abstract: The efficiency of the adaptive immune system is dependent on the diversity of T- and B-cell receptors, which is created by random rearrangement of receptor gene segments. AmpliCot is an experimental technique that allows the measurement of the diversity of the T- and B-cell repertoire. This procedure has the advantage over other cloning and sequencing techniques of being time- and expense-effective. In previous studies, receptor diversity, measured with AmpliCot, has been inferred assuming a second-order kinetics model. The latter implies that the relation between diversity and concentration × time (Cot) values is linear. We show that a more detailed model, involving heteroduplex and transient-duplex formation, leads to significantly better fits of experimental data and to nonlinear diversity-Cot relations. We propose an alternative fitting procedure, which is straightforward to apply and which gives an improved description of the relationship between Cot values and diversity.
authors.affiliation: Laboratory for Computer Communications and Applications, École Polytechnique Fédérale de Lausanne, Switzerland. irina.baltcheva@gmail.com
authors.forename: Irina
authors.initials: I
authors.lastname: Baltcheva
authors.forename: Ellen
authors.initials: E
authors.lastname: Veel
authors.forename: Thomas
authors.initials: T
authors.lastname: Volman
authors.forename: Dan
authors.initials: D
authors.lastname: Koning
authors.forename: Anja
authors.initials: A
authors.lastname: Brouwer
authors.forename: Jean-Yves
authors.initials: JY
authors.lastname: Le Boudec
authors.forename: Kiki
authors.initials: K
authors.lastname: Tesselaar
authors.forename: Rob J
authors.initials: RJ
authors.lastname: de Boer
authors.forename: José A M
authors.initials: JA
authors.lastname: Borghans
mesh_terms: D000465:Algorithms; D007700:Kinetics; D008954:Models, Biological; D017711:Nonlinear Dynamics; D011947:Receptors, Antigen, B-Cell / Q000276:immunology / Q000378:metabolism*; D011948:Receptors, Antigen, T-Cell / Q000276:immunology / Q000378:metabolism*; D013050:Spectrometry, Fluorescence
chemical_list: D011947:Receptors, Antigen, B-Cell; D011948:Receptors, Antigen, T-Cell