Estimating hypermutation rates from clonal tree data.
To understand the mechanisms underlying the varying patterns of mutations that occur during immune and autoimmune responses, estimates of the somatic hypermutation rate are critical. However, despite its significance, precise estimates of the mutation rate do not currently exist. Microdissection studies of mutating B cell clones provide an opportunity to measure this rate more accurately than previously possible. Each microdissection provides a number of clonally related sequences that, through the analysis of shared mutations, can be genealogically related to each other. The shape of these clonal trees is influenced by many processes, including the hypermutation rate. We have developed two different methods to estimate the mutation rate based on these data. These methods are applied to two sets of experimental data, one from an autoimmune response and one from the antihapten response to (4-hydroxy-3-nitrophenyl)acetyl (NP). Comparable mutation rates are estimated for both responses, 0.7-0.9 x 10(-3) and 0.9-1.1 x 10(-3) bp(-1) division(-1) for the autoimmune and NP responses, respectively. In addition to comparing the results of the two procedures, we investigate the effect on our estimate of assumptions, such as the fraction of lethal mutations.
Department of Computer Science, Princeton University, Princeton, NJ 08544, USA. stevenk@cs.princeton.edu
Steven H
SH
Kleinstein
Yoram
Y
Louzoun
Mark J
MJ
Shlomchik
D000818:Animals; D001323:Autoantibodies / Q000096:biosynthesis; D001324:Autoantigens / Q000276:immunology; D001327:Autoimmune Diseases / Q000235:genetics / Q000276:immunology; D016175:B-Lymphocyte Subsets / Q000166:cytology / Q000276:immunology* / Q000378:metabolism*; D002455:Cell Division / Q000235:genetics / Q000276:immunology; D002999:Clone Cells; D003198:Computer Simulation; D003663:Decision Trees; D018095:Germ-Line Mutation / Q000276:immunology; D018655:Lymphocyte Count; D051379:Mice; D019463:Mice, Inbred MRL lpr; D008822:Mice, Transgenic; D018448:Models, Immunological; D009010:Monte Carlo Method; D027041:Somatic Hypermutation, Immunoglobulin
D001323:Autoantibodies; D001324:Autoantigens