Strong intrinsic biases towards mutation and conservation of bases in human IgVH genes during somatic hypermutation prevent statistical analysis of antigen selection.

Immunoglobulin V region genes acquire point mutations during affinity maturation of the T-cell-dependent B-cell response. It has been proposed that both selection by antigen and characteristics of the DNA sequence are involved in determining the distribution of mutations along the genes. There is a tendency for replacement mutations to occur in the complementarity-determining regions and for silent mutations to accumulate in the framework regions of used genes. By analysing a group of highly mutated human IgVH4-34 (VH4. 21) and family 5 genes derived from human gut-associated lymphoid tissues, which were out-of-frame between VH and JH (and therefore not used) we have investigated the distribution of mutations acquired in the absence of selection. We observed that these genes may show the statistical hallmarks of selected genes, suggesting that intrinsic biases alone may be enough to give the appearance of selection. These data suggest that analysis of the distribution of mutations in IgVH genes cannot be used reliably to state whether antigenic selection of the B-cell carrying the genes occurred. In-frame genes had more silent mutations than the out-of-frame genes and lacked stop codons. These characteristics were considered to be indicative of selection in the in-frame genes derived from human gut-associated lymphoid tissue.