Sequencing of the human IG light chain loci from a hydatidiform mole BAC library reveals locus-specific signatures of genetic diversity

Corey T Watson; Karyn Meltz Steinberg; Tina A Graves-Lindsay; Rene L Warren; Maika Malig; Jacqueline E Schein; Richard K Wilson; Rob Holt; Evan Eichler; Felix Breden

Consistent with observations based on V gene allelic variation, SNP density in IGHV (0.0035) was approximately 3-fold higher than in IGLV (0.0012) and 6-fold higher than in IGKV (0.0006); SNP densities were slightly elevated within functional/ORF V genes in each region compared to the calculated locus-wide values ( Table 2 ). An analysis of genomic features in the three loci also showed that the fraction of each locus covered by repeat content was highest in IGHV, whereas that covered by SDs, not surprisingly was highest in IGKV (Table 2 ). However, when SDs associated with the IGKV proximal/distal duplication event were excluded, SD coverage in IGHV (37.7%) was found to be much higher than both of the light chain loci (IGLV, 24.6%; IGKV, 28.2%; Table 2 ). When only SDs exhibiting > 95% sequence identity were considered, this difference was even more striking (IGHV, 28.8%; IGLV, 12.9%; IGKV, 1.0%).