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

Previous analysis of sequence similarity between shared homology blocks of proximal and distal segmental duplication units, which comprise the majority of the IGK locus, revealed that these two regions are >98% similar over most of the region 17 . Segmental duplications are known to facilitate sequence exchange via non-allelic homologous recombination and interlocus gene conversion 29, 30 ; however, given the lack of reference sequence data this has not been investigated in the IGK locus. To address this, we conducted pair-wise comparisons of distal and proximal regions from CH17 and Kawasaki haplotypes to search for large tracts of shared sequence ( Figure 3A ). The expectation is that sequence should be most similar between homologous regions in the alternate haplotype, whereas higher similarity between proximal and distal regions within a haplotype would suggest the occurrence of sequence exchange. Using this approach, we identified a large ~16.7 Kbp region that showed higher identity between the proximal and distal units of the Kawasaki haplotype than between the CH17 distal and Kawasaki proximal units ( Figure 3A ). This region included two IGKV genes for which we observed allelic variants between the Kawasaki and CH17 haplotypes. Four-way sequence alignments of this region show that the CH17 distal unit was most unique compared to the other three sequences The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/006866 doi: bioRxiv preprint haplotype. It is important to note, however, that the Kawasaki distal fragment harbors many unique bp differences compared to the other three sequences (blue tick marks, Figure 3B ), which could be suggestive of the occurrence of mutation following the predicted sequence exchange event. Further analysis of this multi-sequence alignment using the DSS method for recombination detection also predicted two potential flanking recombination breakpoints within the expected regions based on visual inspection of the sequence alignment and comparison of sequence similarities. We also analyzed sequence from two BAC clones in the proximal and distal clusters from the RPCI-11 BAC library 18 ; this analysis revealed that these carried the same variants observed in the Kawasaki haplotype.