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

We analyzed sequences from 17 CH17 BAC clones (IGL, 9; IGK, 8) comprising tiling paths across the two loci (Figures 1 and 2 ) --one of the clones in IGK, CH17-198L18, had been sequenced previously. Clones unique to either IGK or IGL were then used to construct locuswide contigs; clones in IGKV proximal and distal regions were aligned separately because the gap separating these two regions was not completely filled by the current sequencing effort. Figure 1) . In total, we identified 37 of the 38 known functional/ORF IGLV genes, seven functional J genes, and four functional C genes. The remaining IGLV gene, IGHV5-39 was not found in CH17, consistent with it being an insertion polymorphism 15, 21 . Sequence comparisons within IGLV, IGLJ, and IGLC genes revealed allelic differences between CH17 and the Kawasaki haplotype at six V genes, two J genes, and one C gene (Figure 1 ; Supplementary Table 1 ). Six of these alleles, five of which were novel (IGLV6-57, IGLV11-55, IGLV5-45, IGLV5-48, and IGLC7), included non-synonymous changes. Notably, the novel allele identified at IGHV5-48 included a nonsense mutation that introduced a premature stop codon in the framework 3 region of the protein; 15 additional SNPs were also characterized within the exons of this gene. Prior to this study, only a single allele of IGLV5-48 had been described, classified as an ORF due to an uncharacteristic single nucleotide difference in the heptamer portion of the recombination signal (RS: TACAGT instead of CACAGTG 24 ). SNPs characterized in the remaining four novel functional/ORF alleles were represented in the 1000 genomes project (1KG) dataset 25 . Previously described regulatory motifs 13 , including RS sequences, associated with each of the 37 identified functional/ORF IGLV genes were also inspected for previously uncharacterized variants in the CH17 haplotype, but no SNPs in these regions were identified.