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

Locus-wide SNPs were first called in the IGLV, IGKV, and IGHV regions of the CH17 haplotypes by conducting global alignments of the CH17 and Kawasaki or Matsuda haplotypes. The copyright holder for this preprint (which was not peer-reviewed) is the author/funder.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 (https://hyperbrowser.uio.no). We created "case-control" tracks including coordinates overlapped (SD) and not overlapped (non-SD) by SDs in the IGHV/IGKV regions, and then carried out tests for enrichments of CH17 SNPs in these regions by permuting the SD and non-SD status for each IGHV and IGKV set of coordinates (Monte Carlo Simulations = 10,000). The observed enrichments were then compared to the simulated datasets to calculate P values for IGHV and IGKV region analyses. For genome-wide centromere/telomere analysis, we used CHM1 variants, and SNP densities in telomeric/centromeric regions were estimated twice independently using telomere/centromere coordinates extended by either 1Mbp or 3Mbp.