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

Sequences of all functional and open reading frame (ORF) C, J, and V genes (based on IMGT classification) were downloaded from IMGT and Vega databases (www.imgt.org, vega.sanger.ac.uk). All sequences were aligned to the completed contigs of each locus using SeqMan Pro, the positions of which were confirmed using BLAST 52 . Sequences corresponding to each of the mapped C, J, and V genes were extracted from the CH17 contigs, and alleles at each locus were assigned using IMGT V-QUEST 53, 54 . "Novel" alleles were defined as those not found in the IMGT database. To search for potential variants in previously characterized regulatory sequences, SNPs determined from alignments of the CH17 haplotype and references The copyright holder for this preprint (which was not peer-reviewed) is the author/funder.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 from UCSC (www.genome.ucsc.edu), and SNP/gene region overlap was assessed using BEDTools version 2.1 55 . For those genes in which a SNP was found to occur within the defined regions, sequences in question from the CH17 and Kawasaki haplotypes were aligned, visually inspected, and compared to previously identified motifs.