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

Base pair differences were collated based on pair-wise global alignments made between the Kawasaki proximal sequence and all other proximal and distal sequences from the Kawasaki and The copyright holder for this preprint (which was not peer-reviewed) is the author/funder.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 CH17 haplotypes. Global alignments and variant calls were carried out using "run-mummer3" and "combineMUMs" commands in MUMmer3.0 58 . A sequence similarity plot was then generated for each pair-wise comparison using 10 kbp windows with a sliding size of 500 bp, as reported previously 17 . Sequences, ~22.5 kbp in length, from the region suspected to harbor a potential recombination event between proximal and distal regions, were extracted from each haplotype (proximal and distal) and aligned using ClustalW 59 within ebioX (http://www.ebioinformatics.org/ebiox/). Recombination/gene conversion analysis based on this alignment was conducted using the Difference of Sums of Squares (DSS) method within TOPALi v2 60, 61 . This method is based on comparing the branching patterns of two trees constructed using the first and second halves of sequence alignments within a given window of a larger alignment being analyzed; the fit between these two trees and the calculation of DSS is measured using the sum of squares. Windows in which trees differ significantly between the two halves are scored with high DSS values, and are thus candidate sites for recombination. The parameters used here for this analysis were as follows: a window size of 2.5 Kbp with a step size of 100 bp; the Jukes-Cantor substitution model for calculating distance matrices; 500 bootstrap iterations to test for significance; and the analysis was conducted in both forward and reverse directions along the alignment.