Figure 1

Meiotic recombination in pedigrees with two children. Analysis of meiotic recombination for chromosome 5 in two-generation pedigrees having two parents (Fa, Mo) and two children (B1, B2 for brothers 1 and 2). (A) Identity-by-state analysis in which each data point corresponded to a pairwise comparison between biallelic SNPs from siblings B1 and B2. This analysis showed regions of identical (ID) allele sharing, characterized by pairwise matches such as AA to AA for a given SNP. Regions in which the siblings had one shared allele included IBS1 signal (e.g. AA matching AB). Regions in which the siblings inherited opposite alleles included IBS0 in which there were zero shared alleles (e.g. AA aligned to BB). (B) pediSNP analysis. Panels 1 and 2 show SNPtrio results from normal trios (provided as part of the pediSNP analysis) of Fa/Mo/B1 and Fa/Mo/B2. The y-axis labels include Mendelian inconsistencies that are double (MI-D) or single (MI-S), uniparental inheritance that is maternal (UPI-M) or paternal (UPI-P), and biparental inheritance (BPI). Panels 3 and 4 show the results form "reverse pedigree" of B1/B2/Fa and B1/B2/Mo. By inspection of panels 3 and 4, distinct patterns are evident including identical inheritance (note two overlapping blocks from the ID 2 track), opposite inheritance (note overlapping blocks from the OPP 4 track), and one shared allele (note ID 2 pattern in one panel aligned with a blank region in the other panel). Rarely, a region is completely blank (arrow). This may be caused by the absence of SNP data (as at a centromere), the sharing of one allele by the parents (IBS 1), or the occurrence of "no calls" in that region due to homozygous deletion. (C) Implementation of the Wirtenberger et al. schema (defined in Additional File 4) showed patterns of allele sharing that were consistent with those identified by pediSNP. For all three approaches in panels A-C the edge of each block revealing allele sharing corresponded exactly to the nearest informative SNP (see positions marked *, ‡).