Fig. 2

High-resolution and accurate phasing of MHC and KIR loci. a (i) Top chart demonstrates enrichment of targeted HaploSeq reads at the 100 kb binned MHC locus and the bottom plot shows number of probes in 100 kb bins used across the MHC locus. Visually, we can observe a high correlation between these plots, demonstrating the expected relationship between density of probes and the sequencing depth of targeted HaploSeq reads. (ii) To illustrate the sensitivity of probes, we virtually created random probes flanking HindIII cut sites and compared the enrichment in targeted HaploSeq data from these regions to the data from regions containing true probes. We observe ~100 fold more reads from true regions (on target, yellow) than the random regions (off target, green) and this fold-enrichment suggests high-sensitivity of our probes. b High correlation of targeted HaploSeq and the previously published HaploSeq datasets from GM12878 cells at the MHC locus (r² = 0.8). c An example of haplotype inconsistency in the parent-child trio WGS data. Specifically, HapA (TGT-blue) and HapB (CAG-red) represent two haplotypes inferred from the trio dataset. Single-end reads from targeted HaploSeq (top) and Moleculo long-fragment reads (bottom) support a case of an inter-haplotype adjacent SNP-pair (green) and therefore raises an inconsistency with the parent-child trio haplotype inference. d Overall, ~95 % of the targeted HaploSeq reads representing homologous-trans (h-trans) interacting SNVs are concordant with the Moleculo LFR data. e High-resolution phasing capabilities of targeted HaploSeq method at the MHC locus. Completeness represents the collection of all heterozygous SNVs (red) within the MHC locus. Resolution represents the set of phased or resolved heterozygous SNVs in a single haplotype structure. While we observe ~1 % error, these errors are highly concentrated in the high variant density regions. The bottom section represents phasing of only exonic variants. f Similar figure as e) for the KIR locus