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Improved genome inference in the MHC using a population reference graph


Although much is known about human genetic variation, such information is typically ignored in assembling new genomes. Instead, reads are mapped to a single reference, which can lead to poor characterization of regions of high sequence or structural diversity. We introduce a population reference graph, which combines multiple reference sequences and catalogs of variation. The genomes of new samples are reconstructed as paths through the graph using an efficient hidden Markov model, allowing for recombination between different haplotypes and additional variants. By applying the method to the 4.5-Mb extended MHC region on human chromosome 6, combining 8 assembled haplotypes, the sequences of known classical HLA alleles and 87,640 SNP variants from the 1000 Genomes Project, we demonstrate using simulations, SNP genotyping, and short-read and long-read data how the method improves the accuracy of genome inference and identified regions where the current set of reference sequences is substantially incomplete.

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Figure 1: Read mapping in the MHC class II region.
Figure 2: Schematic showing the construction and application of a PRG.
Figure 3: Simulation study and empirical validation.
Figure 4: Recovery of chromotype k-mers from HTS data.
Figure 5: Spatial recovery of k-mers within the HLA class II region.
Figure 6: Alignment of synthetic long-read data to chromotypes.

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NCBI Reference Sequence


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We thank M. Eberle and colleagues at Illumina for early access to the Moleculo data. The study was funded by grants from GlaxoSmithKline and grant 100956/Z/13/Z from the Wellcome Trust to G.M., a Nuffield Department of Medicine Fellowship to Z.I. and a Sir Henry Dale Fellowship jointly awarded by the Wellcome Trust and the Royal Society to Z.I. (102541/Z/13/Z).

Author information

Authors and Affiliations



G.M. designed the experiment. A.D. and C.C. performed analyses. Z.I., M.R.N. and G.M. supervised the research. A.D. and G.M. wrote the manuscript with the assistance of co-authors.

Corresponding authors

Correspondence to Alexander Dilthey or Gil McVean.

Ethics declarations

Competing interests

C.C. and M.R.N. are employed by GlaxoSmithKline (GSK) and may own GSK stock. GSK does not sell or market any software or services related to genetic analysis or the generation of genetic data. G.M. is a founder and shareholder of Genomics, Ltd. G.M. and A.D. are partners in Peptide Groove, LLP.

Integrated supplementary information

Supplementary Figure 1 Relationship between the nucleotide and k-mer PRGs.

The nucleotide PRG is a directed, acyclic graph constructed from a multiple-sequence alignment reflecting variation within the aligned sequences. A k-mer PRG is constructed from the nucleotide PRG by enumerating the possible paths of length k and their relationship. A multi-PRG is generated by combining all non-branching stretches of levels in the k-mer PRG into single levels for the multi-PRG, with edges labeled with multiple k-mers.

Supplementary Figure 2 NA12878 k-mer recovery within classical HLA loci for four approaches.

Each panel shows the fraction of k-mers recovered at single-nucleotide resolution from chromotypes inferred by the four methods using the high-coverage data from NA12878. The average over the locus is also shown.

Supplementary Figure 3 Example of a non-MHC region with low k-mer recovery from mapping-based analysis.

k-mer recovery on chromosome 8 in a region containing multiple members of the ubiquitin-specific peptidase 17–like gene family where there are several 10-kb intervals where <90% of k-mers predicted to exist from the Platypus VCF are recovered from high-coverage sequencing data on NA12878.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–3, Supplementary Tables 1–9 and Supplementary Note (PDF 3181 kb)

Supplementary Data Set: Discrepancies between SNP array and PRG genotypes in NA12878.

Compressed (zip) file with screenshots showing read mapping at the 55 sites where the Viertbi-inferred genotype from the PRG disagrees with the SNP array genotype and where the PRG specifies a gap character. A manual evaluation of these sites is also provided as an Excel file. (ZIP 792 kb)

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Dilthey, A., Cox, C., Iqbal, Z. et al. Improved genome inference in the MHC using a population reference graph. Nat Genet 47, 682–688 (2015).

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