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As a control, we selected nine genes in the genome, chosen randomly, but matched in length with a classical HLA gene, so a control gene of similar length matched each classical HLA gene. The variant call sets were then updated to account for changes in variant lengths.

Our haplotypes are remarkable because they are built from de novo assemblies and phased essentially without the reference genome. Chase is the U. In contrast, our new haplotypes contain fewer sequencing gaps Supplemental Fig.

The procedure of mapping and phasing is iterated, as each inferred phased haplotype improves mapping and in turn phasing. The study protocol was reviewed and approved by The Danish National Committee on Health Research Ethics file numbersubmission numbers and Samples of the chain were taken every iterations after the burn-in. After phasing, we created a sequence for each nontransmitted parental haplotype and created a consensus sequence between transmitted parental haplotypes and inherited child haplotypes by multiple global alignments of segments between phased bubbles steps 4 and 5.

Discovery, genotyping and characterization of structural variation and novel sequence at single nucleotide resolution from de novo genome assemblies on a population scale. Alignment of novel and alternative reference haplotypes to the pgf and cox reference haplotypes was performed using MAFFT 7. We conclude that identification of structural variation in this region by alignment to the reference haplotype is not reliable Dilthey et al.

We report full MHC haplotypes and call a large set of structural variants in the regions for future use in imputation with GWAS data. This approach works especially well for studying small variants but is limited in the ability to detect new structural variation, because the quality of the graph is largely reliant on the quality of the sequence alignment, which can be poor in some regions such as near the C4 genes.


J Mol Biol Sequencing and de novo assembly of genomes from Denmark as a population reference. Proc Natl Acad Sci Alert me to new issues of Genome Research.

As a control, we randomly selected nine genes from the MHC region and compared the same metric but found no significant correlation between MAF and distance to the nearest control 50021 for synonymous variants and, although significant for nonsynonymous variants, 502 slope was in the opposite direction, i. We detected strong LD extending upstream of the gene Fig. Genome-wide association studies have revealed the MHC to be the most important region in the human genome for disease associations, in particular for autoimmune diseases Trowsdale and Knight ; Zhou et al.

About Us Chase is the U. Genotypes were called using GenomeStudio software v Basic local alignment search tool. In order to study the importance of selection and the frequency of coding variants in linked genes in general, we calculated the average minor allele frequency MAF of synonymous and nonsynonymous variants as a function of distance to the closest of nine HLA genes classical HLA loci previously shown to be under balancing selection DeGiorgio et al.

Because of the complexity and inaccessibility of the MHC region, most previous studies have bgii on specific regions of the MHC. Auton AMcVean G.

Assessing structural variation in a personal genome—towards a human reference diploid genome. Although we see a minor peak in recombination rate between the genes, recombination rate is generally much lower compared to the entire region Fig.

The approaches to studying variation in the MHC have different advantages and drawbacks. Articles by Schierup, M. Subsequent analysis was done in R 0521 3.

Assembly and analysis of full MHC haplotypes from the Danish population

Genotyping and phase restoration was then performed again for all individuals in a joint call set in order to rescue missed genotypes. Chase today announced efforts to help its customers who are U. When we align to the cox haplotype, we can improve alignment in this region significantly for most haplotypes Supplemental Fig. The six existing haplotypes from the human reference genome 5012 included for comparison, showing that these contain many sequencing gaps. The entire scaffolds were used and not only the parts mapping to 55021 reference.


Upstream flanking sequences UFS of length 40 bases were extracted for each variant 0521 from the assembly graphs. Search for related content. View source version on businesswire. Integrating mapping- assembly- and haplotype-based approaches for calling variants in clinical sequencing applications. Nucleotide diversity, Tajima’s Dr 2and minor allele frequencies were computed using VCFtools version 0. Trowsdale JKnight JC.

Assembly and analysis of 100 full MHC haplotypes from the Danish population

Deep sequencing of the MHC region in the Chinese population contributes to studies of complex disease. S5 ; however, for some haplotypes, alignment is still poor. Previous Section Next Section. The content of repetitive elements was calculated using RepeatMasker Smit et al.

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For instance, the addition of our haplotypes to population reference graphs will make it possible to study novel sequences using mapping-based approaches and will enable us to place them more accurately in the reference genome.

Variants within the classical MHC genes are not included. For population genetics analyses, we chose to focus on the haplotypes with the most phased variants and the least amount of sequence gaps—the 50 haplotypes transmitted to the children.

We calculate the validation rate as the fraction of variants that have the same phase as we predicted out of the total number of variants of which we could correctly identify an allele. Indels occur with higher relative frequency outside classical loci compared to SNVs and with higher minor allele frequencies also Fig.

We then mapped reads to the transmitted consensus haplotypes and genotyped and phased them using transmission information and read-backed phasing step 6.