Building a population-specific catalogue of single nucleotide variants (SNVs), indels and structural variants (SVs) with frequencies, termed a national pan-genome, is critical for further advancing clinical and public health genetics in large cohorts. Here we report a Danish pan-genome obtained from sequencing 10 trios to high depth (50 × ). We report 536k novel SNVs and 283k novel short indels from mapping approaches and develop a population-wide de novo assembly approach to identify 132k novel indels larger than 10 nucleotides with low false discovery rates. We identify a higher proportion of indels and SVs than previous efforts showing the merits of high coverage and de novo assembly approaches. In addition, we use trio information to identify de novo mutations and use a probabilistic method to provide direct estimates of 1.27e−8 and 1.5e−9 per nucleotide per generation for SNVs and indels, respectively.

Hundreds of thousands of human genomes are now being sequenced to characterize genetic variation and use this information to augment association mapping studies of complex disorders and other phenotypic traits 1-4 . Genetic variation is identified mainly by mapping short reads to the reference genome or by performing local assembly 2,5-7 . However, these approaches are biased against discovery of structural variants and variation in the more complex parts of the genome. Hence, large-scale de novo assembly is needed. Here we show that it is possible to construct excellent de novo assemblies from high-coverage sequencing with mate-pair libraries extending up to 20 kilobases. We report de novo assemblies of 150 individuals (50 trios) from the GenomeDenmark project. The quality of these assemblies is similar to those obtained using the more expensive long-read technology 4,8-13 . We use the assemblies to identify a rich set of structural variants including many novel insertions and demonstrate how this variant catalogue enables further deciphering of known association mapping signals. We leverage the assemblies to provide 100 completely resolved major histocompatibility complex haplotypes and to resolve major parts of the Y chromosome. Our study provides a regional reference genome that we expect will improve the power of future association mapping studies and hence pave the way for precision medicine initiatives, which now are being launched in many countries including Denmark.Using a combination of high-depth (average 78× ) Illumina pairedend and mate-pair libraries, we applied Allpaths-LG 14 to create de novo assemblies of high quality and coverage for each of the 150 individuals with a median scaffold N50 of ~ 21 megabases (Mb; maximum ~ 30 Mb) (Supplementary Table 1). The 100 largest scaffolds in each of the 140 best assemblies typically covered more than 75% (median 77%, Extended Data Fig. 1a) of the genome, with the largest scaffolds exceeding 110 Mb in size (Supplementary Table 1). To evaluate the accuracy of the assemblies, we subsequently aligned the scaffolds for each individual to the human reference genome (GRCh38) 15 . Figure 1 shows an example individual where the euchromatic part of each chromosome was almost completely covered by a few large scaffolds and in several cases scaffolds covered almost entire chromosome arms. Only rarely did we find that large scaffolds break and align to more than one chromosome (Extended Data Fig. 1b), suggesting that even the largest scaffolds are seldom chimaeric. We also compared our de novo assemblies with a published long-read assembly based on BioNano mapping and PacBio sequencing 16 . Extended Data Figs 2a and 3 show that this assembly was less complete than our assemblies, but with similar scaffold lengths. The long-read assembly had 5.38% missing data compared with our median of 4.25% (Extended Data Fig. 3a), but the missing data in our assemblies were found in smaller gaps (Extended Data Fig. 3b, c), and the median contig length was therefore much smaller th...

Genes in the major histocompatibility complex (MHC, also known as HLA) play a critical role in the immune response and variation within the extended 4-Mb region shows association with major risks of many diseases. Yet, deciphering the underlying causes of these associations is difficult because the MHC is the most polymorphic region of the genome with a complex linkage disequilibrium structure. Here, we reconstruct full MHC haplotypes from de novo assembled trios without relying on a reference genome and perform evolutionary analyses. We report 100 full MHC haplotypes and call a large set of structural variants in the regions for future use in imputation with GWAS data. We also present the first complete analysis of the recombination landscape in the entire region and show how balancing selection at classical genes have linked effects on the frequency of variants throughout the region.

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