Article open access publication

Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios

Nature Communications, Springer Nature, ISSN 2041-1723

Volume 6, 1, 2015

DOI:10.1038/ncomms6969, Dimensions: pub.1016362455, PMC: PMC4309431, PMID: 25597990,



  1. (1) Aarhus University, grid.7048.b, AU
  2. (2) University of Copenhagen, grid.5254.6, KU
  3. (3) BGI Europe (Denmark), grid.493273.8
  4. (4) Technical University of Denmark, grid.5170.3, DTU
  5. (5) Lundbeck Foundation, grid.452548.a
  6. (6) South China University of Technology, grid.79703.3a
  7. (7) Copenhagen University Hospital, grid.4973.9, Capital Region
  8. (8) University of Southern Denmark, grid.10825.3e, SDU








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.


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