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

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Søren Besenbacher, Siyang Liu, Jose Maria Gonzalez-Izarzugaza, Jakob Grove, Kirstine G Belling, Jette Bork-Jensen, Shujia Huang, Thomas Damm Als, Shengting Li, Rachita Yadav, Arcadio Rubio García, Francesco Lescai, Ditte Demontis, Junhua Rao, Weijian Ye, Thomas Mailund, Rune Møllegaard Friborg, Christian N. S. Pedersen, Ruiqi Xu, Jihua Sun & 27 others Hao Liu, Ou Wang, Xiaofang Cheng, David Flores, Emil Karol Rydza, Kristoffer Rapacki, John Damm Sørensen, Piotr Jaroslaw Chmura, David Westergaard, Piotr Dworzynski, Thorkild I. A. Sørensen, Ole Lund, Torben Hansen, Xun Xu, Ning Li, Lars Bolund, Oluf Pedersen, Hans Eiberg, Anders Krogh, Anders D. Børglum, Søren Brunak, Karsten Kristiansen, Mikkel H Schierup, Jun Wang, Ramneek Gupta, Palle Villesen, Simon Rasmussen

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.

Original languageEnglish
Article number5969
JournalNature Communications
Number of pages9
Publication statusPublished - 2015

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