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

Søren Besenbacher, Siyang Liu, José M. G. Izarzugaza, Jakob Grove, Kirstine Belling, Jette Bork-Jensen, Shujia Huang, Thomas D. Als, Shengting Li, Rachita Yadav, Arcadio Rubio-García, Francesco Lescai, Ditte Demontis, Junhua Rao, Weijian Ye, Thomas Mailund, Rune M. Friborg, Christian N. S. Pedersen, Ruiqi Xu, Jihua Sun, Hao Liu, Ou Wang, Xiaofang Cheng, David Flores, Emil Rydza, Kristoffer Rapacki, John Damm Sørensen, Piotr 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 () and Simon Rasmussen ()
Additional contact information
Søren Besenbacher: Bioinformatics Research Center, Aarhus University
Siyang Liu: BGI Europe
José M. G. Izarzugaza: Center for Biological Sequence Analysis, Technical University of Denmark
Jakob Grove: Bioinformatics Research Center, Aarhus University
Kirstine Belling: Center for Biological Sequence Analysis, Technical University of Denmark
Jette Bork-Jensen: The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen
Shujia Huang: BGI Europe
Thomas D. Als: Centre for Integrative Sequencing, iSEQ, Aarhus University
Shengting Li: BGI Europe
Rachita Yadav: Center for Biological Sequence Analysis, Technical University of Denmark
Arcadio Rubio-García: Center for Biological Sequence Analysis, Technical University of Denmark
Francesco Lescai: Centre for Integrative Sequencing, iSEQ, Aarhus University
Ditte Demontis: Centre for Integrative Sequencing, iSEQ, Aarhus University
Junhua Rao: BGI Europe
Weijian Ye: BGI Europe
Thomas Mailund: Bioinformatics Research Center, Aarhus University
Rune M. Friborg: Bioinformatics Research Center, Aarhus University
Christian N. S. Pedersen: Bioinformatics Research Center, Aarhus University
Ruiqi Xu: BGI Europe
Jihua Sun: BGI Europe
Hao Liu: BGI Europe
Ou Wang: BGI Europe
Xiaofang Cheng: BGI Europe
David Flores: Center for Biological Sequence Analysis, Technical University of Denmark
Emil Rydza: Center for Biological Sequence Analysis, Technical University of Denmark
Kristoffer Rapacki: Center for Biological Sequence Analysis, Technical University of Denmark
John Damm Sørensen: Center for Biological Sequence Analysis, Technical University of Denmark
Piotr Chmura: Center for Biological Sequence Analysis, Technical University of Denmark
David Westergaard: Center for Biological Sequence Analysis, Technical University of Denmark
Piotr Dworzynski: Center for Biological Sequence Analysis, Technical University of Denmark
Thorkild I. A. Sørensen: The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen
Ole Lund: Center for Biological Sequence Analysis, Technical University of Denmark
Torben Hansen: The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen
Xun Xu: BGI Europe
Ning Li: BGI Europe
Lars Bolund: Centre for Integrative Sequencing, iSEQ, Aarhus University
Oluf Pedersen: The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen
Hans Eiberg: Panum Institute, University of Copenhagen
Anders Krogh: University of Copenhagen
Anders D. Børglum: Centre for Integrative Sequencing, iSEQ, Aarhus University
Søren Brunak: Center for Biological Sequence Analysis, Technical University of Denmark
Karsten Kristiansen: University of Copenhagen
Mikkel H. Schierup: Bioinformatics Research Center, Aarhus University
Jun Wang: BGI Europe
Ramneek Gupta: Center for Biological Sequence Analysis, Technical University of Denmark
Palle Villesen: Bioinformatics Research Center, Aarhus University
Simon Rasmussen: Center for Biological Sequence Analysis, Technical University of Denmark

Nature Communications, 2015, vol. 6, issue 1, 1-9

Abstract: Abstract 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.

Date: 2015
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DOI: 10.1038/ncomms6969

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