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

Søren Besenbacher, Siyang Liu, Jose Maria Gonzalez-Izarzugaza, Jakob Grove, Kirstine C. Belling, Jette Bork-Jensen, Shujia Huang, Thomas Dam-Als, Shengting Li, Rachita Yadav, Rachita Yadav, Arcadio Rubio García, Francesco Lescai, Ditte Demontis, Junhua Rao, Weijian Ye, Thomas Mailund, Rune M. Friborg, Christian N. S. Pedersen, Ruiqi XuJihua Sun, Hao Liu, Ou Wang, Xiaofang Cheng, David Flores Santa Cruz, 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, Wang Jun, Ramneek Gupta, Palle Villesen, Simon Rasmussen

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    Abstract

    Building a population-specific catalogue of single nucleotide variants (SNVs), indels andstructural variants (SVs) with frequencies, termed a national pan-genome, is critical forfurther advancing clinical and public health genetics in large cohorts. Here we report a Danishpan-genome obtained from sequencing 10 trios to high depth (50). We report 536k novelSNVs and 283k novel short indels from mapping approaches and develop a population-widede novo assembly approach to identify 132k novel indels larger than 10 nucleotides with lowfalse discovery rates. We identify a higher proportion of indels and SVs than previous effortsshowing the merits of high coverage and de novo assembly approaches. In addition, we usetrio information to identify de novo mutations and use a probabilistic method to providedirect estimates of 1.27e8 and 1.5e9 per nucleotide per generation for SNVs and indels, respectively.
    Original languageEnglish
    Article number5969
    JournalNature Communications
    Volume6
    Number of pages9
    ISSN2041-1723
    DOIs
    Publication statusPublished - 2015

    Bibliographical note

    This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

    Keywords

    • Biological sciences
    • Genetics

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