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 Xu; Jihua  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

doi:10.1038/ncomms6969

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 language	English
Article number	5969
Journal	Nature Communications
Volume	6
Number of pages	9
ISSN	2041-1723
DOIs	https://doi.org/10.1038/ncomms6969
Publication status	Published - 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

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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Besenbacher, S., Liu, S., Gonzalez-Izarzugaza, J. M., Grove, J., Belling, K. C., Bork-Jensen, J., Huang, S., Dam-Als, T., Li, S., Yadav, R., Yadav, R., Rubio García, A., Lescai, F., Demontis, D., Rao, J., Ye, W., Mailund, T., Friborg, R. M., Pedersen, C. N. S., ... Rasmussen, S. (2015). Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios. Nature Communications, 6, Article 5969. https://doi.org/10.1038/ncomms6969

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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.",

keywords = "Biological sciences, Genetics",

author = "S{\o}ren Besenbacher and Siyang Liu and Gonzalez-Izarzugaza, {Jose Maria} and Jakob Grove and Belling, {Kirstine C.} and Jette Bork-Jensen and Shujia Huang and Thomas Dam-Als and Shengting Li and Rachita Yadav and Rachita Yadav and {Rubio Garc{\'i}a}, Arcadio and Francesco Lescai and Ditte Demontis and Junhua Rao and Weijian Ye and Thomas Mailund and Friborg, {Rune M.} and Pedersen, {Christian N. S.} and Ruiqi Xu and Jihua Sun and Hao Liu and Ou Wang and Xiaofang Cheng and {Flores Santa Cruz}, David and Rydza, {Emil Karol} and Kristoffer Rapacki and S{\o}rensen, {John Damm} and Chmura, {Piotr Jaroslaw} and David Westergaard and Piotr Dworzynski and S{\o}rensen, {Thorkild I. A.} and Ole Lund and Torben Hansen and Xun Xu and Ning Li and Lars Bolund and Oluf Pedersen and Hans Eiberg and Anders Krogh and B{\o}rglum, {Anders D.} and S{\o}ren Brunak and Karsten Kristiansen and Schierup, {Mikkel H} and Wang Jun and Ramneek Gupta and Palle Villesen and Simon Rasmussen",

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{\textquoteright}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/",

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doi = "10.1038/ncomms6969",

language = "English",

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journal = "Nature Communications",

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Besenbacher, S, Liu, S, Gonzalez-Izarzugaza, JM, Grove, J, Belling, KC, Bork-Jensen, J, Huang, S, Dam-Als, T, Li, S, Yadav, R, Yadav, R, Rubio García, A, Lescai, F, Demontis, D, Rao, J, Ye, W, Mailund, T, Friborg, RM, Pedersen, CNS, Xu, R, Sun, J, Liu, H, Wang, O, Cheng, X, Flores Santa Cruz, D, Rydza, EK, Rapacki, K, Sørensen, JD, Chmura, PJ, Westergaard, D, Dworzynski, P, Sørensen, TIA, Lund, O, Hansen, T, Xu, X, Li, N, Bolund, L, Pedersen, O, Eiberg, H, Krogh, A, Børglum, AD, Brunak, S, Kristiansen, K, Schierup, MH, Jun, W, Gupta, R, Villesen, P & Rasmussen, S 2015, 'Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios', Nature Communications, vol. 6, 5969. https://doi.org/10.1038/ncomms6969

TY - JOUR

T1 - Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios

AU - Besenbacher, Søren

AU - Liu, Siyang

AU - Gonzalez-Izarzugaza, Jose Maria

AU - Grove, Jakob

AU - Belling, Kirstine C.

AU - Bork-Jensen, Jette

AU - Huang, Shujia

AU - Dam-Als, Thomas

AU - Li, Shengting

AU - Yadav, Rachita

AU - Rubio García, Arcadio

AU - Lescai, Francesco

AU - Demontis, Ditte

AU - Rao, Junhua

AU - Ye, Weijian

AU - Mailund, Thomas

AU - Friborg, Rune M.

AU - Pedersen, Christian N. S.

AU - Xu, Ruiqi

AU - Sun, Jihua

AU - Liu, Hao

AU - Wang, Ou

AU - Cheng, Xiaofang

AU - Flores Santa Cruz, David

AU - Rydza, Emil Karol

AU - Rapacki, Kristoffer

AU - Sørensen, John Damm

AU - Chmura, Piotr Jaroslaw

AU - Westergaard, David

AU - Dworzynski, Piotr

AU - Sørensen, Thorkild I. A.

AU - Lund, Ole

AU - Hansen, Torben

AU - Xu, Xun

AU - Li, Ning

AU - Bolund, Lars

AU - Pedersen, Oluf

AU - Eiberg, Hans

AU - Krogh, Anders

AU - Børglum, Anders D.

AU - Brunak, Søren

AU - Kristiansen, Karsten

AU - Schierup, Mikkel H

AU - Jun, Wang

AU - Gupta, Ramneek

AU - Villesen, Palle

AU - Rasmussen, Simon

N1 - 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/

PY - 2015

Y1 - 2015

N2 - 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.

AB - 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.

KW - Biological sciences

KW - Genetics

U2 - 10.1038/ncomms6969

DO - 10.1038/ncomms6969

M3 - Journal article

C2 - 25597990

SN - 2041-1723

VL - 6

JO - Nature Communications

JF - Nature Communications

M1 - 5969

ER -

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

Abstract

Bibliographical note

Keywords

UN SDGs

Access to Document

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