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

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.

SUBMITTER: Besenbacher S 

PROVIDER: S-EPMC4309431 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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

Besenbacher Søren S   Liu Siyang S   Izarzugaza José M G JM   Grove Jakob J   Belling Kirstine K   Bork-Jensen Jette J   Huang Shujia S   Als Thomas D TD   Li Shengting S   Yadav Rachita R   Rubio-García Arcadio A   Lescai Francesco F   Demontis Ditte D   Rao Junhua J   Ye Weijian W   Mailund Thomas T   Friborg Rune M RM   Pedersen Christian N S CN   Xu Ruiqi R   Sun Jihua J   Liu Hao H   Wang Ou O   Cheng Xiaofang X   Flores David D   Rydza Emil E   Rapacki Kristoffer K   Damm Sørensen John J   Chmura Piotr P   Westergaard David D   Dworzynski Piotr P   Sørensen Thorkild I A TI   Lund Ole O   Hansen Torben T   Xu Xun X   Li Ning N   Bolund Lars L   Pedersen Oluf O   Eiberg Hans H   Krogh Anders A   Børglum Anders D AD   Brunak Søren S   Kristiansen Karsten K   Schierup Mikkel H MH   Wang Jun J   Gupta Ramneek R   Villesen Palle P   Rasmussen Simon S  

Nature communications 20150119

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  ...[more]

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