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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.

journal_name

Nat Commun

journal_title

Nature communications

authors

Besenbacher S,Liu S,Izarzugaza JM,Grove J,Belling K,Bork-Jensen J,Huang S,Als TD,Li S,Yadav R,Rubio-García A,Lescai F,Demontis D,Rao J,Ye W,Mailund T,Friborg RM,Pedersen CN,Xu R,Sun J,Liu H,Wang O,Cheng X,Fl

doi

10.1038/ncomms6969

subject

Has Abstract

pub_date

2015-01-19 00:00:00

pages

5969

issn

2041-1723

pii

ncomms6969

journal_volume

6

pub_type

杂志文章

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