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.

Visualizing the origins of selfish de novo mutations in individual seminiferous tubules of human testes

“…Importantly, clonal growth occurs one-dimensionally, along the highly convoluted tubules (40), reminiscent of normal spermatogonial clonal dynamics in the murine testis (41,42) and consistent with a previous experimental study (43). The lower bounds of the length of mutant clones found in the proof-of-principle study (4.4-15.3 mm), correspond to 1-4 × 10 −5 of the estimated total length (350-400 m) of seminiferous tubules in a human testis (44), similar to figures for mutation prevalence previously attributed to selfish spermatogonial selection (10), but much higher than the background germline mutation rate (5,6). The majority of the mutations were present in the heterozygous state (taking into account dilution by nonmutant cells including Sertoli and extratubular cells); we propose that these mutations are necessary and sufficient to drive the clonal growth observed.…”

“…Recent whole genome sequencing studies of parent-child trios show that most mutations (such as nucleotide substitutions) originate from the paternal germline and increase in frequency with the father's age (5,6), an issue of particular significance given the demographic shift to delayed reproduction in many populations (7). The deduction that the testes of older men harbor a greater burden of mutations, compared with younger men, is consistent with indirect measures of genetic decline, ranging from high indices of arrested germ cell divisions to complete involution of the seminiferous tubules (7)(8)(9).…”

Characteristics of de novo structural changes in the human genome

“…Previous estimates of the human indel mutation rate range from 0.53 to 1.5 × 10 −9 per base per generation (Kondrashov 2003;Lynch 2010;Campbell and Eichler 2013;Ramu et al 2013;Besenbacher et al 2015). The mutation rate for copy number variants was estimated to be 0.03 for CNVs larger than 500 bp ) and 0.012 for CNVs larger than 100 kbp (Itsara et al 2010) per haploid genome.…”

“…Whereas interspecies comparisons provide us with insight into long-range processes such as genetic drift and selection, the information derived from direct measurements of the de novo mutation spectrum and rates across generations is crucial for understanding mechanisms of mutation formation and inter-individual differences (Scally and Durbin 2012). While several projects have started to investigate the rates and characteristics of de novo SNVs (Kong et al 2012;Michaelson et al 2012;Francioli et al 2014;Besenbacher et al 2015), those of de novo short insertions and deletions (indels) and large structural variants (SVs) have been much less studied (Campbell and Eichler 2013).…”

Comprehensive variation discovery and recovery of missing sequence in the pig genome using multiple de novo assemblies

“…Nonetheless, resequencing is limiting in terms of capturing genetic variation and assessing gaps and misassigned regions of the reference genome (Weisenfeld et al 2014). In contrast, multiple de novo assemblies of pig genomes from different regions and breeds promise a more accurate and comprehensive understanding of genetic variation within this species (Besenbacher et al 2015;Chaisson et al 2015b). Among populations of plants (coccolithophores [Read et al 2013], Arabidopsis thaliana [Gan et al 2011], soybean , and rice ), animals (mosquitoes [Neafsey et al 2015] and macaques [Yan et al 2011]), and even modern humans (Li et al 2010a), a surprisingly large amount of variation has been uncovered by de novo assemblies.…”