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Genome-wide patterns and properties of de novo mutations in humans

Abstract

Mutations create variation in the population, fuel evolution and cause genetic diseases. Current knowledge about de novo mutations is incomplete and mostly indirect1,2,3,4,5,6,7,8,9,10. Here we analyze 11,020 de novo mutations from the whole genomes of 250 families. We show that de novo mutations in the offspring of older fathers are not only more numerous11,12,13 but also occur more frequently in early-replicating, genic regions. Functional regions exhibit higher mutation rates due to CpG dinucleotides and show signatures of transcription-coupled repair, whereas mutation clusters with a unique signature point to a new mutational mechanism. Mutation and recombination rates independently associate with nucleotide diversity, and regional variation in human-chimpanzee divergence is only partly explained by heterogeneity in mutation rate. Finally, we provide a genome-wide mutation rate map for medical and population genetics applications. Our results provide new insights and refine long-standing hypotheses about human mutagenesis.

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Figure 1: Mutations in the offspring of younger fathers are biased toward later-replicating regions.
Figure 2: The offspring of older fathers harbor a higher percentage of de novo mutations in genes.
Figure 3: Mutation clusters exhibit a unique mutational spectrum.
Figure 4: Influence of mutation and recombination rates on human-chimpanzee divergence.

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Acknowledgements

We thank D. Gordenin for very helpful comments. The Genome of the Netherlands (GoNL) Project is funded by the Biobanking and Biomolecular Research Infrastructure (BBMRI-NL), which is financed by the Netherlands Organization for Scientific Research (NWO project 184.021.007). S.R.S., P.P.P. and S.C. are funded by US National Institutes of Health grants 1 R01 MH101244 and 1 R01 GM078598.

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Contributions

S.R.S. and P.I.W.d.B. planned and directed the research. L.C.F. called and filtered the mutations. W.P.K. and I.R. validated candidate mutations. L.C.F. designed and executed the simulations. A.K., L.C.F. and A.M. performed replication timing analyses. P.P.P., L.C.F. and A.M. analyzed factors influencing regional mutation rates and spectra. L.C.F. and P.P.P. analyzed mutation clusters. P.P.P. and P.F.A. computed the comparative genomics model and compared it against observed mutation rates. S.C. and P.P.P. created the mutation rate map. L.C.F., P.P.P., A.K., P.I.W.d.B. and S.R.S. wrote the manuscript. A.M., S.C., C.M.v.D., M.S., C.W., G.v.O., P.E.S., D.I.B., K.Y., V.G., P.F.A. and W.P.K. provided critical feedback on the manuscript.

Corresponding authors

Correspondence to Paul I W de Bakker or Shamil R Sunyaev.

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The authors declare no competing financial interests.

Additional information

A full list of members and affiliations appears in the Supplementary Note.

Integrated supplementary information

Supplementary Figure 1 Association of paternal age of de novo mutation location with epigenetic variables.

Using a linear regression model, we tested the association of seven epigenetic variables (DNA replication timing, expression levels, recombination rates, and the H3K27ac, H3K4me1 and H3K4me3 histone modifications), while correcting for GC content, CpG status and sequence coverage. Here we plot the significance of the associations we found with the different epigenetic variables along with the significance threshold level after Bonferroni correction for the six tests we performed (gray dashed line).

Supplementary Figure 2 Separation of replication timing profiles between the offspring of younger and older fathers.

We separated our de novo mutation data in two groups based on paternal age. To select a threshold that maximizes the difference in the groups, we considered every integer age in our study as a possible threshold and applied a Kolmogorov-Smirnoff test to compare the distribution of replication timing of de novo mutations between the groups. This plot shows the P values obtained for each of the 27 tests as well as the significance threshold after Bonferroni correction (gray dashed line).

Supplementary Figure 3 Paternal age effect on de novo mutation replication timing measured in six cell types.

The distribution of replication timing around de novo mutations in the offspring of younger fathers (orange curves; <28 years old), older fathers (blue curves; ≥28 years old) and simulations (gray areas; 200 simulation sets of 11,020 mutations) in 3 cell types from 4 cell lines41: embryonic stem cells (BG01 ESC, H7 ESC), induced pluripotent stem cells (iPS4) and neural precursor cells (BG01 NPC).

Supplementary Figure 4 Paternal and maternal age effect estimates on replication timing based on de novo mutations with known parental origin.

All effect estimates were computed using a linear regression model. The red line represents the effect estimate from the 630 maternal mutations. The black curve shows the effect estimate for 10,000 samplings of 630 paternal mutations out of the 1,991 available. The effect estimate is significantly larger for paternal mutations (P = 0.0019) when considering the same number of mutations.

Supplementary Figure 5 Power to detect non-CpG mutation depletion in regulatory regions marked by DNase I–hypersensitive sites (DHSs).

The graph shows the power to detect non-CpG mutation depletion in regulatory regions marked by DNase I–hypersensitive sites (DHSs) using the 9,048 non-CpG observed de novo mutations in our data and 177,347 uniformly simulated mutations. The y axis illustrates the power for detecting an effect at the 0.05 significance level using a χ2 test for different effect sizes (here expressed as the relative depletion of mutations in DHSs when compared to other regions).

Supplementary Figure 6 Comparison of nucleotide context–specific mutation rates based on comparative genomics and observed de novo mutations.

Each point represents one of the 96 substitutions in a specific trinucleotide context. The black line shows the best fit (r2 = 0.993). The rate of transition mutations is 2.15 times greater than the transversion rate (Ti/Tv ratio). The highest mutation rates are observed for cytosine bases in a CpG context.

Supplementary Figure 7 Mutational spectrum in transcribed regions.

The proportion of de novo mutations of each substitution type in transcribed regions classified based on their corresponding strand (transcribed or non-transcribed). There is a strong asymmetry of mutations between the two strands, with significantly elevated A>G substitutions on the transcribed strand, consistent with the action of transcription-coupled nucleotide excision repair.

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Supplementary Figures 1–7, Supplementary Tables 1–4 and Supplementary Note. (PDF 1185 kb)

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Francioli, L., Polak, P., Koren, A. et al. Genome-wide patterns and properties of de novo mutations in humans. Nat Genet 47, 822–826 (2015). https://doi.org/10.1038/ng.3292

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