Overlooked roles of DNA damage and maternal age in generating human germline mutations

Abstract

The textbook view that most germline mutations in mammals arise from replication errors is indirectly supported by the fact that there are both more mutations and more cell divisions in the male than in the female germline. When analyzing large de novo mutation datasets in humans, we find multiple lines of evidence that call that view into question. Notably, despite the drastic increase in the ratio of male to female germ cell divisions after the onset of spermatogenesis, even young fathers contribute three times more mutations than young mothers, and this ratio barely increases with parental age. This surprising finding points to a substantial contribution of damage-induced mutations. Indeed, C-to-G transversions and CpG transitions, which together constitute over one-fourth of all base substitution mutations, show genomic distributions and sex-specific age dependencies indicative of double-strand break repair and methylation-associated damage, respectively. Moreover, we find evidence that maternal age at conception influences the mutation rate both because of the accumulation of damage in oocytes and potentially through an influence on the number of postzygotic mutations in the embryo. These findings reveal underappreciated roles of DNA damage and maternal age in the genesis of human germline mutations.

Keywords: DNA damage and repair; DNA replication; germline mutation; male mutation bias; maternal age effect.

Fig. 1.

The fraction of paternal mutations among phased mutations, as a function of paternal age at conception. Each point represents the data for one child (proband) with similar parental ages (paternal-to-maternal age ratio between 0.9 and 1.1; 719 trios in total with a minimum of 6 and an average of 23.5 phased mutations per trio). The x-axis position, but not the y-axis position, is slightly jittered to show overlapping points. The blue line is the predicted fraction of paternal mutations by binomial regression with logit link, with the shaded area representing the 95% confidence interval (calculated with the “predict” function in R).

Fig. 2.

Inferred sex and age dependencies of germline mutations (based on a linear model applied to trios with maternal age no greater than 40 y). In all panels, shaded areas and bars represent 95% CIs of the corresponding quantities obtained from bootstrapping. (A) Inferred sex-specific mutation rates as a function of parental ages. Parental ages are measured since birth, that is, birth corresponds to age 0 (throughout the paper). The extrapolated intercepts at age 0 are small but significantly positive for both sexes, implying a weak but significant effect of reproductive age on yearly mutation rates (16). (B) Predicted male-to-female mutation ratio (α) as a function of the ratio of paternal to maternal ages. For reference, the ratio of parental ages is centered around 1.10 in the deCODE DNM dataset (SD = 0.20). (C) Contrast between male-to-female mutation ratio (purple) and the ratio of male to female cell divisions (green), assuming the same paternal and maternal ages. Estimates of the cell division numbers for the two sexes in humans are from Drost and Lee (11).

Fig. 3.

Distinctive sex and age dependencies for C > G and CpG > TpG DNMs. The shaded areas in all panels represent 95% CIs. See SI Appendix, Fig. S6 for similar plots for other mutation types. The male-to-female mutation ratio at age 17 is significantly lower for CpG > TpG than for other mutation types (discussed in the main text). (A) Fraction of paternal mutations in phased DNMs (similar to Fig. 1). (B) Predicted male-to-female mutation ratio (α). (C) Predicted parental age effects.

Fig. 4.

Maternal age effect on mutations that occur on paternally inherited chromosomes. (A) An illustration of mutations occurring during development and gametogenesis. Adapted from ref. . Filled stars represent mutations that arise in the parents and hollow stars mutations in the child. The standard trio approach requires allelic balance in the child and no or few reads carrying the alternative allele in the parent, leading to inclusion of some early postzygotic mutations in the child (brown open) and exclusion of a fraction of early mutations in the parents (brown filled). (B) An illustration of a potential maternal age effect on the number of postzygotic mutations. The shade of the oocyte represents its cellular quality, with a darker color indicating a worse condition of the replication or repair machinery. (C) Pairwise comparison conditional on the same paternal age. Each point represents a pair of trios, with the x axis showing the difference in maternal ages and the y axis the difference in paternal mutation counts (Left; older mother – younger mother) or maternal mutation counts (Right; older mother – younger mother); point position is slightly jittered to show overlapping points. P values are evaluated by 10,000 permutations, using Kendall’s rank correlation test statistic (Materials and Methods). (D) Pairwise comparison conditional on the same maternal age, similar to C. The ranges of y axis differ for the plots on the left and right for visualization purposes.