Properties and rates of germline mutations in humans

Abstract

All genetic variation arises via new mutations; therefore, determining the rate and biases for different classes of mutation is essential for understanding the genetics of human disease and evolution. Decades of mutation rate analyses have focused on a relatively small number of loci because of technical limitations. However, advances in sequencing technology have allowed for empirical assessments of genome-wide rates of mutation. Recent studies have shown that 76% of new mutations originate in the paternal lineage and provide unequivocal evidence for an increase in mutation with paternal age. Although most analyses have focused on single nucleotide variants (SNVs), studies have begun to provide insight into the mutation rate for other classes of variation, including copy number variants (CNVs), microsatellites, and mobile element insertions (MEIs). Here, we review the genome-wide analyses for the mutation rate of several types of variants and suggest areas for future research.

Keywords: de novo mutation; genome wide; germline mutation rate; paternal age; paternal bias.

Figure I. Methods to discover new mutations and estimate mutation rate

a) Sequence data from parent-offspring trios can be used to find mutations present in the child but not observed in either parent (red star). b) Fixed differences between closely related species can be identified and counted; red and green stars represent mutations occurring in the lineage leading to humans and orange and yellow stars represent mutations in the lineage leading to chimpanzees. This value, in combination with the estimated number of generations between the species, can be used to calculate mutation rate. A modification of this approach can be used within species if the coalescent time of haplotypes can be estimated[12]. c) Mutations in regions of autozygosity appear as heterozygous variants in long stretches of homozygous DNA[7, 120]. With known pedigree information, the MRCA of the autozygous haplotype can be identified and the mutation rate calculated[7].

Figure 1. Comparison of the frequency and scale of different forms of genetic variation

There is an inverse relationship between mutation size and frequency. Although SNVs occur more frequently, each mutation affects only a single base pair. In contrast, large mutations such as CNVs or chromosomal aneuploidy are rare, yet affect thousands to millions of base pairs, and even though these mutations are rare, they affect more base pairs per birth on average than SNVs. a) Average number of mutations of each type of variant per birth. b) Average number of mutated bases contributed by each type of variant per birth. (Y-axis is log₁₀ scaled in both panels).

Figure 2. Common mechanisms leading to biases in mutation

a) CpG dinucleotides are the sites of cytosine methylation and frequent mutation. 5-methyl-cytosine can be deaminated to thymine (red). This mutation can either be repaired by mismatch repair pathways (reviewed in [121]) or be replicated to yield a cytosine to thymine mutation. b) Indels can occur by polymerase slippage during replication if these events are not repaired by mismatch repair (reviewed in [121]), especially in regions of low complexity such as microsatellites. Replication slippage is shown (red) on the newly synthesized strand leading to an insertion. c) Regions flanked by highly identical SDs (black boxes) are prone to NAHR. Recombination between homologous chromosomes (blue and magenta) occurs in paralogous regions leading to duplication of genes ABC in one of the recombined chromosomes and deletion on the other. d) Replicated homologous chromosomes are shown in black and gray. Premature loss of cohesion between sister chromatids can lead to separation of chromatids in meiosis I (black) leading to cells with only one chromatid or three chromatids. Trisomy results after meiosis II when one gamete ends up with an extra chromatid (red).

Figure 3. Larger CNVs are more likely to be de novo

Size distributions of CNVs from over 15,000 children with developmental delay are plotted. Inherited CNVs are in black and de novo CNVs are in red with the number of CNVs on the left-hand y-axis. The proportion of CNVs that are de novo is plotted in blue with the de novo proportion on the right-hand y-axis. Reproduced from [82].

Figure 4. Relationship between paternal age and de novo mutations

Current fitted models are shown of the increase in SNV mutations with paternal age from whole-exome and whole-genome sequencing of parent-offspring trios. There is some difference between the studies in regards to the magnitude of this effect, but sample sizes were relatively low and more studies, especially with elderly fathers, are needed to achieve a more precise estimate. The paternal age is on the x-axis, the left-hand y-axis shows the number of mutations per genome per birth and the right-hand y-axis shows the number of mutations per exome per birth. Exome data from 189 trios yielded an increase of 0.04 exonic mutations per year of paternal age (dashed green line)[15]; the smaller number of mutations compared to the whole-genome studies is consistent with the smaller target (protein-coding exons). Whole-genome data from 78 trios yielded an increase of 2.01 mutations per year (blue)[6]. Whole-genome data from 10 families yielded an increase of 1.02 mutations per year (red)[8].