27 August 2012. As a man ages, the chance that his children will carry new, spontaneously occurring mutations grows, according to a study published 23 August in Nature. Led by Kari Stefansson of deCODE Genetics in Reykjavik, Iceland, the study sequenced the entire genomes of 78 families consisting mainly of unaffected parents and their children with autism or schizophrenia. The study identified an average of 63 single-nucleotide changes per person that were not inherited from their parents, but arose “de novo,” likely in parental sperm or egg cells. More de novo mutations were found in people with older fathers than with younger fathers, with an effect size of about two mutations per year of a father’s age; a mother’s age did not have an influence.
The study offers an explanation for epidemiological studies that find older fathers are more likely to have children with schizophrenia (see SRF Current Hypothesis) or autism (Croen et al., 2007). Researchers suspect things go wrong at the level of sperm cells, which are made throughout a man’s life, unlike a woman’s egg cells. Each round of DNA replication prior to cell division could introduce copying errors. If these mutations accumulate in sperm cells with age, then the chances of disrupting a gene involved in either disorder would increase. In line with this idea of sperm as crucibles for mutation, a study published July 20 in Cell sequenced the genome within individual sperm cells from a single man, and found 25-36 point mutations in each cell (Wang et al., 2012).
Though previous studies reported a similar effect of a father’s age on de novo mutations in the protein-coding exome of people with autism (see SRF related news story), the extent to which the new findings explain the paternal age epidemiology is unclear. This will depend on how many schizophrenia or autism cases actually result from de novo mutations in the first place—though exome sequencing studies have reported an excess of de novo mutations in schizophrenia (see SRF related news story and SRF news story), these kinds of mutations turn up in healthy people, too. An alternative explanation for the epidemiology hinges on inherited mutations: fathers carrying disease-related mutations may show subclinical signs of schizophrenia, which could delay their married-with-kids stage of life. Last year, a study suggested that a father’s age at the birth of his first child—rather than the birth of the child who eventually develops schizophrenia—matters more (Petersen et al., 2011).
All in the family
First author Augustine Kong and colleagues sequenced the genomes of 44 people with autism, 21 with schizophrenia, 13 without a disorder, and both parents of each. Scanning the entire genome for nucleotide changes present in offspring but not in parents, the researchers identified 4,933 de novo mutations in total, with an average of 63 new mutations in each child in the family. With 2.63 billion base pairs effectively scanned, the researchers pegged the de novo mutation rate at 1.2 x 10-8 per nucleotide per generation, in line with other studies. Though this rate relies largely on data from autism and schizophrenia samples, it may not differ in healthy people.
For five of these families, three generations' worth of data were available because the offspring had children themselves. This allowed the researchers to trace which chromosome—mother’s or father’s—harbored the de novo mutation, thus clarifying where the trouble began. Identifying the de novo mutations that were then inherited by the third generation, the researchers looked for maternal or paternal markers nearby that originated from the first generation. This analysis pointed to the fathers, who contributed an average of 55 mutations to their child, whereas mothers added only 14. The number was substantially more variable in fathers than in mothers, too, leading the researchers to examine age as a factor in this variability.
The father effect
Considering the 4,933 de novo mutations from all the families, the researchers found that the number of mutations increased nearly linearly as the father’s age increased (p = 3.6 x 10-19). For example, children born when their dads were 20 years old carried around 40 mutations, whereas those born when their dads were 40 years old carried about 80. The father’s age could explain up to 97 percent of the variance in de novo mutation number, which seems to limit contributions by other factors, including the mother’s age. Though the mother’s age correlates with the father’s age (r = 0.83), removing the effect of the mother did not change the relationship between the father’s age and de novo mutations. This suggests the mother’s age matters less for point mutations, and more for larger genetic glitches like the extra chromosome found in Down’s syndrome.
The researchers noted some de novo mutations in interesting places. Seventy-three landed in protein-coding parts of genes, and, of interest to schizophrenia, one person with schizophrenia carried a protein-truncating mutation in neurexin. Neurexin is thought to help wire synapses together (see SRF related news story), and several studies have found small deletions within the gene in people with schizophrenia, autism, and other psychiatric disorders (Schaaf et al., 2012; see SRF related news story).
The authors suggest that the influence of a father’s age is so profound that it might not make sense to talk about a stable mutation rate across the genome, but instead to consider it a time-dependent variable. This malleability highlights how societal factors, like shifts in the age when people first become parents, can shape the genome, but whether this influences risk for schizophrenia or autism remains an interesting question.—Michele Solis.
Kong A, Frigge ML, Masson G, Besenbacher S, Sulem P, Magnusson G, Gudjonsson SA, Sigurdsson A, Jonasdottir A, Jonasdottir A, Wong WS, Sigurdsson G, Walters GB, Steinberg S, Helgason H, Thorleifsson G, Gudbjartsson DF, Helgason A, Magnusson OT, Thorsteinsdottir U, Stefansson K. Rate of de novo mutations and the importance of father's age to disease risk. Nature. 2012 Aug 22; 488: 471-475. Abstract