Estimating the genome-wide mutation rate from thousands of unrelated individuals

We provide a method for estimating the genome-wide mutation rate from sequence data on unrelated individuals by using segments of identity by descent (IBD). The length of an IBD segment indicates the time to shared ancestor of the segment, and mutations that have occurred since the shared ancestor result in discordances between the two IBD haplotypes. Previous methods for IBD-based estimation of mutation rate have required the use of family data for accurate phasing of the genotypes. This has limited the scope of application of IBD-based mutation rate estimation. Here, we develop an IBD-based method for mutation rate estimation from population data, and we apply it to whole-genome sequence data on 4,166 European American individuals from the TOPMed Framingham Heart Study, 2,996 European American individuals from the TOPMed My Life, Our Future study, and 1,586 African American individuals from the TOPMed Hypertension Genetic Epidemiology Network study. Although mutation rates may differ between populations as a result of genetic factors, demographic factors such as average parental age, and environmental exposures, our results are consistent with equal genome-wide average mutation rates across these three populations. Our overall estimate of the average genome-wide mutation rate per 108 base pairs per generation for single-nucleotide variants is 1.24 (95% CI 1.18-1.33).