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e-Article

De novo structural mutation rates and gamete-of-origin biases revealed through genome sequencing of 2,396 families
Document Type
article
Source
American Journal of Human Genetics. 108(4)
Subject
Genetics
Biotechnology
Human Genome
Pediatric
Contraception/Reproduction
Brain Disorders
Intellectual and Developmental Disabilities (IDD)
2.1 Biological and endogenous factors
Aetiology
Aging
Autistic Disorder
Bias
DNA Copy Number Variations
DNA Mutational Analysis
Family
Female
Genome
Human
Germ Cells
Germ-Line Mutation
Humans
Male
Mutation Rate
Paternal Age
Point Mutation
autism
copy number variation
de novo mutation
genetic diversity
genomic structure
genomics
germline mutation
structural variation
Biological Sciences
Medical and Health Sciences
Genetics & Heredity
Language
Abstract
Each human genome includes de novo mutations that arose during gametogenesis. While these germline mutations represent a fundamental source of new genetic diversity, they can also create deleterious alleles that impact fitness. Whereas the rate and patterns of point mutations in the human germline are now well understood, far less is known about the frequency and features that impact de novo structural variants (dnSVs). We report a family-based study of germline mutations among 9,599 human genomes from 33 multigenerational CEPH-Utah families and 2,384 families from the Simons Foundation Autism Research Initiative. We find that de novo structural mutations detected by alignment-based, short-read WGS occur at an overall rate of at least 0.160 events per genome in unaffected individuals, and we observe a significantly higher rate (0.206 per genome) in ASD-affected individuals. In both probands and unaffected samples, nearly 73% of de novo structural mutations arose in paternal gametes, and we predict most de novo structural mutations to be caused by mutational mechanisms that do not require sequence homology. After multiple testing correction, we did not observe a statistically significant correlation between parental age and the rate of de novo structural variation in offspring. These results highlight that a spectrum of mutational mechanisms contribute to germline structural mutations and that these mechanisms most likely have markedly different rates and selective pressures than those leading to point mutations.