Abstract
Long-read sequencing improves sensitivity to discover variation in complex repetitive regions, assign parent-of-origin, and distinguish germline from postzygotic mutations. We applied Illumina, Oxford Nanopore Technologies, and PacBio sequencing to discover and validate de novo mutations in 73 children from 42 autism families (157 individuals). We assay 2.77 Gbp of the human genome, yielding on average 95 de novo mutations per transmission (87.5 single-nucleotide substitutions, 7.8 indels), with no significant difference in mutation rate or profile between probands and their unaffected siblings. Long reads increase de novo mutation discovery by 20-40% and double the mutations classified as early embryonic. The germline mutation rate is 1.30×10−8 substitutions/base pair/generation; the postzygotic rate is 0.23×10−8. These rates are significantly increased in repetitive DNA, where segmental duplication mutability is dependent on length and percent identity. Here, we show that enrichment in repeats occurs predominantly postzygotically, likely resulting from faulty DNA repair and interlocus gene conversion.
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Data availability
The data used for analysis, including underlying sequence data, assemblies, and alignment files, are available to approved researchers in the SFARI Base under the accession number SFARI_DS0000104 (https://base.sfari.org/dataset/DS0000104) and through the National Institute of Mental Health Data Archive (NDA) under Collection ID 3780. Source data are provided with this paper.
Code availability
Code and scripts used for the analyses presented in this manuscript are available in GitHub at https://github.com/mdnoyes/denovo_calling69. Any additional information required to reanalyze the data reported in this work paper is available from the lead contact upon request.
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Acknowledgements
This work was supported, in part, by the US National Institutes of Health (NIH R01MH101221 to E.E.E.) and the Simons Foundation (SFARI #810018EE to E.E.E.). E.E.E. is an investigator of the Howard Hughes Medical Institute. We thank Tonia Brown for assistance in editing this manuscript. This article is subject to HHMI’s Open Access to Publications policy. HHMI lab heads have previously granted a nonexclusive CC BY 4.0 license to the public and a sublicensable license to HHMI in their research articles. Pursuant to those licenses, the author-accepted manuscript of this article can be made freely available under a CC BY 4.0 license immediately upon publication.
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E.E.E. and M.D.N. conceptualized the study. K.M.M., K.H., J. Kordosky, G.H.G., J. Knuth, and A.P.L. generated the data. Y.S., Y.K., I.W., and N.K. performed data quality control. M.D.N. and Y.S. conducted the formal analysis. M.D.N. created the visualizations. M.D.N. developed the methodology. M.D.N. wrote the original draft. M.D.N., Y.S., and E.E.E. reviewed and edited the manuscript. E.E.E. supervised the study.
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E.E.E. is a scientific advisory board (SAB) member of Variant Bio, Inc. All other authors declare no competing interests.
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Noyes, M.D., Sui, Y., Kwon, Y. et al. Long-read sequencing of families reveals increased germline and postzygotic mutation rates in repetitive DNA. Nat Commun (2026). https://doi.org/10.1038/s41467-026-70342-1
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DOI: https://doi.org/10.1038/s41467-026-70342-1
