Parental germline mosaicism in genome-wide phased de novo variants: Recurrence risk assessment and implications for precision genetic counselling
François Lecoquierre, Nathalie Drouot, Sophie Coutant, Olivier Quenez, Steeve Fourneaux, Fanny Jumeau, Nathalie Rives, Françoise Charbonnier, Céline Derambure, Anne Boland, Robert Olaso, Vincent Meyer, Jean-François Deleuze, Alice Goldenberg, Anne-Marie Guerrot, Camille Charbonnier, Gaël Nicolas
Abstract
De novo mutations (DNMs) have a significant impact on human health, notably through their contribution to developmental disorders. DNMs occur in both paternal and maternal germlines via diverse mechanisms, including parental early embryonic mosaicism, at high recurrence risk for subsequent pregnancies through germline mosaicism. This phenomenon has been studied mostly on isolated pathogenic variants, but its contribution to genome-wide phased variants in individual genomes is underexplored. We aimed to categorize DNMs and their recurrence risk by detecting and phasing a large set of DNMs via short- and long-read genome sequencing followed by systematic deep sequencing of parental blood and sperm DNA.
Introduction
De novo mutations are defined as variants in an individual that are absent from their parents’ genomes, reflecting the germline’s mutability. While all types of variants may occur de novo, sequence variants including single nucleotide variants (SNVs) and small insertions deletions (indels) are both common in our genomes, in the range of 60–80 per individual [1,2] and have high impact on health. Indeed, while de novo SNVs and indels (thereafter referred to as de novo mutations, DNM) are a natural and evolutionary constrained phenomenon [3], they represent a major source of genetic diseases [4].
Materials and method
Ethics statement
This study was approved by the Comité de Protection des Personnes Ouest V (CPP) ethics committee, reference 20/043-2. Informed written consent was obtained from all participants or their legal guardians. The GERMETHEQUE biobank (BB-0033–00081), site of Rouen, provided 5 samples of spermatozoa and their associated data for this project. GERMETHEQUE obtained consent from each patient to use their sperm samples (CPP 2.15.27). The GERMETHEQUE steering committee approved the study design on 17/11/2020. The Biobank has the declaration DC-2021–4820 and the authorization AC-2019–3487. The number of requests made to Germethèque is 20201117.
Results
Establishment of a set of high-quality phased de novo mutations
We used short-read genome sequencing to call a set of 428 high-confidence DNMs in five families (S2 Table), ranging from 56 to 119 per individual, with a mean of 77 SNVs and 9 indels (Fig 1). Targeted sequencing of smMIP (single molecule molecular inversion probes) libraries on 349 variations accessible to a MIP design was primarily performed to detect mosaic events, but also served as an independent estimation of precision of de novo variant calling. SmMIP sequencing revealed a very low false positive rate, with only 1 variant that appeared to be inherited and 348 true de novo variants.
Discussion
Embryonic mosaicism is a common source of DNMs
To explore the timing of mutational events in the human germline, we used a three-step method to detect genome-wide DNMs, attribute a parental haplotype and assess parental blood and sperm mosaicism in five individuals. We found that parental embryonic mosaicism is a common source of DNMs that are detectable in every genome. Pre-PGC events (detected in blood) contributed to 3.90% of all DNMs analyzed (13/334) and appeared equally distributed on paternal and maternal haplotypes.
Acknowledgments
We thank the participants and their family members. This study was supported by the Germethèque Biobank (France – Site of Rouen), which provided samples. This work was conducted as part of the collaborative efforts between CEA‐DRF‐Jacob‐CNRGH and CHU de Rouen.
Citation: Lecoquierre F, Drouot N, Coutant S, Quenez O, Fourneaux S, Jumeau F, et al. (2025) Parental germline mosaicism in genome-wide phased de novo variants: Recurrence risk assessment and implications for precision genetic counselling. PLoS Genet 21(3): e1011651. https://doi.org/10.1371/journal.pgen.1011651
Editor: Kevin E. Glinton,, Baylor College of Medicine, UNITED STATES OF AMERICA
Received: October 29, 2024; Accepted: March 8, 2025; Published: March 31, 2025
Copyright:© 2025 Lecoquierre et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Data Copyright: Availability: All relevant data are in the manuscript and its supporting information qlecoquierre/de_novo_tools.
Funding: This study was funded by a grant from GIRCI Nord-Ouest (AAP-AE_19-36 to FL). This study was co-supported by the European Union and Région Normandie in the context of Recherche Innovation Normandie (RIN2018 to GN and FL). This work did benefit from support from the France Génomique National Infrastructure, funded as part of the “Investissements d'Avenir” program managed by the Agence Nationale pour la Recherche (contract ANR-10-INBS-09 to JFD). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
