scholarly journals Large, three-generation human families reveal post-zygotic mosaicism and variability in germline mutation accumulation

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Thomas A Sasani ◽  
Brent S Pedersen ◽  
Ziyue Gao ◽  
Lisa Baird ◽  
Molly Przeworski ◽  
...  
Keyword(s):  
Germline Mutation ◽  
De Novo ◽  
Primordial Germ Cell ◽  
Mutation Accumulation ◽  
Sequencing Data ◽  
De Novo Mutations ◽  
Cell Specification ◽  
Mutational Spectra ◽  
Germ Cell Specification ◽  
Human Gametes

The number of de novo mutations (DNMs) found in an offspring's genome increases with both paternal and maternal age. But does the rate of mutation accumulation in human gametes differ across families? Using sequencing data from 33 large, three-generation CEPH families, we observed significant variability in parental age effects on DNM counts across families, ranging from 0.19 to 3.24 DNMs per year. Additionally, we found that ~3% of DNMs originated following primordial germ cell specification in a parent, and differed from non-mosaic germline DNMs in their mutational spectra. We also discovered that nearly 10% of candidate DNMs in the second generation were post-zygotic, and present in both somatic and germ cells; these gonosomal mutations occurred at equivalent frequencies on both parental haplotypes. Our results demonstrate that rates of germline mutation accumulation vary among families with similar ancestry, and confirm that post-zygotic mosaicism is a substantial source of human DNM.

scholarly journals Large, three-generation CEPH families reveal post-zygotic mosaicism and variability in germline mutation accumulation

2019 ◽  
Author(s):  
Thomas A. Sasani ◽  
Brent S. Pedersen ◽  
Ziyue Gao ◽  
Lisa Baird ◽  
Molly Przeworski ◽  
...  
Keyword(s):  
Germ Cell ◽  
Germline Mutation ◽  
De Novo ◽  
Primordial Germ Cell ◽  
Mutation Accumulation ◽  
De Novo Mutations ◽  
Cell Specification ◽  
Mutational Spectra ◽  
Germ Cell Specification ◽  
Data Files

AbstractThe number of de novo mutations (DNMs) found in an offspring’s genome is known to increase with both paternal and maternal age. But does the rate of mutation accumulation in parental gametes differ across families? To answer this question, we analyzed DNMs in 33 large, three-generation families collected in Utah by the Centre d’Etude du Polymorphisme Humain (CEPH) consortium. We observed significant variability in parental age effects on DNM counts across families, ranging from 0.24 to 3.33 additional DNMs per year. Using up to 14 grandchildren in these families, we find that 3% of DNMs originated following primordial germ cell specification (PGCS) in a parent, and differ from non-mosaic germline DNMs in their mutational spectra. We also identify a median of 3 gonosomal mutations per sample in the F1 generation, which, along with post-PGCS DNMs, occur at equivalent frequencies on the paternal and maternal haplotypes. These results demonstrate that the rate of germline mutation accumulation varies among families with similar ancestry, and confirm that parental mosaicism is a substantial source of de novo mutations in children.Data and code availabilityCode used for statistical analysis and figure generation has been deposited on GitHub as a collection of annotated Jupyter Notebooks: https://github.com/quinlan-lab/ceph-dnm-manuscript. Data files containing germline de novo mutations, as well as the gonosomal and post-primordial germ cell specification (PGCS) mosaic mutations, are included with these Notebooks. To mitigate compatibility/version issues, we have also made all notebooks available in a Binder environment, accessible at the above GitHub repository.

scholarly journals Not All H3K4 Methylations Are Created Equal: Mll2/COMPASS Dependency in Primordial Germ Cell Specification

2017 ◽  
Vol 65 (3) ◽  
pp. 460-475.e6 ◽  
Author(s):  
Deqing Hu ◽  
Xin Gao ◽  
Kaixiang Cao ◽  
Marc A. Morgan ◽  
Gloria Mas ◽  
...  
Keyword(s):  
Germ Cell ◽  
Primordial Germ Cell ◽  
Cell Specification ◽  
Germ Cell Specification

scholarly journals Spontaneous rate of clonal mutations in Daphnia galeata

2020 ◽  
Author(s):  
Markus Pfenninger ◽  
Halina Binde Doria ◽  
Jana Nickel ◽  
Anne Thielsch ◽  
Klaus Schwenk ◽  
...  
Keyword(s):  
Mutation Rate ◽  
De Novo ◽  
Mutation Accumulation ◽  
Parental Genotype ◽  
De Novo Mutations ◽  
Daphnia Galeata ◽  
Short Term ◽  
Heritable Variation ◽  
Nucleotide Mutation ◽  
Ultimate Source

AbstractMutations are the ultimate source of heritable variation and therefore the fuel for evolution, but direct estimates exist only for few species. We estimated the spontaneous nucleotide mutation rate among clonal generations in the waterflea Daphnia galeata with a short term mutation accumulation approach. Individuals from eighteen mutation accumulation lines over five generations were deep genome sequenced to count de novo mutations that were not present in a pool of F1 individuals, representing the parental genotype. We identified 12 new nucleotide mutations in 90 clonal generational passages. This resulted in an estimated haploid mutation rate of 0.745 x 10-9 (95% c.f. 0.39 x 10-9 − 1.26 x 10-9), which is slightly lower than recent estimates for other Daphnia species. We discuss the implications for the population genetics of Cladocerans.

scholarly journals Trio deep-sequencing does not reveal unexpected off-target and on-target mutations in Cas9-edited rhesus monkeys

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Xin Luo ◽  
Yaoxi He ◽  
Chao Zhang ◽  
Xiechao He ◽  
Lanzhen Yan ◽  
...  
Keyword(s):  
Rhesus Monkeys ◽  
De Novo ◽  
Preclinical Model ◽  
Structural Variants ◽  
Sequencing Data ◽  
De Novo Mutations ◽  
Target Region ◽  
Long Read ◽  
Target Effect

AbstractCRISPR-Cas9 is a widely-used genome editing tool, but its off-target effect and on-target complex mutations remain a concern, especially in view of future clinical applications. Non-human primates (NHPs) share close genetic and physiological similarities with humans, making them an ideal preclinical model for developing Cas9-based therapies. However, to our knowledge no comprehensive in vivo off-target and on-target assessment has been conducted in NHPs. Here, we perform whole genome trio sequencing of Cas9-treated rhesus monkeys. We only find a small number of de novo mutations that can be explained by expected spontaneous mutations, and no unexpected off-target mutations (OTMs) were detected. Furthermore, the long-read sequencing data does not detect large structural variants in the target region.

Sall4 Is Essential for Mouse Primordial Germ Cell Specification by Suppressing Somatic Cell Program Genes

Stem Cells ◽  
2014 ◽  
Vol 33 (1) ◽  
pp. 289-300 ◽  
Author(s):  
Yasuka L. Yamaguchi ◽  
Satomi S. Tanaka ◽  
Maho Kumagai ◽  
Yuka Fujimoto ◽  
Takeshi Terabayashi ◽  
...  
Keyword(s):  
Germ Cell ◽  
Somatic Cell ◽  
Primordial Germ Cell ◽  
Cell Specification ◽  
Germ Cell Specification ◽  
Mouse Primordial Germ Cell

scholarly journals Selection bias in mutation accumulation

2021 ◽  
Author(s):  
Lindi M Wahl ◽  
Deepa Agashe
Keyword(s):  
Positive Selection ◽  
Negative Selection ◽  
De Novo ◽  
Mutation Accumulation ◽  
Microbial Populations ◽  
Single Individual ◽  
Deleterious Mutations ◽  
De Novo Mutations ◽  
Fitness Effects ◽  
Wide Range

Mutation accumulation (MA) experiments, in which de novo mutations are sampled and subsequently characterized, are an essential tool in understanding the processes underlying evolution. In microbial populations, MA protocols typically involve a period of population growth between severe bottlenecks, such that a single individual can form a visible colony. While it has long been appreciated that the action of positive selection during this growth phase cannot be eliminated, it is typically assumed to be negligible. Here, we quantify the effect of both positive and negative selection in MA studies, demonstrating that selective effects can substantially bias the distribution of fitness effects (DFE) and mutation rates estimated from typical MA protocols in microbes. We then present a simple correction for this bias which applies to both beneficial and deleterious mutations, and can be used to correct the observed DFE in multiple environments. Finally, we use simulated MA experiments to illustrate the extent to which the MA-inferred DFE differs from the underlying true DFE, and demonstrate that the proposed correction accurately reconstructs the true DFE over a wide range of scenarios. These results highlight that positive selection during microbial MA experiments is in fact not negligible, but can be corrected to gain a more accurate understanding of fundamental evolutionary parameters.

scholarly journals Resf1 supports embryonic stem cell self-renewal and effective germline entry

2021 ◽  
Author(s):  
Matus Vojtek ◽  
Ian Chambers
Keyword(s):  
Stem Cells ◽  
Germ Cell ◽  
Germ Line ◽  
Primordial Germ Cell ◽  
Embryonic Stem ◽  
Cell Specification ◽  
Self Renewal ◽  
Downstream Target ◽  
Germ Cell Specification

Retroelement silencing factor 1 (Resf1) interacts with the key regulators of mouse embryonic stem cells (ESCs) Oct4 and Nanog, and its absence results in sterility of mice. However, the function of Resf1 in ESCs and germ line specification is poorly understood. In this study, we used Resf1 knockout cell lines to determine the requirements of RESF1 for ESCs self-renewal and for in vitro specification of ESCs into primordial germ cell-like cells (PGCLCs). We found that deletion of Resf1 in ESCs cultured in serum and LIF reduces self-renewal potential whereas episomal expression of RESF1 has a modest positive effect on ESC self-renewal. In addition, RESF1 is not required for the capacity of NANOG and its downstream target ESRRB to drive self-renewal in the absence of LIF. However, Resf1 deletion reduces efficiency of PGCLC differentiation in vitro. These results identify Resf1 as a novel player in the regulation of pluripotent stem cells and germ cell specification.

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