Unbiased mosaic variant assessment in sperm: a cohort study to test predictability of transmission
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Curated by eLife
Evaluation Summary:
This manuscript analyzes human blastocysts from in vitro fertilization for three subjects (a total of 55 blastocysts), demonstrating transmission of mosaic mutations at close to expected frequencies. These studies are the first of their kind and of translational relevance for the field of clinical genetics and prenatal genetic testing, with the potential to contribute to strategies to reduce genetic disease risk in future offspring.
(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)
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Abstract
De novo mutations underlie individually rare but collectively common pediatric congenital disorders. Some of these mutations can also be detected in tissues and from cells in a parent, where their abundance and tissue distribution can be measured. We previously reported that a subset of these mutations is detectable in sperm from the father, predicted to impact the health of offspring.
Methods:
As a cohort study, in three independent couples undergoing in vitro fertilization, we first identified male gonadal mosaicism through deep whole genome sequencing. We then confirmed variants and assessed their transmission to preimplantation blastocysts (32 total) through targeted ultra-deep genotyping.
Results:
Across 55 gonadal mosaic variants, 15 were transmitted to blastocysts for a total of 19 transmission events. This represented an overall predictable but slight undertransmission based upon the measured mutational abundance in sperm. We replicated this conclusion in an independent, previously published family-based cohort.
Conclusions:
Unbiased preimplantation genetic testing for gonadal mosaicism may represent a feasible approach to reduce the transmission of potentially harmful de novo mutations. This—in turn—could help to reduce their impact on miscarriages and pediatric disease.
Funding:
No external funding was received for this work.
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Evaluation Summary:
This manuscript analyzes human blastocysts from in vitro fertilization for three subjects (a total of 55 blastocysts), demonstrating transmission of mosaic mutations at close to expected frequencies. These studies are the first of their kind and of translational relevance for the field of clinical genetics and prenatal genetic testing, with the potential to contribute to strategies to reduce genetic disease risk in future offspring.
(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)
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Reviewer #1 (Public Review):
This manuscript confirms and extends a recent study from this same group analyzing mosaicism in sperm and transmission of new mutations to relevant offspring. The current work extends this analysis to human blastocysts from in vitro fertilization for three subjects (a total of 55 blastocysts), demonstrating transmission of mosaic mutations at close to expected frequencies. The experiments represent a carefully performed genetic study by cutting edge genetic sequence analysis in a uniquely relevant, but very limited set of human samples. The weakness of this study is that the findings are largely expected and represent an incremental advance relative to the analysis of sperm mosaicism recently published by the same group (Yang et al, Cell, 184:4772, 2021). Nonetheless, these valuable data from primary human …
Reviewer #1 (Public Review):
This manuscript confirms and extends a recent study from this same group analyzing mosaicism in sperm and transmission of new mutations to relevant offspring. The current work extends this analysis to human blastocysts from in vitro fertilization for three subjects (a total of 55 blastocysts), demonstrating transmission of mosaic mutations at close to expected frequencies. The experiments represent a carefully performed genetic study by cutting edge genetic sequence analysis in a uniquely relevant, but very limited set of human samples. The weakness of this study is that the findings are largely expected and represent an incremental advance relative to the analysis of sperm mosaicism recently published by the same group (Yang et al, Cell, 184:4772, 2021). Nonetheless, these valuable data from primary human blastocysts are the first of their kind and of translational relevance for the field of clinical genetics and prenatal genetic testing, with the potential to contribute to strategies to reduce genetic disease risk in future offspring. The computational genomic analysis is cutting-edge and the methods protocol reported here could prove useful to other workers in the field.
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Reviewer #2 (Public Review):
The goal of this study is to examine the transmission of mosaic genetic variants identified in sperm. The authors first perform genome sequencing of DNA from sperm (and blood) at 300x depth to identify putative mosaic variants. They then validate each and simultaneously test blastocysts obtained via IVF using ddPCR to determine whether/which variants were transmitted.
This study differs from previous studies in that mosaic variants are first identified in sperm, rather than identifying de novo variants in offspring and retrospectively testing for germline mosaicism in the parent(s). The experimental approach is solid, though the depth of coverage is modest at 300x. The overall findings are consistent with expectations: they do observe transmission of a subset of variants, and those with higher allele …
Reviewer #2 (Public Review):
The goal of this study is to examine the transmission of mosaic genetic variants identified in sperm. The authors first perform genome sequencing of DNA from sperm (and blood) at 300x depth to identify putative mosaic variants. They then validate each and simultaneously test blastocysts obtained via IVF using ddPCR to determine whether/which variants were transmitted.
This study differs from previous studies in that mosaic variants are first identified in sperm, rather than identifying de novo variants in offspring and retrospectively testing for germline mosaicism in the parent(s). The experimental approach is solid, though the depth of coverage is modest at 300x. The overall findings are consistent with expectations: they do observe transmission of a subset of variants, and those with higher allele frequencies are more likely to be transmitted. They perform a similar analysis in eight previously studied families with 14 offspring and find overall similar results.
An underlying premise of the study is that a priori testing could be performed to prevent transmission of disease-causing variants that usually occur de novo in the affected offspring. A potential weakness is the sample size, as only three cases (sperm + blastocyst) are evaluated. Furthermore, all mosaic variants identified in these cases were deemed likely benign; with the goal of preventing the transmission of deleterious variants, it would be important to expand the cohort in the future and, when possible, evaluate the transmission of potentially deleterious variants.
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