A method for low-coverage single-gamete sequence analysis demonstrates adherence to Mendel’s first law across a large sample of human sperm

Carioscia, Sara A.; Weaver, Kathryn J.; Bortvin, Andrew N; Pan, Hao; Ariad, Daniel; Bell, Avery Davis; McCoy, Rajiv C.

doi:10.7554/elife.76383

Cited by 5 publications

(4 citation statements)

References 68 publications

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“…S3d ). The ratio of X sperm and Y sperm was close to 1:1, which was consistent with Mendel’s Law of Segregation 27 .…”

Section: Resultssupporting

confidence: 82%

Mapping crossover events of mouse meiotic recombination by restriction fragment ligation-based Refresh-seq

Wang,

Chen,

Gao

et al. 2024

Cell Discov

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Single-cell whole-genome sequencing methods have undergone great improvements over the past decade. However, allele dropout, which means the inability to detect both alleles simultaneously in an individual diploid cell, largely restricts the application of these methods particularly for medical applications. Here, we develop a new single-cell whole-genome sequencing method based on third-generation sequencing (TGS) platform named Refresh-seq (restriction fragment ligation-based genome amplification and TGS). It is based on restriction endonuclease cutting and ligation strategy in which two alleles in an individual cell can be cut into equal fragments and tend to be amplified simultaneously. As a new single-cell long-read genome sequencing method, Refresh-seq features much lower allele dropout rate compared with SMOOTH-seq. Furthermore, we apply Refresh-seq to 688 sperm cells and 272 female haploid cells (secondary polar bodies and parthenogenetic oocytes) from F1 hybrid mice. We acquire high-resolution genetic map of mouse meiosis recombination at low sequencing depth and reveal the sexual dimorphism in meiotic crossovers. We also phase the structure variations (deletions and insertions) in sperm cells and female haploid cells with high precision. Refresh-seq shows great performance in screening aneuploid sperm cells and oocytes due to the low allele dropout rate and has great potential for medical applications such as preimplantation genetic diagnosis.

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“…S3d ). The ratio of X sperm and Y sperm was close to 1:1, which was consistent with Mendel’s Law of Segregation 27 .…”

Section: Resultssupporting

confidence: 82%

Mapping crossover events of mouse meiotic recombination by restriction fragment ligation-based Refresh-seq

Wang,

Chen,

Gao

et al. 2024

Cell Discov

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“…1 . There are several methods to obtain haplotypes for sperm data; for example, Carioscia et al developed the rhapsodi method suitable for low coverage of single-gamete sequence analysis 22 . Li et al developed Hapi, which utilizes sperm data to obtain haplotypes by employing the PHMM (pairwise Hidden Markov Model) method 23 .…”

Section: Resultsmentioning

confidence: 99%

Haplotype-resolved assembly of a pig genome using single-sperm sequencing

Niu,

Fan,

Yang

et al. 2024

Commun Biol

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Single gamete cell sequencing together with long-read sequencing can reliably produce chromosome-level phased genomes. In this study, we employed PacBio HiFi and Hi-C sequencing on a male Landrace pig, coupled with single-sperm sequencing of its 102 sperm cells. A haplotype assembly method was developed based on long-read sequencing and sperm-phased markers. The chromosome-level phased assembly showed higher phasing accuracy than methods that rely only on HiFi reads. The use of single-sperm sequencing data enabled the construction of a genetic map, successfully mapping the sperm motility trait to a specific region on chromosome 1 (105.40–110.70 Mb). Furthermore, with the assistance of Y chromosome-bearing sperm data, 26.16 Mb Y chromosome sequences were assembled. We report a reliable approach for assembling chromosome-level phased genomes and reveal the potential of sperm population in basic biology research and sperm phenotype research.

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“…Independent random assortment is a major principle of Mendelian genetics [ 60 ]. There is excellent evidence from large-scale allelic segregation studies at many loci that this random assortment of meiotic products is the mechanism that prevails [ 61 ]. Obviously, there may appear to be segregation anomalies due to selection at loci where alleles deleterious for survival arise.…”

Section: Meiotic Segregationmentioning

confidence: 99%

Stochasticity in genetics and gene regulation

van Heyningen

2024

Phil. Trans. R. Soc. B

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Development from fertilized egg to functioning multi-cellular organism requires precision. There is no precision, and often no survival, without plasticity. Plasticity is conferred partly by stochastic variation, present inherently in all biological systems. Gene expression levels fluctuate ubiquitously through transcription, alternative splicing, translation and turnover. Small differences in gene expression are exploited to trigger early differentiation, conferring distinct function on selected individual cells and setting in motion regulatory interactions. Non-selected cells then acquire new functions along the spatio-temporal developmental trajectory. The differentiation process has many stochastic components. Meiotic segregation, mitochondrial partitioning, X-inactivation and the dynamic DNA binding of transcription factor assemblies—all exhibit randomness. Non-random X-inactivation generally signals deleterious X-linked mutations. Correct neural wiring, such as retina to brain, arises through repeated confirmatory activity of connections made randomly. In immune system development, both B-cell antibody generation and the emergence of balanced T-cell categories begin through stochastic trial and error followed by functional selection. Aberrant selection processes lead to immune dysfunction. DNA sequence variants also arise through stochastic events: some involving environmental fluctuation (radiation or presence of pollutants), or genetic repair system malfunction. The phenotypic outcome of mutations is also fluid. Mutations may be advantageous in some circumstances, deleterious in others. This article is part of a discussion meeting issue ‘Causes and consequences of stochastic processes in development and disease’.

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A method for low-coverage single-gamete sequence analysis demonstrates adherence to Mendel’s first law across a large sample of human sperm

Cited by 5 publications

References 68 publications

Mapping crossover events of mouse meiotic recombination by restriction fragment ligation-based Refresh-seq

Mapping crossover events of mouse meiotic recombination by restriction fragment ligation-based Refresh-seq

Haplotype-resolved assembly of a pig genome using single-sperm sequencing

Stochasticity in genetics and gene regulation

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