ArticleNucleic acids research2023
Long-read-based single sperm genome sequencing for chromosome-wide haplotype phasing of both SNPs and SVs.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 18 citations in OpenAlex.
- Epigenetic dynamics of human spermatogenesis and their dysregulation in non-obstructive azoospermia.Protein & cell · 2026Article
- Article
- Single-Cell and Spatial Omics: Methods and Applications.MedComm · 2026Review
- Genetic diversity of infertile males in India.Journal of assisted reproduction and genetics · 2026Article
- Matched whole-genome sequencing of blood (10×) and five single sperm cells (1×) per individual in 53 men.Scientific data · 2026Article
- Direct detection of meiotic recombination events in the highly heterozygous amphioxus genome.Advanced biotechnology · 2025Article
- Single-cell long-read Hi-C, scNanoHi-C2, details 3D genome reorganization in embryonic-stage germ cells.Nature structural & molecular biology · 2025Article
- A high-resolution meiotic crossover map from single-nucleus ATAC-seq reveals insights into the recombination landscape in mammals.NAR genomics and bioinformatics · 2025Article
- Enhanced identification of novel pathogenic variants in hereditary hearing loss through physical phasing with integrated short and long-read sequencing data.Molecular genetics and genomics : MGG · 2025Article
- Review
- Simultaneous de novo calling and phasing of genetic variants at chromosome-scale using NanoStrand-seq.Cell discovery · 2024Article
- Insights into non-crossover recombination from long-read sperm sequencing.bioRxiv : the preprint server for biology · 2024Article
- Low-input PacBio sequencing generates high-quality individual fly genomes and characterizes mutational processes.Nature communications · 2024Article
- Chasing Sequencing Perfection: Marching Toward Higher Accuracy and Lower Costs.Genomics, proteomics & bioinformatics · 2024Review
- Understanding the Genetic Basis of Variation in Meiotic Recombination: Past, Present, and Future.Molecular biology and evolution · 2024Review
Corrections and comments
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Although localized haploid phasing can be achieved using long read genome sequencing without parental data, reliable chromosome-scale phasing remains a great challenge. Given that sperm is a natural haploid cell, single-sperm genome sequencing can provide a chromosome-wide phase signal. Due to the limitation of read length, current short-read-based single-sperm genome sequencing methods can only achieve SNP haplotyping and come with difficulties in detecting and haplotyping structural variations (SVs) in complex genomic regions. To overcome these limitations, we developed a long-read-based single-sperm genome sequencing method and a corresponding data analysis pipeline that can accurately identify crossover events and chromosomal level aneuploidies in single sperm and efficiently detect SVs within individual sperm cells. Importantly, without parental genome information, our method can accurately conduct de novo phasing of heterozygous SVs as well as SNPs from male individuals at the whole chromosome scale. The accuracy for phasing of SVs was as high as 98.59% using 100 single sperm cells, and the accuracy for phasing of SNPs was as high as 99.95%. Additionally, our method reliably enabled deduction of the repeat expansions of haplotype-resolved STRs/VNTRs in single sperm cells. Our method provides a new opportunity for studying haplotype-related genetics in mammals.
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