ArticleNucleic acids research2022
Single-cell genome-wide concurrent haplotyping and copy-number profiling through genotyping-by-sequencing.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 40 citations in OpenAlex.
- A medium throughput approach for single cell copy number variation sequencing towards efficient application in clinics.Journal of advanced research · 2026Article
- PEStimate: predicting offspring disease risk after polygenic embryo screening.Bioinformatics (Oxford, England) · 2026Article
- Preimplantation genetic testing for polygenic diseases: A novel paradigm in embryo selection.Biochemistry and biophysics reports · 2026Review
- Underrecognized triploidy and genome-wide uniparental disomy in human blastocysts revealed by a concurrent preimplantation genetic testing approach.Human reproduction open · 2026Article
- Comparative Genomic Hybridization (CGH) in Genotoxicology: From the Basics to Modern Approaches.Methods in molecular biology (Clifton, N.J.) · 2026Review
- Preimplantation genetic testing for cardiomyopathies: a case series illustrating the clinical and technological perspective.European heart journal. Case reports · 2025Article
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- Uncovering Molecular and Genetic Drivers of Dental Caries Via scRNA-seq and Mendelian Randomisation.International dental journal · 2025Article
- Reproductive Choices in Haemoglobinopathies: The Role of Preimplantation Genetic Testing.Genes · 2025Review
- Long-read whole-genome sequencing-based concurrent haplotyping and aneuploidy profiling of single cells.Nucleic acids research · 2025Article
- Benign mosaic chromosomal structural variants across generations: evidence for a developmental correction mechanism from clinical and computational models.Frontiers in genetics · 2025Article
- Preimplantation genetic testing for structural rearrangements by genome-wide SNP genotyping and haplotype analysis: a prospective multicenter clinical study.EBioMedicine · 2025Article
- Screening embryos for polygenic disease risk: a review of epidemiological, clinical, and ethical considerations.Human reproduction update · 2024Review
- Clinical-grade whole genome sequencing-based haplarithmisis enables all forms of preimplantation genetic testing.Nature communications · 2024Article
- A healthy live birth after mosaic blastocyst transfer in preimplantation genetic testing for GATA1-related cytopenia combined with HLA matching.BMC medical genomics · 2024Article
- Genome-wide equine preimplantation genetic testing enabled by simultaneous haplotyping and copy number detection.Scientific reports · 2024Article
- Single-cell DNA sequencing reveals a high incidence of chromosomal abnormalities in human blastocysts.The Journal of clinical investigation · 2024Article
- OneGene PGT: comprehensive preimplantation genetic testing method utilizing next-generation sequencing.Journal of assisted reproduction and genetics · 2024Article
- Case report: Successful PGT-M based on the identification of a spliceogenic variant in theFrontiers in genetics · 2024Article
Corrections and comments
- Erratum issued
Authors and funding
10 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Single-cell whole-genome haplotyping allows simultaneous detection of haplotypes associated with monogenic diseases, chromosome copy-numbering and subsequently, has revealed mosaicism in embryos and embryonic stem cells. Methods, such as karyomapping and haplarithmisis, were deployed as a generic and genome-wide approach for preimplantation genetic testing (PGT) and are replacing traditional PGT methods. While current methods primarily rely on single-nucleotide polymorphism (SNP) array, we envision sequencing-based methods to become more accessible and cost-efficient. Here, we developed a novel sequencing-based methodology to haplotype and copy-number profile single cells. Following DNA amplification, genomic size and complexity is reduced through restriction enzyme digestion and DNA is genotyped through sequencing. This single-cell genotyping-by-sequencing (scGBS) is the input for haplarithmisis, an algorithm we previously developed for SNP array-based single-cell haplotyping. We established technical parameters and developed an analysis pipeline enabling accurate concurrent haplotyping and copy-number profiling of single cells. We demonstrate its value in human blastomere and trophectoderm samples as application for PGT for monogenic disorders. Furthermore, we demonstrate the method to work in other species through analyzing blastomeres of bovine embryos. Our scGBS method opens up the path for single-cell haplotyping of any species with diploid genomes and could make its way into the clinic as a PGT application.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.