Single-cell genome-wide concurrent haplotyping and copy-number profiling through genotyping-by-sequencing

Area of Science:

• Genomics
• Reproductive Biology
• Bioinformatics

Background:

• Single-cell whole-genome haplotyping is crucial for detecting genetic disorders and mosaicism in early development.
• Current preimplantation genetic testing (PGT) methods like karyomapping and haplarithmisis, often rely on SNP arrays.
• There is a need for more accessible and cost-effective sequencing-based PGT methods.

Purpose of the Study:

• To develop a novel, sequencing-based methodology for concurrent haplotyping and copy-number profiling of single cells.
• To establish technical parameters and an analysis pipeline for accurate single-cell genetic analysis.
• To demonstrate the utility of the method for PGT applications in humans and other species.

Main Methods:

• Developed a single-cell genotyping-by-sequencing (scGBS) approach involving DNA amplification, restriction enzyme digestion, and sequencing.
• Integrated scGBS data with the haplarithmisis algorithm for analysis.
• Validated the method using human blastomere and trophectoderm samples, and bovine embryo blastomeres.

Main Results:

• Established a robust scGBS method enabling accurate, concurrent haplotyping and copy-number profiling of single cells.
• Demonstrated successful application of scGBS for PGT in human samples, identifying monogenic disorders.
• Showcased the method's cross-species applicability by analyzing bovine embryos.

Conclusions:

• The scGBS method offers a powerful, sequencing-based alternative for single-cell genetic analysis.
• This approach has significant potential as a clinical PGT application for monogenic disorders.
• scGBS is adaptable for single-cell haplotyping in any species with diploid genomes.