Direct chromosome-length haplotyping by single-cell sequencing.

Area of Science:

• Genomics
• Molecular Biology
• Genetics

Background:

• Phasing diploid genomes accurately is crucial for understanding individual genetic makeup.
• Existing methods often lack the resolution or require generational data.
• Directly charting parental chromosome contributions remains a challenge.

Purpose of the Study:

• Introduce single-cell DNA template strand sequencing (Strand-seq) for complete diploid genome phasing.
• Demonstrate Strand-seq's capability in high-accuracy haplotype construction.
• Utilize Strand-seq to analyze meiotic recombination and structural variants.

Main Methods:

• Single-cell DNA template strand sequencing (Strand-seq) was employed.
• Haplotype phasing was performed on a HapMap individual (NA12878).
• Meiotic recombination events were mapped in a family trio.

Main Results:

• Achieved highly accurate haplotype phasing (99.3% concordance) without generational data.
• Mapped meiotic recombination events with high resolution (median range ~14 kb).
• Phased large structural variants including deletions, indels, and inversions.
• Observed loss of heterozygosity in single cells, revealing cellular heterogeneity.

Conclusions:

• Strand-seq is a powerful, novel approach for complete diploid genome phasing.
• The method accurately maps inheritance patterns and genetic variations.
• Single-cell resolution of Strand-seq is advantageous for studying heterogeneous cell populations like cancer cells.