Single-cell paired-end genome sequencing reveals structural variation per cell cycle

Area of Science:

• Genomics
• Molecular Biology
• Cancer Research

Background:

• The rate and nature of genome mutations at the single-cell level are poorly understood.
• Traditional population-based DNA sequencing obscures individual cell genetic changes and mutation mechanisms.
• Existing single-cell genome analyses are limited by whole-genome amplification (WGA) artifacts and mutation detection capabilities.

Purpose of the Study:

• To develop novel methods for analyzing single-cell whole-genome amplification (WGA) products.
• To enable detection of diverse DNA mutations and characterization of structural variants.
• To overcome limitations of current single-cell sequencing for studying genome mutation dynamics.

Main Methods:

• Development of paired-end sequence analysis for single-cell WGA products.
• Distinguishing copy number changes from allelic WGA amplification artifacts using aberrantly mapping read pairs.
• Delineation of structural variant breakpoints and architecture.

Main Results:

• Successfully captured DNA copy number changes within a single cell cycle in breast cancer cells.
• Detected DNA copy number changes in blastomeres from a human zygote post-in vitro fertilization.
• Discovered and fine-mapped a heritable inter-chromosomal rearrangement t(1;16)(p36;p12) in a single blastomere.

Conclusions:

• The developed paired-end sequencing methods provide a robust approach for single-cell genome mutation analysis.
• These methods accurately detect various mutation classes and structural variants, including copy number changes.
• The approach offers a significant advancement for basic genome research and holds potential for clinical genetic diagnostics.