Clonal Evolution and Changes in Two AML Patients Detected with A Novel Single-Cell DNA Sequencing Platform

Area of Science:

• Genomics
• Cancer Biology
• Hematology

Background:

• Next-generation sequencing (NGS) in cancer typically uses bulk analysis, averaging variant allele frequencies and missing rare cells or mutational co-occurrences.
• Single-cell genome analysis offers a higher resolution to understand clonal architecture and disease progression.

Purpose of the Study:

• To develop and apply a novel single-cell DNA sequencing approach for analyzing acute myeloid leukemia (AML) patient samples.
• To resolve clonal architecture, monitor engraftment post-bone marrow transplantation (BMT), and track clonal evolution in AML.

Main Methods:

• Longitudinal sampling of peripheral blood mononuclear cells from AML patients.
• Generation of single-cell DNA sequencing libraries using a droplet-based microfluidics technique.
• Molecular profiling of single nucleotide variants (SNVs) and hierarchical clustering analysis.

Main Results:

• The approach successfully profiled thousands of single cells, revealing genetic chimerism post-BMT.
• Hierarchical clustering identified distinct oncogenic clones with mutations in tumor-suppressor genes and/or oncogenes.
• Precise monitoring of engraftment and detection of clonal evolution during disease progression and treatment were achieved.

Conclusions:

• Single-cell DNA sequencing provides a powerful tool for detailed analysis of cancer genomes.
• This method enables precise monitoring of engraftment and reveals the clonal dynamics of oncogenic cells in AML.
• The findings highlight the potential for single-cell sequencing in understanding disease progression and treatment response.