Challenges of chimerism analysis using Next-Generation Sequencing in a patient with complex chromosomal alterations

Area of Science:

• Hematology
• Genetics
• Oncology

Background:

• Chimerism analysis is crucial for monitoring engraftment after allogeneic stem cell transplantation.
• The influence of chromosomal abnormalities on chimerism testing, particularly with next-generation sequencing (NGS), remains underexplored.

Purpose of the Study:

• To investigate the impact of chromosomal abnormalities in leukemic cells on NGS-based chimerism analysis.
• To report a case of cutaneous T-cell lymphoma (CTCL)/Sézary syndrome with atypical chimerism findings.

Main Methods:

• Cytogenetics analysis revealed a near-triploid karyotype with multiple abnormalities in leukemic cells.
• Chimerism testing was performed using the NGS-based One Lambda Devyser Chimerism assay.
• Analysis compared pre-transplant samples with and without detectable leukemic cells, and post-transplant samples.

Main Results:

• Pre-transplant samples with leukemic cells showed aberrant variant allele frequencies (VAF) at multiple DNA markers.
• A sample devoid of leukemic cells exhibited normal allele ratios, indicating accurate baseline assessment.
• Post-transplantation, the absence of leukemic cells enabled precise donor chimerism evaluation.

Conclusions:

• Leukemic cell genotypic abnormalities can significantly affect the accuracy of NGS chimerism analysis.
• Post-transplant monitoring requires consideration of potential leukemia recurrence impacting chimerism results.
• Accurate chimerism assessment relies on the absence of confounding factors like chromosomal abnormalities in leukemic cells.