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

The impact of chromosomal abnormalities on chimerism analysis by next generation sequencing (NGS) has not been explored. Here we report a case of cutaneous T-cell lymphoma (CTCL)/ Sézary syndrome with unusual chimerism findings caused by genotypic abnormalities of the leukemic cells. Cytogenetics analysis indicated a near-triploid karyotype with multiple numerical and structural abnormalities in the leukemic cells. Allogeneic stem cell transplantation was considered. Chimerism testing was performed using NGS-based One Lambda Devyser Chimerism assay. In pre-transplant samples containing leukemic cells, chimerism analysis indicated out-of-range variant allele frequencies (VAF) at 9 out of 11 heterozygous DNA markers. In contrast, a pre-transplant sample with no detectable leukemic cells showed normal allele ratios. After transplantation, the absence of circulating leukemic cells allowed accurate assessment of donor chimerism. However, the possibility that leukemia recurrence may impact the accuracy of chimerism results has to be considered in follow-up testing.