STP — Cancer Genomics

Validation and preliminary implementation of short tandem repeat (STR) chimerism status testing in patients treated with allogenic haematopoietic stem cell transplantation (HSCT)

Allo-HSCT has become a well-established, effective method for the treatment of several malignant and non-malignant haematological malignancies. Though the incidence of improved donor availability and better supportive care has resulted in an increase in the use of HSCT, it continues to be a high-risk procedure, with risks of GVHD, graft failure and infections. Relapse is the main cause of patient death following allo-HSCT. An increase in recipient alleles is usually indicative of a relapse of the patient’s malignant cells, and therefore, the likelihood of relapse can be predicted following two successive increases in recipient chimerism within post-transplant whole blood or bone marrow samples: a phenomenon known as mixed chimerism.

Currently, the method of choice for monitoring chimerism is short tandem repeat (STR) PCR, a technique capable of determining the percentage of both donor and recipient cells. Their increased polymorphism means there is a high probability that a panel of STR markers will enable the differentiation of individual genomes. BHSCT currently has no in-house chimerism testing in place for HSCT patients. Using the PowerPlex® 16 STR system, we sort to establish chimerism analysis on NEQAS, retrospective and WB, CD3+ and CD15+ cell subsets samples.

In this thesis, we have confirmed that the wide range of sensitivity, in addition to the flexibility of the protocol ensures that chimerism analysis in patient samples with minimal DNA material can be performed. We show that, the use of more than 3 informative markers increases the quality of chimerism analysis, and highlighted that, reducing the reaction volume is a viable option for chimerism analysis in patients with minimal DNA concentration or template volume, albeit with extreme care. With continuous training on analysis, chimerism monitoring assessments will be implemented and performed on a weekly basis in our department using the quantitative fluorescence-based STR-PCR with capillary electrophoresis for PCR product resolution presented herein. Chimerism analysis will be performed during engraftment in PB, CD3+ T-cell subsets and CD15+ myeloid subsets, in line with published guidelines, to aid clinicians to implement clinical interventions to ensure optimal patient management.

Last updated on 4th October 2022