P014 Next generation sequencing is capable of detecting contaminating alleles from malignancy for a bone marrow transplant recipient

HLA typing using Next Generation Sequencing (NGS) for bone marrow transplant (BMT) patients has been recognized to outperform traditional molecular typing methodologies in detecting contaminating alleles from malignancy. Here we report a case with ambiguous HLA typing that was clearly resolved by NGS. A 61 year old female with atypical chronic myeloid leukemia was evaluated for allogeneic BMT. Initial HLA typing by NGS on peripheral blood (PB) of the patient and her 2 siblings showed that one sibling was most likely HLA identical, and the other was haplo-identical to the patient, except an extra HLA-DRB1* allele was detected in the patient. NGS presented a mixture of DRB1*03:01 and 03:16 for the patient and DRB1*03:01 only for both siblings (Table 1a). The difference between DRB1*03:01 and 03:16 is located in Exon 2 at NT 229 as C and T, respectively. The number of NGS reads (R#345) from the patients’ PB at this position showed 10 reads mapping to DRB1*03:01 and 335 to DRB1*03:16, indicating 2.9% DRB1*03:01 and 97.1% DRB1*03:16. To investigate the possible involvement of malignant cells, DNA from the patients’ buccal swab (BS) was typed by NGS and also revealed a mixture of DRB1*03:01 and 03:16. The number of NGS reads (R#543) showed 420 and 123 reads (77.3% and 22.7%) mapped to the DRB1*03:01 and 03:16, respectively (Table 1b). Confirmatory typing of the patients’ PB and BS verified the initial typing result, thus concluding the DRB1*03:16 allele originated in the malignancy of the patient. BMT was performed with the HLA identical sibling. Parallel testing by NGS typing and engraftment monitoring by short tandem repeat (STR) was performed with post-BMT PB. Interestingly, NGS analysis indicated 63.1% of DRB1*03:01 and 36.9% of DRB1*03:16, which presented a close correlation with 61% and 39% donor and recipient chimerism, respectively, as detected by STR (Table 1c). This case study highlights the great potential of NGS in detecting minor component alleles from malignancy in a semi-quantitative manner.