Germline Mutations in Patients Receiving Unrelated Donor Hematopoietic Cell Transplant for Severe Aplastic Anemia

Background. The correct classification of patients presenting with aplastic anemia is essential for proper clinical management. This study aimed to identify patients with unrecognized pathogenic variants associated with inherited bone marrow failure syndromes (IBMFS) in patients receiving hematopoietic cell transplant (HCT) for acquired aplastic anemia (AAA), and to evaluate their impact on patient survival.

Methods. We performed whole exome sequencing (WES) and genome-wide SNP array genotyping on pre-HCT blood samples from 608 patients who received unrelated donor HCT for severe aplastic anemia in 175 centers reporting to the Center for International Blood and Marrow Transplant Research (CIBMTR) and research samples available in the CIBMTR Repository. An IBMFS was the reported diagnosis in 92/608 patients. From generated genomic data and mode of IBMFS inheritance, we developed a bioinformatic algorithm to identify deleterious mutations in 52 known IBMFS genes. Cox proportional hazard models were used for survival analyses. Variables included in the model were selected by a stepwise backward procedure with a p-threshold of 0.05 for entry and 0.1 for retention.

Results. We validated our algorithm in 16 patients with genetically confirmed dyskeratosis congenita (DC, n=12) and Fanconi anemia (FA, n=4) from the NCI IBMFS cohort. Our algorithm was 88% sensitive and 100% specific in identifying the exact mutation in those patients. In HCT recipients, analysis of 52 IBMFS genes identified 130 pathogenic variants in the 92 patients with reported IBMFS and 277 in the 516 patients with reported AAA. Our algorithm combining WES and SNP array data identified genetic evidence of an IBMFS in 59.8% (55/92) of patients reported to have an IBMFS. In patients originally classified as AAA, 10.5% (54/516) had genetic evidence of an IBMFS; 88.7% of them received HCT at ≤ 40 years old, and DC was the most commonly unrecognized disorder (n=26, 5%). Other identified IBMFS by our algorithm included: Diamond-Blackfan anemia (n=8, 1.5%), and FA, myelodysplastic syndrome, or severe congenital neutropenia with 6 patients each (1.2% each), and 1 patient with amegakaryocytic thrombocytopenia (0.2%). Among patients with reported AAA who were ≤ 40 years old, the 3 years survival probability for patients with DC-associated genetic variants (n=26) was 53% (95% CI=35-73%), for patients with genetic variants in other IBMFS (n=20, 4 had FA) was 75% (95% CI=56-94%), and for those with no genetic evidence of IBMFS was 69% (95% CI=64-74%), p log-rank= 0.02. Compared to patients with no genetic evidence of IBMFS, worse post-HCT survival was noted with DC-associated genetic variants (HR=1.75, 95% CI=1.03-2.97, p=0.04), but no survival difference was noted with other IBMFS variants (HR=0.42, 95% CI=0.16-1.15, p=0.09)

Conclusions. We identified a high incidence of unidentified IBMFS in patients undergoing HCT for AAA, which was associated with worse post-HCT survival in those with unrecognized DC. Our study supports the importance of comprehensive genetic testing for patients presenting with AA, given the high incidence of underlying genetic abnormalities that have implications for donor selection, family counseling and selection of the preparative regimen