46. Clinical SNP-array adds value to diagnosis and surveillance of bone marrow failure syndromes

Cytogenomic SNP microarray (SNP-A) utilization for diagnosis and monitoring of bone marrow failure syndromes (BMFS) is increasing. Understanding the biology of these heterogeneous diseases is required to appropriately identify, interpret, and track prognostically significant clones, some of which may represent revertant somatic genetic rescue (SGR) events. We reviewed SNP-A findings from our encounter of over 100 BMFS cases tested at our institution. Abnormal results were reported in 30 cases, including nine aplastic anemia (AA, 30%), eleven Shwachman-Diamond syndrome (SDS, 37%), six SAMD9/SAMD9L-related syndrome (20%), and four Diamond-Blackfan anemia (DBA, 13%) cases. In 15 (50%) cases, the SNP-A profile was consistent with SGR and acquired correction of the disease-causing variant. Isolated CN-LOH of the chromosome containing the disease-causing gene was observed in 12 (40%) cases, including CN-LOH 7q in two individuals with SDS (SBDS gene) and three individuals with SAMD9/SAMD9L-associated syndromes, and CN-LOH 2p and 19q in two individuals with RPS7 and RPS19-associated DBA, respectively. SGR-associated CNVs included isochromosome 7q (SBDS) and 20q deletion (EIF6 gene) in three cases of SDS. Malignant transformation SNP-A findings were observed in 4/30 (13%) cases, including CN-LOH 17p with TP53 Tier 1 variant in an SDS case and monosomy 7 in three cases of SAMD9/SAMD9L-related syndromes. Concurrent review of cytogenetic/FISH, NGS, and/or germline BMFS results, where available; identification of low-level, complex and/or coexisting clones; and accurate clonal estimation for sequential tracking are essential, and add value to clinical management. Our results emphasize the value of SNP-A in the diagnosis, prognosis, and monitoring of BMFS.