Whole genome transcriptome sequencing in inherited bone marrow failure syndromes and related diseases – the ibmdx study

Abstract

Abstract Inherited bone marrow failure syndromes (IBMFS) are a group of monogenic diseases of diverse pathogenesis manifesting as single or multilineage cytopenia typically due to hypoproliferative dyshematopoiesis. Accurately diagnosing IBMFS is challenging given the overlapping clinicopathological features between individual genetic syndromes as well as with acquired BMFS (e.g. immune aplastic anemia). Accurate genetic diagnosis in IBMFS is critical and most commonly involves targeted panel DNA sequencing or whole exome sequencing. These approaches do not cover the full spectrum of possible genomic abnormalities which in turn may contribute to a significant proportion of patients with IBMFS remaining undiagnosed. We aimed to comprehensively evaluate the unbiased upfront approach of whole genome transcriptome sequencing (WGTS) in patients with suspected IBMFS (the IBMDx study). The IBMDx study aimed to (i) determine the diagnostic rate and clinical impact of upfront WGTS (ii) assess the acceptability of WGTS to patients and physicians through an implementation science framework (iii) evaluate the health-economic impact and cost-effectiveness of the approach and (iv) discover and functionally characterize novel genes and variants in IBMFS. 237 patients were enrolled from March 2022 to March 2025. The median age of the cohort was 30 years (range 6m-78 years; M:F 0.93:1). 70/237 (29.5%) were under 18 years. WGS was performed exclusively on non-hematological DNA (hair follicle DNA [n=178], skin biopsy/cultured skin fibroblasts [n=59]). Trio WGS was performed in 18 families. WGS was performed by a clinically accredited service and results returned to physicians/patients in real time for patient management and segregation/predictive testing as required. A genomic diagnosis for the hematological phenotype was established in 88/237 (37.1%) patients. Diagnoses made included hereditary thrombocytopenia (n=19), telomere biology disorders (TBDs) (n=14), Diamond-Blackfan anemia (n=12), primary red cell disorders (n=6), severe congenital neutropenia (n=6), Shwachman Diamond Syndrome (n=5) and Fanconi anemia (n=4). Targeted sequencing of the hematological compartment demonstrated clonal hematopoiesis in 32/217 (14.7%) patients. In addition, four patients had genetic diagnoses made of symptomatic and clinically significant diseases unrelated to the hematological phenotype (TAP2, IRF2BP2, ACADM and mosaic trisomy 7). Secondary genomic findings requiring further management were detected in 7 patients (TNNI3, MSH6, Monosomy X mosaic, BRCA1, BRIP1, ATM, FBN1). WGTS revealed novel genomic abnormalities not previously established in IBMFS such as retrotransposon-mediated gene disruption, polyadenylation site loss and disruption of novel regulatory regions. Novel genomic abnormalities in genes associated with Diamond-Blackfan anaemia (RPL31), TBDs (TERT/TERC) and hereditary thrombocytopenia (TPM4) underwent in vivo and in vitro functional assessment to inform pathogenicity. Finally, novel associations were identified with primary IBMFS-like presentations (THRA) as well as definitive evidence of gene-disease association were established (MEIS1, TUBB). Using a formal Theoretical Framework of Acceptability, WGTS was found to be highly acceptable to patients and carers as evidenced by positive perceptions of clinicians, alignment with healthcare expectations, and minimal effort required to participate. However, concern regarding equity of access to technology for all patients with suspected IBMFS was a recurrent theme amongst patients and carers interviewed. Health economic analysis showed that the cost of achieving maximum diagnostic yield, incorporating varied diagnostic strategies, to be between $7,800 - $8,200 USD per hematological diagnosis. In summary, we have comprehensively evaluated upfront WGTS in a large cohort of adult and pediatric patients with suspected IBMFS and have found this approach has a high diagnostic rate (37.1%), is highly acceptable to patients, and uncovered multiple genomic abnormalities that would have been missed with more traditional diagnostic approaches. Moreover, we have uncovered new genomic mechanisms of disease and genes associated with IBMFS leading to new areas of research into the underlying biology of these challenging diseases.