Improved Molecular Diagnosis of Aplastic Anemia/Bone Marrow Failure Syndromes Using a Novel Comprehensive Next Generation Sequencing Gene Panel

Introduction: Various forms of aplastic anemia (AA)/bone marrow failure syndromes (IBMFs) show significant clinical and molecular heterogeneity with significant clinical overlap and are often diagnosed based on established clinical and pathological criteria. While >70 genes have been identified in patients with AA/IBMFs, most cases have are labelled as idiopathic with no identifiable genetic abnormlaity found. Precise detection of genetic abnormalities in these patients may assist in more accurate molecular diagnosis in these patients, proper counseling, cancer surveillance and personalized clinical intervention.

Method: As part of the Saudi Human Genome Project, we developed a comprehensive 405 gene panel encompassing all known Mendelian hematological disorders (hemolytic anemias, aplastic anemias/bone marrow failure syndromes, coagulation disorders) using the Ion Torrent AmpliSeq technology. Patients who met the clinical diagnosis of aplastic anemia/bone marrow failure syndrome were enrolled into this study. Peripheral blood samples were subjected to this next-generation sequencing analysis.

Results: We validated the Saudi Mendeliome assay using 642 samples with known mutations across various medical specialties. We then tested 37 patients with AA/IBMFS using this Proton-Ion sequencing platform. Mutations were identified in 7/37 (19%) of patients, followed by whole exome sequencing (WES) in those patients without identifiable mutations.

Conclusion: Compared with clinical WES and/or whole genome sequencing (WGS), which are still expensive, time consuming and difficult to interpret, this novel and comprehensive targeted gene panel is more economical (< $150), faster (3-4 weeks), upgradable (by spiking in newly identified AA/IBMFs genes) and can be used to genotype patients with acquired aplastic anemia/bone marrow failure syndromes and guide their management. Second tier testing using WES/WGS is recommended for cases without identifiable mutations.