Utility of clinical comprehensive genomic characterization for diagnostic categorization in patients presenting with hypocellular bone marrow failure syndromes

Piers Blombery, Lucy Fox, Georgina L Ryland, Ella R Thompson, Jennifer Lickiss, Michelle McBean, Satwica Yerneni, David Hughes, Anthea Greenway, Francoise Mechinaud, Erica M Wood, Graham J Lieschke, Jeff Szer, Pasquale Barbaro, John Roy, Joel Wight, Elly Lynch, Melissa Martyn, Clara Gaff, David Ritchie, Piers Blombery, Lucy Fox, Georgina L Ryland, Ella R Thompson, Jennifer Lickiss, Michelle McBean, Satwica Yerneni, David Hughes, Anthea Greenway, Francoise Mechinaud, Erica M Wood, Graham J Lieschke, Jeff Szer, Pasquale Barbaro, John Roy, Joel Wight, Elly Lynch, Melissa Martyn, Clara Gaff, David Ritchie

Abstract

Bone marrow failure (BMF) related to hypoplasia of hematopoietic elements in the bone marrow is a heterogeneous clinical entity with a broad differential diagnosis including both inherited and acquired causes. Accurate diagnostic categorization is critical to optimal patient care and detection of genomic variants in these patients may provide this important diagnostic and prognostic information. We performed real-time, accredited (ISO15189) comprehensive genomic characterization including targeted sequencing and whole exome sequencing in 115 patients with BMF syndrome (median age 24 years, range 3 months - 81 years). In patients with clinical diagnoses of inherited BMF syndromes, acquired BMF syndromes or clinically unclassifiable BMF we detected variants in 52% (12/23), 53% (25/47) and 56% (25/45) respectively. Genomic characterization resulted in a change of diagnosis in 30/115 (26%) including the identification of germline causes for 3/47 and 16/45 cases with pre-test diagnoses of acquired and clinically unclassifiable BMF respectively. The observed clinical impact of accurate diagnostic categorization included choice to perform allogeneic stem cell transplantation, disease-specific targeted treatments, identification of at-risk family members and influence of sibling allogeneic stem cell donor choice. Multiple novel pathogenic variants and copy number changes were identified in our cohort including in TERT, FANCA, RPS7 and SAMD9. Whole exome sequence analysis facilitated the identification of variants in two genes not typically associated with a primary clinical manifestation of BMF but also demonstrated reduced sensitivity for detecting low level acquired variants. In conclusion, genomic characterization can improve diagnostic categorization of patients presenting with hypoplastic BMF syndromes and should be routinely performed in this group of patients.

Figures

Figure 1.
Figure 1.
Genes involved in inherited and acquired bone marrow failure syndromes. Genes causative of an inherited bone marrow failure syndrome (IBMFS), and genes associated with a risk of transformation to hematological malignancy or response to immunosuppression in patients with acquired aplastic anemia (aAA) and hypoplastic myelodysplastic syndrome (hMDS) were assessed in this study. Four genes, CSF3R, GATA2, MPL and RUNX1, were assessed in both germline and acquired settings. Genes targeted by whole exome sequencing (WES) only (i.e., not included on targeted panel) are denoted with an asterisk. Genes KMT2D and PSTPIP1 are not represented in this figure; variants detected in these two genes were considered ‘off-target’ findings.
Figure 2.
Figure 2.
Pre- and post-test diagnosis classification of patients. Numbers of patients classified into each diagnostic group, (i) inherited bone marrow failure syndrome (IBMFS), (ii) acquired aplastic anemia (aAA) or hypoplastic MDS (hMDS) or (iii) clinically unclassifiable bone marrow failure (UBMF) as evaluated prior to genomic testing (pre-test diagnosis) and again following genomic testing (posttest diagnosis) with transitions indicated by the connecting lines (in addition three patients changed diagnosis within the aAA/hMDS category from aAA to MDS). RCC: refractory cytopenia of childhood; tMN: therapy related myeloid neoplasm.

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