Clinical usefulness of next-generation sequencing-based target gene sequencing in diagnosis of inherited bone marrow failure syndrome

Abstract

Inherited bone marrow failure syndromes are genetic hematologic disorders with increased cancer risk. Accurate diagnosis is crucial for appropriate management. This study assessed the clinical usefulness of next-generation sequencing (NGS)-based target gene sequencing in pediatric and AYA (adolescent and young adult) patients with hematologic abnormalities. From December 2019 to June 2023, 93 patients with suspected congenital hematologic diseases at a single institution underwent NGS-based testing. Medical records were retrospectively reviewed. The median age at diagnosis was 9.3 years (range 0.2-31.4), with 59.1% males. Indications for testing included specific medical histories (28 patients), persistent cytopenia or recurrent neutropenic fever (22 patients), changes in cytopenia patterns (11 patients), and other reasons (32 patients). Pathogenic variants were identified in 9/28 (32.1%), 3/22 (13.6%), 4/11 (36.4%), and 0/32 (0%). Overall, 16 patients (17.2%) had pathogenic variants, including FANCA, BRCA2, PMS2, ELANE, G6PC3 and VPS13B in patients with idiopathic neutropenia, and GATA2 in patients with suspected myelodysplastic syndrome. Genetic findings led to diagnostic revisions in 12 patients (12.9%), including reclassification of aplastic anemia (AA) as Fanconi anemia, Diamond-Blackfan anemia, or Shwachman-Diamond syndrome, prompting hematopoietic stem cell transplantation and altering cancer surveillance. Pathogenic variants were more frequently observed in patients with a specific medical history or changes in cytopenia, and in those with additional clinical features (cytogenetic abnormalities or non-severe AA). This study demonstrated the diagnostic usefulness of NGS-based target gene sequencing for pediatric and AYA patients with suspected genetic hematologic disorders, supporting the need for multicenter studies and standardized guideline development.

Keywords: Cytopenia; Inherited bone marrow failure syndrome; Next-generation sequencing.

Fig. 1

Patient selection and testing outcomes in suspected Inherited bone marrow failure syndromes. NGS = next-generation sequencing, IBMFS = inherited bone marrow failure syndromes, AA = aplastic anemia, MDS = myelodysplastic syndromes

Fig. 2

Distribution of pathogenic variants and variants of unknown significance (VUS) in 93 patients. A The horizontal axis category represents presumed diagnoses of the patients at the time of next-generation sequencing-based target gene sequencing. Non-severe AA is categorized within the cytopenia (affecting ≥ 2 lineages) group. HM includes acute lymphoblastic leukemia and acute myeloid leukemia, while Others include hemophagocytic lymphohistiocytosis, Langerhans cell histiocytosis, and other conditions such as isolated anemia. Dark green indicates pathogenic variants, black diamonds (◆) represent carriers of pathogenic variants, and light mint green denotes cases with variants of uncertain significance (VUS) (B) Frequency and patterns of 16 pathogenic variants identified in 93 patients. MDS = myelodysplastic syndromes, HM = hematologic malignancy, AA = aplastic anemia