Next-generation Sequencing in Bone Marrow Failure Syndromes and Isolated Cytopenias: Experience of the Spanish Network on Bone Marrow Failure Syndromes

Abstract

Inherited bone marrow failure syndromes (IBMFSs) are a group of congenital rare diseases characterized by bone marrow failure, congenital anomalies, high genetic heterogeneity, and predisposition to cancer. Appropriate treatment and cancer surveillance ideally depend on the identification of the mutated gene. A next-generation sequencing (NGS) panel of genes could be 1 initial genetic screening test to be carried out in a comprehensive study of IBMFSs, allowing molecular detection in affected patients. We designed 2 NGS panels of IBMFS genes: version 1 included 129 genes and version 2 involved 145 genes. The cohort included a total of 204 patients with suspected IBMFSs without molecular diagnosis. Capture-based targeted sequencing covered > 99% of the target regions of 145 genes, with more than 20 independent reads. No differences were seen between the 2 versions of the panel. The NGS tool allowed a total of 91 patients to be diagnosed, with an overall molecular diagnostic rate of 44%. Among the 167 patients with classified IBMFSs, 81 patients (48%) were diagnosed. Unclassified IBMFSs involved a total of 37 patients, of whom 9 patients (24%) were diagnosed. The preexisting diagnosis of 6 clinically classified patients (6%) was amended, implying a change of therapy for some of them. Our NGS IBMFS gene panel assay is a useful tool in the molecular diagnosis of IBMFSs and a reasonable option as the first tier genetic test in these disorders.

Syndromes predisposing to leukemia are a major cause of inherited cytopenias in children

“…38 Using an NGS panel, Galvez et al successfully diagnosed only three of 25 patients with prolonged neutropenia. 18 Overlap with primary immunodeficiencies, 49 new unrecognized genes (estimated to be the cause in about 25% of patients with SCN) 50 and acquired neutropenia probably contribute to the low yield of pathogenic variant detection among these patients. The overall poor results that we and others achieved calls for better selection of candidates for genetic diagnosis due to isolated neutropenia.…”

“…However, due to the non-specific clinical and laboratory presentation of syndromes causing cytopenias, an unbiased diagnosis, as offered by next-generation sequencing (NGS) technologies, is usually essential. 11,15,16 Indeed, several studies have demonstrated advantages of NGS technologies for improving diagnosis, 11,13,[15][16][17][18] and reported genetic diagnostic rates of 13-54%. However, differences were evident in the patient populations (IBMFS only, MDS only, IT only or all these conditions), age (children, adults or both), sequencing method (NGS panel or whole exome sequencing [WES]), the type of variants detected (germline variants or both somatic and germline variants) and the types of sequence variants reported (pathogenic and likely pathogenic [P/LP]) only or also variants of unknown significance [VOUS]).…”

Fludarabine-based Reduced Intensity Conditioning for Allogeneic Hematopoietic Stem Cell Transplantation in a Pediatric Patient With Bone Marrow Failure Syndrome Type 3

“…1 However, many patients remain underdiagnosed because of the wide range of the phenotype which overlap with other diseases. 2,3 Now with the advent of whole-exome sequencing, it is possible to identify the novel genetic defects of unclassificated BMFS in the societies with high-rate consanguinity. [1][2][3] Shwachman-Diamond syndrome (SDS) is one of BMFS related to ribosomopathies.…”

“…2,3 Now with the advent of whole-exome sequencing, it is possible to identify the novel genetic defects of unclassificated BMFS in the societies with high-rate consanguinity. [1][2][3] Shwachman-Diamond syndrome (SDS) is one of BMFS related to ribosomopathies. 4,5 Most cases are associated with biallelic mutations in the SBDS gene.…”

“…3,5 However, about 10% to 20% of patients have shown classic phenotype of SDS with negative SBDS mutations. 2,3,5 Recent reports shown homozygous variants in a novel gene known as DNAJC21. DNAJC21 that belongs to J-proteins family (named after the founder, E. coli DnaJ), is required for nucleolar rRNA biogenesis, and has essential role in the late cytoplasmic step of 60S ribosome subunit maturation.…”