Genomic analysis of bone marrow failure and myelodysplastic syndromes reveals phenotypic and diagnostic complexity

A novel 33‐Gene targeted resequencing panel provides accurate, clinical‐grade diagnosis and improves patient management for rare inherited anaemias

“…While the approach of choosing a narrow set of genes can speed up diagnosis and allow appropriate genetic counselling, it can, at best, confirm the clinically‐suspected diagnosis, as shown in previously published studies which reported >80% diagnostic yields (Gerrard et al , 2013; Collopy et al , 2014; De Rocco et al , 2014; Christensen et al , 2015; Ghemlas et al , 2015; Zhang et al , 2015). Similarly, for most of our cases, confirmation of a suspected diagnosis by molecular analysis also allowed provision of accurate information for genetic counselling for the first time in 17/57 (~30%) of cases.…”

“…Of the 44 variants tested, 11% were insertions and 8% deletions, satisfying ACMG guidelines that positive controls include variants representative of naturally‐occurring disease‐causing traits. Robustness and assay precision : To test within‐run and between‐run variability, we took a much more stringent approach than used in research‐grade targeted NGS panels (Gerrard et al , 2013; Collopy et al , 2014; De Rocco et al , 2014; Christensen et al , 2015; Ghemlas et al , 2015; Zhang et al , 2015) by assaying 13 samples in duplicate and 4 in triplicate (66 variants in total, 100% of which were found on repeat sequencing).…”

“…Meanwhile, targeted next‐generation‐sequencing (NGS) is a popular approach for providing rapid and accurate mutation analysis as the use of a limited panel of genes facilitates the interpretation and reduces incidental findings (Sun et al , 2015). While targeted NGS has been reported for the investigation of various anaemias and/or pancytopenia (Gerrard et al , 2013; Collopy et al , 2014; De Rocco et al , 2014; Christensen et al , 2015; Ghemlas et al , 2015; Zhang et al , 2015), these studies have reported only research‐grade validation strategies, usually by ensuring that a small number of variants or single nucleotide polymorphisms (SNPs; ranging from 2 to 53 variants) identified by Sanger sequencing could also be detected by NGS. While these panels are valuable in the research context for the positive identification of novel mutations in known genes, they cannot be reliably used in a clinical context because ‘negative’ results do not distinguish between the absence of mutations on the one hand and lack of adequate sequencing reads at the locations of known mutations on the other.…”

Next-Generation Sequencing (NGS)-Based Clinical Testing is Recommended for the Detection of Gene Mutations Associated with Familial Myelodysplastic Syndrome and Acute Myeloid Leukemia Predisposition Syndromes

“…For example, a recent study of pediatric and young adult patients with idiopathic bone marrow failure or MDS identified pathogenic germline mutations in eight of 71 patients (11.3%) who lacked a diagnosis after clinical evaluation and standard clinically-directed genetic testing using a custom targeted NGS gene panel [8]. Another retrospective analysis of pediatric and young adult patients that had undergone bone marrow stem cell transplantation for aplastic anemia or MDS using a multiplexed targeted NGS gene panel identified a pathogenic mutation in five of 98 (5.1%) aplastic anemia patients and 15 of 110 (13.6%) MDS patients, with all of the mutations present in the germline except for one somatically acquired RUNX1 gene Table 1: Genes involved in hereditary MDS and AML predisposition disorders.…”

“…For the purposes of clinical diagnostic testing, NGS-based clinical testing using custom targeted gene panels is recommended for screening and identification of pathogenic mutations associated with familial MDS/AML syndromes [8][9][10][11]. However, once gene mutations associated with specific genetically defined hereditary MDS/AML syndromes have been identified using NGS gene panels, additional confirmatory clinical germline testing is recommended to be performed using DNA samples obtained from cultured skin fibroblasts obtained from skin punch biopsy or skin ellipse biopsies [11].…”