Targeted re-sequencing analysis of 25 genes commonly mutated in myeloid disorders in del(5q) myelodysplastic syndromes

Abstract

Interstitial deletion of chromosome 5q is the most common chromosomal abnormality in myelodysplastic syndromes. The catalogue of genes involved in the molecular pathogenesis of myelodysplastic syndromes is rapidly expanding and next-generation sequencing technology allows detection of these mutations at great depth. Here we describe the design, validation and application of a targeted next-generation sequencing approach to simultaneously screen 25 genes mutated in myeloid malignancies. We used this method alongside single nucleotide polymorphismarray technology to characterize the mutational and cytogenetic profile of 43 cases of early or advanced del(5q) myelodysplastic syndromes. A total of 29 mutations were detected in our cohort. Overall, 45% of early and 66.7% of advanced cases had at least one mutation. Genes with the highest mutation frequency among advanced cases were TP53 and ASXL1 (25% of patients each). These showed a lower mutation frequency in cases of 5q-syndrome (4.5% and 13.6%, respectively), suggesting a role in disease progression in del(5q) myelodysplastic syndromes. Fifty-two percent of mutations identified were in genes involved in epigenetic regulation (ASXL1, TET2, DNMT3A and JAK2). Six mutations had allele frequencies <20%, likely below the detection limit of traditional sequencing methods. Genomic array data showed that cases of advanced del(5q) myelodysplastic syndrome had a complex background of cytogenetic aberrations, often encompassing genes involved in myeloid disorders. Our study is the first to investigate the molecular pathogenesis of early and advanced del(5q) myelodysplastic syndromes using next-generation sequencing technology on a large panel of genes frequently mutated in myeloid malignancies, further illuminating the molecular landscape of del(5q) myelodysplastic syndromes.

Retroviral insertional mutagenesis identifies the del(5q) genes, CXXC5, TIFAB and ETF1, as well as the Wnt pathway, as potential targets in del(5q) myeloid neoplasms

“…The complex cytogenetic abnormalities and recurrent somatic mutations, such as ASXL1, NF1, TET2 and TP53 associated with advanced MDS and AML with a del(5q), has provided some insight; however, the complete genetic profile, and consequences thereof, are not yet known. 3,7 Whether prior cytotoxic therapy induces mutations and/or promotes expansion of pre-existing genetic mutations in t-MNs is also poorly understood. We used a mutagenesis approach in mice, heterozygous for Egr1 (Egr1 +/-) to identify genes and signaling pathways that predispose to developing del(5q) myeloid neoplasms (MNs).…”

What lies beyond del(5q) in myelodysplastic syndrome?

“…8 More will be learned as additional patients are examined and as more agnostic approaches, such as exome and whole genome techniques, are applied. Next-generation sequencing is rapidly moving from research laboratories into clinical settings.…”

“…8 8 demonstrate the molecular genetic heterogeneity of this group which include additional mutations in many genes, including TP53 which has been associated with a very poor prognosis. This may lead us to reconsider how we assess MDS patients we previously put into discrete risk categories based on cytogenetics alone.…”

“…Its targets are to improve outcomes, ensure cost-effective therapy, and to reduce adverse effects of antimicrobial use, including resistance. 8 Control of infection is closely related to antimicrobial stewardship programs, as it aims to prevent the spread of the resistant organisms, when these are selected locally or introduced via patient transfers. The successful implementation of antimicrobial stewardship and infection control programs complement each other in limiting the number of infections caused by multidrug-resistant organisms.…”

Mutational profiling in patients with MDS: Ready for every-day use in the clinic?

“…In more advanced MDS cases, the proportions of mutation carriers were higher as compared to early MDS cases. This suggested a role of the respective mutations for disease progression in MDS with 5q deletion [39,40]. Additionally, gene alterations were recently identified within the Cohesin complex in patients with MDS and other myeloid malignancies such as AML or chronic myelomonocytic leukemia (CMML).…”