Somatic Mutations Predict Poor Prognosis in Myelodysplastic Syndrome Patients with Normal Karyotypes

Purpose: Somatic mutations are common in myelodysplastic syndrome (MDS), but its risk stratification is mainly based on cytogenetics. This study was to explore the prognostic significance of somatic mutations in MDS patients with normal karyotypes. Patients and Methods: Three hundred and four patients with MDS were enrolled in this retrospective study. A genomic panel of 127 gene targets were detected by next-generation sequencing. Results: Two hundred and Eighty-one (92.4%) patients carried at least one somatic mutation, while cytogenetics identified abnormalities in 140 (46.1%) patients. The 5 most frequently mutated genes were TET2, ASXL1, EZH2, TET1, FAT1, and TET2, TP53, TET1, EP300, SF3B1 in the patients with normal karyotypes and aberrant karyotypes, respectively. When mutations detected in >5% of the whole cohort, they were included in analysis and the results showed that the frequency of TET2, TP53, ASXL1, CD101, KDM6A, SH2B3 and IL-3RA mutations was different between two groups(all P<0.05). ASXL1, CD101, KDM6A, SH2B3, IL-3RA mutations were more common in normal karyotype group, while TET2 and TP53 were more common in aberrant karyotype group. Multivariable analysis showed that age (HR 1.02; P=0.027), IPSS-R(HR 1.80; P<0.0001), TP53(HR 2.36; P<0.0001) and DNMT3A (HR 1.83, P=0.044) were the risk factors while allo-HSCT(HR 0.50; P=0.001) was a protect factor for OS in the whole cohort. For sub-group analysis, IPSS-R(HR 1.54; P=0.005; HR 1.80; P<0.0001, respectively), TP53 mutation(HR 2.49; P=0.030; HR 2.13; P=0.005, respectively) and allo-HSCT(HR 0.52; P=0.040; HR 0.37; P<0.0001, respectively) retained the prognostic significance in both the normal karyotype and aberrant karyotype group. FAT1(HR 2.32; P=0.019), DNMT3A(HR 3.32; P=0.006) and IL-7R(HR 4.35; P=0.002) mutations were unfavorable factors for OS only in the normal karyotype group. Conclusion: FAT1, IL-7R and DNMT3A mutations pretict poor prognosis in MDS patients with normal karyotypes. Key words: Somatic mutation, Next-generation sequencing, Prognosis, Myelodysplastic syndrome Disclosures No relevant conflicts of interest to declare.

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Clinical Implications of Copy Number Alteration Detection Using Panel-Based Next-Generation Sequencing Data in Myelodysplastic Syndrome

10.21203/rs.3.rs-72329/v1 ◽

2020 ◽

Author(s):

Yoo-Jin Kim ◽

SeungHyun Jung ◽

Eun-Hye Hur ◽

Eun-Ji Choi ◽

Kyoo-Hyung Lee ◽

...

Keyword(s):

Next Generation Sequencing ◽

Myelodysplastic Syndrome ◽

Somatic Mutation ◽

Copy Number ◽

Somatic Mutations ◽

Clinical Implications ◽

Next Generation ◽

Clinical Variables ◽

Ngs Data ◽

Generation Sequencing

Abstract Background: Recent advancements in next-generation sequencing (NGS) technologies allow the simultaneous identification of targeted copy number alterations (CNAs) as well as somatic mutations using the same panel-based NGS data. We investigated whether CNAs detected by the targeted NGS data provided additional clinical implications, over somatic mutations, in myelodysplastic syndrome (MDS). Methods: Targeted deep sequencing of 28 well-known MDS-related genes was performed for 266 patients with MDS. Results: Overall, 215 (80.8%) patients were found to have at least one somatic mutation; 67 (25.2%) had at least one CNA; 227 (85.3%) had either a somatic mutation or CNA; 160 had somatic mutations without CNA; and 12 had CNA without somatic mutations. Considering the clinical variables and somatic mutations alone, multivariate analysis demonstrated that sex, revised International Prognostic Scoring System (IPSS-R) and NRAS and TP53 mutations were independent prognostic factors for overall survival. For AML-free survival, these factors were sex, IPSS-R, and mutations in NRAS, DNMT3A, and complex karyotype/TP53 mutations. When we consider clinical variables along with somatic mutations and CNAs, genetic alterations in TET2, LAMB4, U2AF1, and CBL showed additional significant impact on the survivals. Conclusions: Our study suggests that the concurrent detection of somatic mutations and targeted CNAs may provide clinically useful information for the prognosis of MDS patients.

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Spectrum of somatic mutations detected by targeted next-generation sequencing and their prognostic significance in adult patients with acute lymphoblastic leukemia

Journal of Hematology & Oncology ◽

10.1186/s13045-017-0431-1 ◽

2017 ◽

Vol 10 (1) ◽

Cited By ~ 11

Author(s):

Juan Feng ◽

Yan Li ◽

Yujiao Jia ◽

Qiuyun Fang ◽

Xiaoyuan Gong ◽

...

Keyword(s):

Next Generation Sequencing ◽

Acute Lymphoblastic Leukemia ◽

Somatic Mutations ◽

Lymphoblastic Leukemia ◽

Prognostic Significance ◽

Adult Patients ◽

Next Generation ◽

Targeted Next Generation Sequencing ◽

Generation Sequencing

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Comprehensive molecular screening by next generation sequencing reveals a distinctive mutational profile ofKIT/PDGFRAgenes and novel genomic alterations: results from a 20-year cohort of patients with GIST from north-western Greece

ESMO Open ◽

10.1136/esmoopen-2018-000335 ◽

2018 ◽

Vol 3 (3) ◽

pp. e000335 ◽

Cited By ~ 2

Author(s):

Leonidas Mavroeidis ◽

Vassiliki Metaxa-Mariatou ◽

Alexandra Papoudou-Bai ◽

Angeliki Maria Lampraki ◽

Lida Kostadima ◽

...

Keyword(s):

Next Generation Sequencing ◽

Growth Factor ◽

Poor Prognosis ◽

Prognostic Significance ◽

Growth Factor Receptor ◽

Next Generation ◽

Survival Difference ◽

North Western ◽

Generation Sequencing ◽

Western Greece

IntroductionGastrointestinal stromal tumours (GIST) are mesenchymal neoplasms that usually carry an activating mutation inKITor platelet-derived growth factor receptor alpha (PDGFRA) genes with predictive and prognostic significance. We investigated the extended mutational status of GIST in a patient population of north-western Greece in order to look at geopraphic/genotypic distinctive traits.Patient and methodsClinicopathological and molecular data of 38 patients diagnosed from 1996 to 2016 with GIST in the region of Epirus in Greece were retrospectively assessed. Formalin-fixed paraffin-embedded tumours were successfully analysed for mutations in 54 genes with oncogenic potential. Next generation sequencing was conducted by using the Ion AmpliSeqCancer Hotspot Panel V.2 for DNA analysis (Thermofisher Scientific).ResultsAmong 38 tumours, 24 (63.16%) and seven (18.42%) of the tumours harboured mutations in theKITandPDGFRAgenes, respectively, while seven (18.42%) tumours were negative for eitherKITorPDGFRAmutation. No mutations were detected in five (13.16%) cases. Concomitant mutations ofBRAFand fibroblast growth factor receptor 3 (FGFR3) genes were observed in two patients withKITgene mutation. Two patients withKIT/PDGFRAwild-type GIST had mutations in eitherKRASor phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) genes. There was no significant survival difference regarding the exonic site of mutation in eitherKITorPDGFRAgene. The presence of a mutation in pathway effectors downstream ofKITorPDGFRA, such asBRAF,KRASorPIK3CA, was associated with poor prognosis. Adverse prognosticators were also high mitotic index and the advanced disease status at diagnosis.ConclusionsWe report comparable incidence ofKITandPDGFRAmutation in patients with GIST from north-western Greece as compared with cohorts from other regions. Interestingly, we identified rare mutations onRAS,BRAFandPIK3CAgenes in patients with poor prognosis.

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Reevaluating the Role of Cytogenetic Testing in Patients with Suspected Myelodysplastic Syndrome in the Era of Next Generation Sequencing

Blood ◽

10.1182/blood-2019-128507 ◽

2019 ◽

Vol 134 (Supplement_1) ◽

pp. 3438-3438

Author(s):

Eri Kawata ◽

Anargyros Xenocostas ◽

Cyrus C. Hsia ◽

Alejandro Lazo-Langner ◽

Kang Howson-Jan ◽

...

Keyword(s):

Next Generation Sequencing ◽

Myelodysplastic Syndrome ◽

Board Of Directors ◽

Normal Karyotype ◽

Molecular Diagnostic ◽

Next Generation ◽

Abnormal Karyotype ◽

Advisory Committees ◽

Cytogenetic Testing ◽

Generation Sequencing

Background: In patients with suspected myelodysplastic syndrome (MDS), ancillary tests including cytogenetics (CG) and molecular diagnostics often support the diagnosis and add prognostic value guiding treatment decisions. Frequently, high-cost new technologies such as next generation sequencing (NGS) are added to the existing test menu without consideration for redundancy or added value. In our institution most patients with suspected MDS or cytopenias of undetermined origin will have conventional CG and NGS routinely ordered in addition to bone marrow (BM) morphology and flow cytometry (FCM). In a previous retrospective study, we evaluated combined NGS and CG in 120 patients and we found that our NGS panel had enhanced diagnostic and prognostic advantages over standard karyotyping. Based on these results, we undertook a quality improvement (QI) project to streamline molecular diagnostic testing, reduce test redundancy, turnaround time and cost. Methods: Between February and June 2019 we prospectively evaluated an "NGS first approach" to investigate patients with suspected MDS or cytopenias of undetermined origin. We assessed BM morphology, FCM, NGS testing (Oncomine Myeloid Research Assay, Thermo-Fisher) and CG for all patients. To assess whether BM aspirates can be used to triage appropriate use of NGS and CG, expert morphologists assigned BM samples to either the NGS/CG group or NGS only group, based exclusively on the presence of morphological abnormalities suggesting the possibility of an MDS. Results: We included 50 patients with suspected MDS or cytopenias of undetermined origin. Of these, 33 (66%) were triaged into the NGS/CG group and the remaining 17 (34%) into the NGS only group. In the NGS/CG group NGS testing revealed DNA mutations in 27 (81.8%) patients, whereas CG showed an abnormal karyotype in 12 (36.4%). Among the 21 patients with normal karyotype, NGS revealed mutations in 17 (81%). Two patients (6%) were identified as MDS by morphological examination and had an abnormal karyotype but negative NGS. Of those assigned to the NGS/CG group, 27 (81.8%) were morphologically diagnosed as either MDS (54.5%), acute myeloid leukemia (AML) (15.2%), MDS/myeloproliferative neoplasms (MPN) (6.1%), or therapy related myeloid neoplasms (t-MNs) - MDS/AML (6.1%). Among the patients assigned to the NGS only group, NGS testing showed no abnormalities in 16 (94.1%) patients. One patient was found to carry a BRAF mutation and subsequently diagnosed with hairy cell leukemia. CG testing showed a normal karyotype in 16 (94.1%) patients. One patient was found to carry an inv(2)(p11.2q13) and was diagnosed as clonal B cell lymphocytosis. Conclusion: We proposed and validated a testing algorithm based on an "NGS first approach" with CG restricted to patients with morphological changes suggestive of MDS, in order to reduce the number of samples karyotyped. Overall, in patients with a morphological diagnosis of MDS, NGS defined genetic abnormalities in more patients (84.2%) compared to CG (47.4%) alone. Additional cytogenetic testing only detected chromosomal abnormalities in less than 10% of MDS cases. Most importantly, nearly no mutations or CG abnormalities were detected in patients without dysplastic features. Based on these results we estimated that we could reduce karyotyping by 10% to 20% for patients presenting with probable MDS or cytopenias of undetermined origin using an "NGS first approach". Further studies are warranted to validate and provide cost saving estimates of this approach. Disclosures Hsia: Amgen: Honoraria; Jansen: Honoraria, Membership on an entity's Board of Directors or advisory committees; Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees; Pfizer: Membership on an entity's Board of Directors or advisory committees.

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