scholarly journals 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 ◽  
2018 ◽  
Vol 3 (3) ◽  
pp. e000335 ◽  
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.

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

Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 44-45
Author(s):  
Xiangzong Zeng ◽  
Min Dai ◽  
Yu Zhang ◽  
Lingling Zhou ◽  
Ya Zhou ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Myelodysplastic Syndrome ◽  
Somatic Mutation ◽  
Poor Prognosis ◽  
Somatic Mutations ◽  
Prognostic Significance ◽  
Multivariable Analysis ◽  
Normal Karyotype ◽  
Next Generation ◽  
Generation Sequencing

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.

scholarly journals Genomics of medulloblastoma: from Giemsa-banding to next-generation sequencing in 20 years

2010 ◽  
Vol 28 (1) ◽  
pp. E6 ◽  
Author(s):  
Paul A. Northcott ◽  
James T. Rutka ◽  
Michael D. Taylor
Keyword(s):  
Next Generation Sequencing ◽  
Molecular Mechanisms ◽  
Genomic Medicine ◽  
Prognostic Significance ◽  
Next Generation ◽  
Sequencing Technologies ◽  
Disease Stratification ◽  
Insight Into ◽  
Generation Sequencing

Advances in the field of genomics have recently enabled the unprecedented characterization of the cancer genome, providing novel insight into the molecular mechanisms underlying malignancies in humans. The application of high-resolution microarray platforms to the study of medulloblastoma has revealed new oncogenes and tumor suppressors and has implicated changes in DNA copy number, gene expression, and methylation state in its etiology. Additionally, the integration of medulloblastoma genomics with patient clinical data has confirmed molecular markers of prognostic significance and highlighted the potential utility of molecular disease stratification. The advent of next-generation sequencing technologies promises to greatly transform our understanding of medulloblastoma pathogenesis in the next few years, permitting comprehensive analyses of all aspects of the genome and increasing the likelihood that genomic medicine will become part of the routine diagnosis and treatment of medulloblastoma.

scholarly journals Formalin-Fixed and Paraffin-Embedded Samples for Next Generation Sequencing: Problems and Solutions

Genes ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1472
Author(s):  
Gerardo Cazzato ◽  
Concetta Caporusso ◽  
Francesca Arezzo ◽  
Antonietta Cimmino ◽  
Anna Colagrande ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Genetic Material ◽  
Growth Factor Receptor ◽  
Acid Extraction ◽  
Nucleotide Polymorphisms ◽  
Next Generation ◽  
Tissue Samples ◽  
Dna And Rna ◽  
Sequencing Problems ◽  
Generation Sequencing

Over the years, increasing information has been asked of the pathologist: we have moved from a purely morphological diagnosis to biomolecular and genetic studies, which have made it possible to implement the use of molecular targeted therapies, such as anti-epidermal growth factor receptor (EGFR) molecules in EGFR-mutated lung cancer, for example. Today, next generation sequencing (NGS) has changed the approach to neoplasms, to the extent that, in a short time, it has gained a place of absolute importance and diagnostic, prognostic and therapeutic utility. In this scenario, formaldehyde-fixed and paraffin-embedded (FFPE) biological tissue samples are a source of clinical and molecular information. However, problems can arise in the genetic material (DNA and RNA) for use in NGS due to fixation, and work is being devoted to possible strategies to reduce its effects. In this paper, we discuss the applications of FFPE tissue samples in the execution of NGS, we focus on the problems arising with the use of this type of material for nucleic acid extraction and, finally, we consider the most useful strategies to prevent and reduce single nucleotide polymorphisms (SNV) and other fixation artifacts.

Two-Year Experience of Performing a Next-Generation-Sequencing Based Panel Test in an Academic Medical Center and Its Clinical Impact

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 1707-1707 ◽  
Author(s):  
Kuo Frank ◽  
Jon C. Aster ◽  
Coleman Lindsley
Keyword(s):  
Next Generation Sequencing ◽  
Academic Medical Center ◽  
Prognostic Significance ◽  
Turnaround Time ◽  
Genetic Alterations ◽  
Splenic Marginal Zone Lymphoma ◽  
Next Generation ◽  
Lymphoid Malignancies ◽  
Myeloid Neoplasm ◽  
Generation Sequencing

Abstract Our ability to interrogate a broad array of genetic alterations in myeloid neoplasm has increased significantly with the advance in next-generation sequencing (NGS). In addition to morphologic examination, flow cytometry and cytogenetics, NGS-based testing can add additional useful information to the diagnostic workup. With improved turnaround time, decreasing costs and an expanding knowledge of the therapeutic and prognostic significance of the detected variants, NGS-based panel testing has increasingly played a major role in the management of patients with myeloid neoplasm. Rapid Heme Panel (RHP) is a custom, 95-gene, amplicon-based NGS panel (PMID: 27339098) that was launched at the Center for Advanced Molecular Diagnostics (CAMD), Brigham and Women's Hospital and Dana-Farber Cancer Institute in August of 2014. RHP covers a total territory of ~200 KB, including hotspots of oncogenes and whole coding exons of tumor suppressor genes that are frequently mutated in myeloid and lymphoid malignancies. Single nucleotide variants, insertions/deletions up to 52-bp, and copy number variations are detected. In the two years following its launch, over 5,000 RHP was performed and reported with an average turnaround time of 7.2 days from time of receipt into the lab. The specimen failed rate is <0.5% and sample repeat rate is <0.2%. Over half of the specimens came from patients with a known myeloid disease: 25% with acute leukemia, 15% with a myelodysplastic syndrome (MDS), 10% with a myeloproliferative neoplasm (MPN) and a minor fraction each with a variety of other myeloid neoplasms such as paroxysmal nocturnal hemoglobinuria (PNH), aplastic anemia, systemic mastocytosis or chronic myeloid leukemia (CML). Twenty percent of the specimens came from patients with known lymphoid malignancies such as hairy cell leukemia, chronic lymphocytic leukemia, lymphoplasmacytic lymphoma, or splenic marginal zone lymphoma. The remainder 25-30% of the specimens came from patients with abnormal blood count (CBC) such as anemia, neutropenia, thrombocytopenia, leukocytosis, thrombocytosis and/or abnormal serum protein electrophoresis (SPEP) where a myeloid or a lymphoid neoplasm was suspected. Greater than 98% of the time, the test was ordered by a hematologist/oncologist. Among patients with a prior diagnosis, >80% of them had at least one pathogenic alterations identified by RHP while about 30% of the patients with abnormal CBC or abnormal SPEP had positive findings. RHP results have been used to (1) provide eligibility for enrollment into clinical trials of targeted therapies; (2) monitor effect of therapy by quantifying variant allele fraction; (3) identify disease progression with detection of emergence of new variants; (4) evaluate post-transplant status by following allele fractions of pre-transplant pathogenic variants; (5) shorten the time and cost to diagnosis by establishing clonality and identification of disease-defining alterations. Disclosures No relevant conflicts of interest to declare.

scholarly journals Genetic mapping of pancreatic cancer by targeted next-generation sequencing in a cohort of patients managed with nab-paclitaxel-based chemotherapy or agents targeting the EGFR axis: a retrospective analysis of the Hellenic Cooperative Oncology Group (HeCOG)

ESMO Open ◽  
2019 ◽  
Vol 4 (5) ◽  
pp. e000525 ◽  
Author(s):  
George Zarkavelis ◽  
Vassiliki Kotoula ◽  
Georgia-Angeliki Kolliou ◽  
Kyriaki Papadopoulou ◽  
Ioannis Tikas ◽  
...  
Keyword(s):  
Pancreatic Cancer ◽  
Next Generation Sequencing ◽  
Patient Population ◽  
Growth Factor Receptor ◽  
Gene Mutations ◽  
Next Generation ◽  
Pancreatic Tumours ◽  
Targeted Next Generation Sequencing ◽  
Dismal Prognosis ◽  
Generation Sequencing

Pancreatic cancer is one of the most fatal malignancies ranking fourth among the leading causes of cancer death with diagnosis at late stages carrying a dismal prognosis. The aim of our retrospective study was to describe the nature and the incidence of gene mutations and genomic instability in advanced pancreatic adenocarcinomas of a Greek patient population fully annotated with clinicopathological data. We used a targeted next-generation sequencing (NGS) panel encompassing genes commonly mutated in pancreatic tumours in a patient population managed with either nab-paclitaxel regimens or targeted compounds modulating the epidermal growth factor receptor (EGFR)/AKT/mTOR axis. We identified KRAS, TP53, SMAD4 and CDKN2A as being the most prevalent mutations in the study population with the exception of an intriguingly lower incidence regarding KRAS mutants. Homologous recombination gene mutations were found to be mutually exclusive with CDKN2A mutations. The coexistence of both KRAS and TP53 mutation seems to adversely affect the outcome of the patients whether treated with targeted therapy against EGFR/Akt/mTOR axis or cytotoxic drugs. The poor prognosis observed, correlated to late presentation, specific molecular mutations and to high mutational load warrant prospective validating studies and research into the mechanistic pathophysiology of pancreatic tumours for more effective therapeutic targeting.

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