BRAF Mutations and Dysregulation of the MAP Kinase Pathway Associated to Sinonasal Mucosal Melanomas

Sinonasal mucosal melanoma (SNM) is a rare and aggressive type of melanoma, and because of this, we currently have a limited understanding of its genetic and molecular constitution. The incidence among SNMs of somatic mutations in the genes involved in the main molecular pathways, which have been largely associated with cutaneous melanoma, is not yet fully understood. Through a next-generation sequencing (NGS) approach using a panel of 25 genes involved in melanoma pathogenesis customized by our group, we performed a mutation analysis in a cohort of 25 SNM patients. Results showed that pathogenic mutations were found in more than 60% of SNM cases at a somatic level, with strikingly 32% of them carrying deleterious mutations in the BRAF gene. The identified mutations mostly lack the typical UV signature associated with cutaneous melanomas and showed no significant association with any histopathological parameter. Oncogenic activation of the BRAF-depending pathway, which may induce immune tolerance into the tumour microenvironment (i.e., by increasing the VEGF production) was poorly associated with mutations in genes that have been related to diminished clinical benefit of the treatment with BRAF inhibitors. Screening for mutations in BRAF and other MAPK genes should be included in the routine diagnostic test for a better classification of SNM patients.

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Next-Generation Sequencing Mutational Landscape and Clinical Features of Chinese Adults with Myeloproliferative Neoplasms

10.21203/rs.3.rs-483741/v1 ◽

2021 ◽

Author(s):

Shuna Luo ◽

Zanzan Wang ◽

Xiaofei Xu ◽

Lan Zhang ◽

Shengjie Wang ◽

...

Keyword(s):

Next Generation Sequencing ◽

Comprehensive Evaluation ◽

Myeloproliferative Neoplasms ◽

Primary Myelofibrosis ◽

Next Generation ◽

Chinese Adults ◽

Leukocyte Counts ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

Abstract Background: Myeloproliferative neoplasms (MPNs) include three classical subtypes: polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF). Since prefibrotic primary myelofibrosis (pre-PMF) was recognized as a separate entity in the 2016 revised classification of MPN, it has been a subject of debate among experts due to its indefinite diagnosis. However, pre-PMF usually has a distinct outcome compared with either ET or overt PMF. In this study, we examined the clinical, haematologic, genetic, and prognostic differences among pre-PMF, ET, and overt PMF.Methods: We retrospectively reviewed the clinical parameters, haematologic information, and genetic mutations of patients who were diagnosed with pre-PMF, ET, and overt PMF according to the WHO 2016 criteria using next-generation sequencing (NGS).Results: Pre-PMF patients exhibited higher leukocyte counts, higher LDH values, a higher frequency of splenomegaly, and a higher incidence of hypertension than ET patients. On the other hand, pre-PMF patients had higher platelet counts and haemoglobin levels than overt PMF patients. Molecular analysis revealed that the frequency of EP300 mutations was significantly increased in pre-PMF patients compared with ET and overt PMF patients. In terms of outcome, male sex, along with symptoms including MPN-10, anaemia, thrombocytopenia, and KMT2A and CUX1 mutations, indicated a poor prognosis for PMF patients.Conclusion: The results of this study indicated that comprehensive evaluation of BM features, clinical phenotypes, haematologic parameters, and molecular profiles is needed for the accurate diagnosis and treatment of ET, pre-PMF, and overt PMF patients.

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Nemaline myopathy: Next generation sequencing (NGS) significantly improving the molecular classification of Brazilian families

Neuromuscular Disorders ◽

10.1016/j.nmd.2015.06.364 ◽

2015 ◽

Vol 25 ◽

pp. S288

Author(s):

J. Gurgel-Giannetti ◽

M. Lazar ◽

R. Pavanello ◽

E. Concentino ◽

F. Fernandes ◽

...

Keyword(s):

Next Generation Sequencing ◽

Molecular Classification ◽

Nemaline Myopathy ◽

Next Generation ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

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A Framework for the RNA-Seq Based Classification and Prediction of Disease

10.20944/preprints201901.0068.v1 ◽

2019 ◽

Author(s):

Naiyar Iqbal ◽

Pradeep Kumar

Keyword(s):

Microarray Gene Expression Data ◽

Biological Data ◽

Disease Classification ◽

Rna Seq ◽

Microarray Gene Expression ◽

Early Detection Of Disease ◽

Medical Practitioners ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

Disease classification based on biological data is an important area in bioinformatics and biomedical research. It helps the doctors and medical practitioners for the early detection of disease and support them as a computer-aided diagnostic tool for accurate diagnosis, prognosis, and treatment of disease. Earlier Microarray gene expression data have wide application for the classification of disease, but now Next-generation sequencing (NGS) has replaced the Microarray technology. From the last few years, RNA sequence (RNA-Seq) data are widely used for the transcriptomic analysis. Hence, RNA-Seq based classification of disease is in its infancy. In this article, we present a general framework for the classification of disease constructed on RNA-Seq data. This framework will guide the researchers to process RNA-Seq, extract relevant features and apply the appropriate classifier to classify any kind of disease.

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Epithelioid Hyalinizing Sarcoma With MGA-NUTM1 Fusion

American Journal of Clinical Pathology ◽

10.1093/ajcp/aqaa113 ◽

2020 ◽

Vol 154 (6) ◽

pp. 859-866

Author(s):

Caroline I M Underwood ◽

Diana M Cardona ◽

Rex C Bentley ◽

Guomiao Shen ◽

Xiaojun Feng ◽

...

Keyword(s):

Soft Tissue ◽

Immunohistochemical Study ◽

Soft Tissue Sarcomas ◽

Soft Tissue Tumors ◽

Molecular Testing ◽

Molecular Alterations ◽

Poorly Differentiated ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

Abstract Objectives Soft tissue sarcomas are a group of tumors derived from the mesenchymal origin. Historically, they have been classified according to morphologic and immunohistochemical characteristics. The advent of multiplexed next-generation sequencing (NGS), specifically RNA sequencing, has modified the classification of such tumors and others by determining categorization based on molecular alterations. The NUTM1 rearrangement, previously thought to be present only in carcinomas, has recently been reported in poorly differentiated high-grade sarcomas of the soft tissue. We present the first reported case of an epithelioid hyalinizing sarcoma harboring the MGA-NUTM1 fusion in an acral site. Methods Histopathologic, immunohistochemical, and molecular testing were performed on resection tissue. Results Histologically, the tumor showed an epithelioid morphology with prominent background hyalinization. Immunohistochemically, the tumor expressed CD99 and nuclear NUT-1. By NGS the tumor harbors MGA-NUTM1 fusion. Conclusions Our findings support more extensive use of NGS for accurate sarcoma classification and identification of potential therapeutic targets. Furthermore, they corroborate the fact that NUTM1-rearranged soft tissue tumors represent a spectrum of heterogeneous morphologic entities. This case also highlights the utility of NUT-1 immunohistochemical study as a possible screening tool for NUTM1-fused sarcomas.

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NGS-Based Analysis of Atypical Deep Penetrating Nevi

Cancers ◽

10.3390/cancers13123066 ◽

2021 ◽

Vol 13 (12) ◽

pp. 3066

Author(s):

Antonella Manca ◽

Maria Cristina Sini ◽

Anna Maria Cesinaro ◽

Francesca Portelli ◽

Carmelo Urso ◽

...

Keyword(s):

Gene Mutations ◽

Metastatic Potential ◽

Idh1 Mutation ◽

Specific Gene ◽

Nodal Disease ◽

Architectural Features ◽

Frequent Mutations ◽

Map Kinase Pathway ◽

Kinase Pathway ◽

Generation Sequencing

Deep penetrating nevi (DPNs) are rare melanocytic neoplasms consisting of pigmented spindled or epithelioid melanocytes with a distinctive wedge-shaped configuration showing activation of the WNT pathway, with unusual cyto-architectural features. It is unclear whether they show a distinct genomic profile associated with a diverse metastatic potential. We describe herein a cohort of 21 atypical DPNs analyzed by next-generation sequencing using the Ion AmpliSeq™ Comprehensive Cancer Panel. We found that β-catenin exon 3 was mutated in 95% and MAP kinase pathway genes in 71% of the cases. Less frequent mutations were observed in HRAS (19%) and MAP2K1 (24%). Isocitrate dehydrogenases 1 (IDH1) mutations, including R132C, V178I, and S278L, were identified in 38% of cases and co-existed with BRAF/HRAS mutations. The only case with progressive nodal disease carried alterations in the β-catenin pathway and mutations in IDH1 and NRAS (codon 61). By a comprehensive mutation analysis, we found low genetic heterogeneity and a lack of significant associations between specific gene mutations and histopathological features, despite atypical features. Whether the acquisition of an NRAS or IDH1 mutation in an atypical DPN may represent a molecular evolution implying a pathway to melanoma progression should be confirmed in a larger series.

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Effect of matcha consumption on gut microbiota in healthy Japanese individuals: study protocol for a double-blind crossover interventional study

10.21203/rs.3.rs-391684/v1 ◽

2021 ◽

Author(s):

Maya Takegami ◽

Yoshitaka Hashimoto ◽

Tomoki Miyoshi ◽

Chihiro Munekawa ◽

Takashi Yoshimura ◽

...

Keyword(s):

Gut Microbiota ◽

Medical Information ◽

Intestinal Flora ◽

University Hospital ◽

Double Blind ◽

Before And After ◽

Next Generation Sequencing Ngs ◽

Sequence Similarities ◽

Generation Sequencing

Abstract Background: This study compares and clarifies the changes in intestinal flora resulting from the continuous consumption of two types of matcha.Methods: Healthy adults will consume two types of matcha tea for four weeks, and differences in the intestinal microflora before and after drinking will be compared. Gut microbiota will be identified using next-generation sequencing (NGS). Phylogenetic classification of the enterobacteria will be performed based on sequence similarities. The relative proportions of the classified enterobacteria to the total nucleotide sequences will be compared between the samples obtained from the two groups consuming different matcha.Discussion: The continuous consumption of matcha may improve dysbiosis and prevent atherosclerosis. The effects may vary according to the type of matcha used.Trial registration:The study was registered with university hospital medical information network (UMIN) (UMIN000040303), and all participants gave their written informed consent. Registered 1 November 2020, https://upload.umin.ac.jp/cgi-open-bin/ctr/ctr_view.cgi?recptno=R000045982.

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Classification of somatic variants in solid tumors detected by next-generation sequencing (NGS) and the need for clinical guidelines.

Journal of Clinical Oncology ◽

10.1200/jco.2014.32.15_suppl.1555 ◽

2014 ◽

Vol 32 (15_suppl) ◽

pp. 1555-1555

Author(s):

Antonios Papanicolau-Sengos ◽

Edward Hart ◽

Wei Shen ◽

Kenneth F. Grossmann ◽

Cecily Vaughn ◽

...

Keyword(s):

Next Generation Sequencing ◽

Solid Tumors ◽

Clinical Guidelines ◽

Next Generation ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

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SKAP2-BRAF fusion and response to an MEK inhibitor in a patient with metastatic melanoma resistant to immunotherapy

BMJ Case Reports ◽

10.1136/bcr-2020-238494 ◽

2021 ◽

Vol 14 (6) ◽

pp. e238494

Author(s):

Sonya Minmin Chew ◽

Mairi Lucas ◽

Michelle Brady ◽

Catherine Margaret Kelly

Keyword(s):

First Generation ◽

Mek Inhibitor ◽

Mitogen Activated Protein Kinase ◽

Unknown Primary ◽

Braf Inhibitors ◽

Mitogen Activated Protein ◽

Braf Fusion ◽

Kinase Pathway ◽

Generation Sequencing ◽

Dramatic Fall

A woman in her 40s presented to the emergency department with headache and unintentional weight loss in September 2018. Investigations revealed a widely metastatic pan-negative melanoma of unknown primary. She had multiple lines of treatment including combination immunotherapy and chemotherapy. Next-generation sequencing identified an SKAP2-BRAF fusion protein, and she was commenced on an MEK inhibitor in September 2019 with a partial response seen on restaging scans after 6 weeks and a dramatic fall in her lactate dehydrogenase from 2248 IU/L to 576 IU/L. Unfortunately, the response was not maintained and she died from progression of her cancer in January 2020. SKAP2-BRAF fusions have a dimerisation domain that paradoxically activates the mitogen-activated protein kinase pathway, resulting in hyperproliferation if first-generation or second-generation BRAF inhibitors are used. Our knowledge is limited regarding the complex effects of targeted therapy in rare BRAF fusion proteins.

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TERT Immunohistochemistry Expression as a Surrogate of TERT Promoter Mutations in Infiltrating Gliomas

American Journal of Clinical Pathology ◽

10.1093/ajcp/aqab191.303 ◽

2021 ◽

Vol 156 (Supplement_1) ◽

pp. S142-S142

Author(s):

A M Moosvi ◽

A Dono ◽

A Bellman ◽

L Ballester ◽

P Goli ◽

...

Keyword(s):

Sensitivity And Specificity ◽

Surrogate Marker ◽

Study Cohort ◽

Targeted Next Generation Sequencing ◽

Tert Promoter Mutations ◽

Next Generation Sequencing Ngs ◽

Promoter Mutations ◽

Generation Sequencing

Abstract Introduction/Objective Genomic alterations are critical for the diagnosis of infiltrating gliomas. Mutations in the telomerase reverse transcriptase promoter (TERTp) are sufficient for a diagnosis of glioblastoma in some cases, independent of histologic features. Although DNA sequencing is the preferred method for evaluating TERTp mutations, there are limitations with regards to turn-around-time, accessibility, and cost. In this study, we evaluated the efficacy of using TERT immunohistochemistry (IHC) as a surrogate marker for the identification of TERTp mutations in infiltrating gliomas. Methods/Case Report The study cohort consisted of 31 infiltrating gliomas diagnosed following the 2016 WHO classification of CNS tumors by a board-certified neuropathologist. Each case was evaluated by immunohistochemistry (anti-TERT monoclonal antibody) and with a targeted next-generation sequencing (NGS) panel. A systemic literature search was conducted to examine reports of TERT antibody as a surrogate marker of TERTp mutations. TERTp mutation detected by sequencing was considered the gold standard. Results (if a Case Study enter NA) TERT immunohistochemistry demonstrated a sensitivity of 61.1% and specificity of 69.2%. Cases were divided into IDH-WT and IDH-mutant infiltrating gliomas. Among the IDH-WT group, 84% contained the TERTp mutation with a sensitivity of 62.5% and specificity of 33.3% for the TERTp IHC. IDH-mutant gliomas showed a 16.2% TERTp mutation rate, and immunohistochemistry had a sensitivity of 50% and 80% specificity. The probability of TERT immunohistochemistry in diagnosing TERTp mutations exhibited a poor likelihood ratio for both the positive and negative test. Literature review included 5 studies with an overall sensitivity and specificity remaining consistently low (<80%), with 2 of these studies evaluating CNS related tumors giving rise to similar diagnostic performance. Conclusion TERT IHC has suboptimal sensitivity and specificity for identifying TERTp mutations in IDH-WT and IDH- mutant infiltrating gliomas.

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