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Diagnostics
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Next-Generation Sequencing in Tumor Diagnosis and Treatment
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Next-Generation Sequencing in Tumor Diagnosis and Treatment

A special issue of Diagnostics (ISSN 2075-4418). This special issue belongs to the section "Pathology and Molecular Diagnostics".

Deadline for manuscript submissions: closed (31 May 2020) | Viewed by 23994

Special Issue Editors

Dr. Dario De Biase

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Guest Editor
Department of Pharmacy and Biotechnology, University of Bologna, Viale Ercolani 4/2, S. Orsola Hospital, Bologna, Italy
Interests: next-generation sequencing; predictive markers in solid tumors; molecular pathology
Special Issues, Collections and Topics in MDPI journals
Dr. Umberto Malapelle

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Guest Editor
Department of Public Health, University of Naples Federico II, Naples, Italy
Interests: predictive molecular pathology in solid tumors; next generation technologies in molecular biology; liquid biopsies; predictive oncology
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Matteo Fassan

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Guest Editor
Department of Medicine, Surgical Pathology Unit, University of Padua, Padua, Italy
Interests: gastrointestinal pathology; molecular pathology; preinvasive lesions; biomarkers
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Next-Generation Sequencing (NGS) allows for the sequencing of multiple genes at a very high depth of coverage. The principle of targeted therapy consists in the application of drugs targeted against well-defined molecules that play a key role in tumor progression and/or survival. Considering the continuous discovery of new molecules as a putative target or that are responsible for treatment resistance mechanisms, single-gene diagnostics is becoming less effective. Nowadays, precision medicine requires multigene characterization. The introduction of NGS to molecular diagnostics has allowed us to combine high analytical sensitivity with multigene analysis. The aim of this Special Issue is to focus on the application of NGS in characterizing molecular alterations in solid tumors for diagnostic, prognostic, or predictive purposes. We invite researchers and authors to submit original research on the application of NGS in the characterization of molecular alterations in solid tumors. Review articles that describe the state-of-the-art on this topic are also encouraged.

Dr. Dario de Biase
Dr. Umberto Malapelle
Prof. Matteo Fassan
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Diagnostics is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • next generation sequencing
  • lung tumors
  • brain tumors
  • pancreatic tumors
  • liquid biopsy
  • thyroid tumors
  • colorectal carcinomas
  • melanoma
  • molecular techniques.

Related Special Issue

Published Papers (7 papers)

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Editorial

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3 pages, 153 KiB  
Editorial
Next-Generation Sequencing in Tumor Diagnosis and Treatment
by Dario de Biase, Matteo Fassan and Umberto Malapelle
Diagnostics 2020, 10(11), 962; https://doi.org/10.3390/diagnostics10110962 - 17 Nov 2020
Cited by 9 | Viewed by 1969
Abstract
Next-Generation Sequencing (NGS) allows for the sequencing of multiple genes at a very high depth of coverage [...] Full article
(This article belongs to the Special Issue Next-Generation Sequencing in Tumor Diagnosis and Treatment)

Research

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17 pages, 1453 KiB  
Article
Molecular Diagnostic of Solid Tumor Using a Next Generation Sequencing Custom-Designed Multi-Gene Panel
by Dario de Biase, Giorgia Acquaviva, Michela Visani, Viviana Sanza, Chiara M. Argento, Antonio De Leo, Thais Maloberti, Annalisa Pession and Giovanni Tallini
Diagnostics 2020, 10(4), 250; https://doi.org/10.3390/diagnostics10040250 - 23 Apr 2020
Cited by 41 | Viewed by 4118
Abstract
Next generation sequencing (NGS) allows parallel sequencing of multiple genes at a very high depth of coverage. The need to analyze a variety of targets for diagnostic/prognostic/predictive purposes requires multi-gene characterization. Multi-gene panels are becoming standard approaches for the molecular analysis of solid [...] Read more.
Next generation sequencing (NGS) allows parallel sequencing of multiple genes at a very high depth of coverage. The need to analyze a variety of targets for diagnostic/prognostic/predictive purposes requires multi-gene characterization. Multi-gene panels are becoming standard approaches for the molecular analysis of solid lesions. We report a custom-designed 128 multi-gene panel engineered to cover the relevant targets in 22 oncogene/oncosuppressor genes for the analysis of the solid tumors most frequently subjected to routine genotyping. A total of 1695 solid tumors were analyzed for panel validation. The analytical sensitivity is 5%. Analytical validation: (i) Accuracy: sequencing results obtained using the multi-gene panel are concordant using two different NGS platforms and single-gene approach sequencing (100% of 83 cases); (ii) Precision: consistent results are obtained in the samples analyzed twice with the same platform (100% of 20 cases). Clinical validation: the frequency of mutations identified in different tumor types is consistent with the published literature. This custom-designed multi-gene panel allows to analyze with high sensitivity and throughput 22 oncogenes/oncosuppressor genes involved in diagnostic/prognostic/predictive characterization of central nervous system tumors, non-small-cell lung carcinomas, colorectal carcinomas, thyroid nodules, pancreatic lesions, melanoma, oral squamous carcinomas and gastrointestinal stromal tumors. Full article
(This article belongs to the Special Issue Next-Generation Sequencing in Tumor Diagnosis and Treatment)
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17 pages, 2766 KiB  
Article
Identification of the Potential Prognostic Markers from the miRNA-lncRNA-mRNA Interactions for Metastatic Renal Cancer via Next-Generation Sequencing and Bioinformatics
by I-Jeng Yeh, Kuan-Ting Liu, Jheng-Heng Shen, Yen-Hung Wu, Yao-Hua Liu, Meng-Chi Yen and Po-Lin Kuo
Diagnostics 2020, 10(4), 228; https://doi.org/10.3390/diagnostics10040228 - 16 Apr 2020
Cited by 13 | Viewed by 2808
Abstract
The survival rate in patients with metastatic renal cell carcinoma (RCC) is low. In addition, metastatic RCC resists traditional treatment. Therefore, identification of novel biomarkers, signaling pathways, and therapeutic targets is an important issue. The aim of the present study is to identify [...] Read more.
The survival rate in patients with metastatic renal cell carcinoma (RCC) is low. In addition, metastatic RCC resists traditional treatment. Therefore, identification of novel biomarkers, signaling pathways, and therapeutic targets is an important issue. The aim of the present study is to identify novel prognostic markers from the miRNA-mediated network for the regulation of metastasis of RCC. To address this issue, the RNA of human RCC cell lines, 786-O and ACHN, derived from primary and metastatic sites, respectively, were collected and subjected to RNA sequencing and small RNA sequencing. The bioinformatic analysis revealed that the pathways of the genes with different expressions were related to tumor progression, and identified miRNA and miRNA-long non-coding RNA (lncRNA) interactions, and mRNA. The results revealed that the expressions of seven miRNAs were associated with the overall survival rate of patients with RCC. Furthermore, the expressions of two lncRNA and three protein-coding genes (mRNA) were significantly associated with the increased or decreased disease-free survival rate. Although the detailed regulatory mechanism between miRNAs and targeted genes was not fully understood, our findings present novel prognostic markers and novel insight on miRNA-mediated pathways for metastatic RCC. Full article
(This article belongs to the Special Issue Next-Generation Sequencing in Tumor Diagnosis and Treatment)
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11 pages, 769 KiB  
Article
High Genetic Diversity and No Evidence of Clonal Relation in Synchronous Thyroid Carcinomas Associated with Hashimoto’s Thyroiditis: A Next-Generation Sequencing Analysis
by Csaba Molnár, Emese Sarolta Bádon, Attila Mokánszki, Anikó Mónus, Lívia Beke, Ferenc Győry, Endre Nagy and Gábor Méhes
Diagnostics 2020, 10(1), 48; https://doi.org/10.3390/diagnostics10010048 - 17 Jan 2020
Cited by 6 | Viewed by 2895
Abstract
The close association between pre-existing Hashimoto’s thyroiditis and thyroid cancer is well established. The simultaneous occurrence of multiple neoplastic foci within the same organ suggests a common genotoxic effect potentially contributing to carcinogenesis, the nature of which is still not clear. Next-generation sequencing [...] Read more.
The close association between pre-existing Hashimoto’s thyroiditis and thyroid cancer is well established. The simultaneous occurrence of multiple neoplastic foci within the same organ suggests a common genotoxic effect potentially contributing to carcinogenesis, the nature of which is still not clear. Next-generation sequencing (NGS) provides a potent tool to demonstrate and compare the mutational profile of the independent neoplastic foci. Our collection of 47 cases with thyroid carcinoma and Hashimoto’s thyroiditis included 14 with at least two tumorous foci. Detailed histological analysis highlighted differences in histomorphology, immunoprofile, and biological characteristics. Further, a 67-gene NGS panel was applied to demonstrate the mutational diversity of the synchronic tumors. Significant differences could be detected with a wide spectrum of pathogenic gene variants involved (ranging between 5 and 18, cutoff >5.0 variant allele frequencies (VAF)). Identical gene variants represented in both synchronous tumors of the same thyroid gland were found in only two cases (BRAF and JAK3 genes). An additional set of major driver mutations was identified at variable allele frequencies in a highly individual setup suggesting a clear clonal independence. The different BRAF statuses in coincident thyroid carcinoma foci within the same organ outline a special challenge for molecular follow-up and therapeutic decision-making. Full article
(This article belongs to the Special Issue Next-Generation Sequencing in Tumor Diagnosis and Treatment)
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8 pages, 15377 KiB  
Communication
First Glance of Molecular Profile of Atypical Cellular Angiofibroma/Cellular Angiofibroma with Sarcomatous Transformation by Next Generation Sequencing
by Yi-Che Chang Chien, Attila Mokánszki, Hsuan-Ying Huang, Raimundo Geronimo Silva, Jr., Chien-Chin Chen, Lívia Beke, Anikó Mónus and Gábor Méhes
Diagnostics 2020, 10(1), 35; https://doi.org/10.3390/diagnostics10010035 - 09 Jan 2020
Cited by 5 | Viewed by 3313
Abstract
Cellular angiofibroma is a rare benign mesenchymal neoplasm most commonly occurring in the vulvovaginal region in women and the inguinoscrotal region in men with specific genetic deletion involved in the RB1 gene in chromosome 13q14 region. Atypical cellular angiofibroma and cellular angiofibroma with [...] Read more.
Cellular angiofibroma is a rare benign mesenchymal neoplasm most commonly occurring in the vulvovaginal region in women and the inguinoscrotal region in men with specific genetic deletion involved in the RB1 gene in chromosome 13q14 region. Atypical cellular angiofibroma and cellular angiofibroma with sarcomatous transformation are recently described variants showing worrisome morphological features and strong, diffuse p16 expression. Nevertheless, the molecular profile of these tumor entities is largely unknown. We carried out a next generation sequencing (NGS) study from six cases of atypical cellular angiofibroma and cellular angiofibroma with sarcomatous transformation. We were able to identify oncogenic TP53 gene mutations (33%) which may contribute to pathogenesis also resulting in p16 overexpression. In addition, RB1 gene alterations generally present were identified. Since it is a recently described and rare entity, the whole molecular signaling pathway is still largely obscured and the analysis of larger cohorts is needed to elucidate this issue. Full article
(This article belongs to the Special Issue Next-Generation Sequencing in Tumor Diagnosis and Treatment)
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17 pages, 729 KiB  
Article
A Hierarchical Machine Learning Model to Discover Gleason Grade-Specific Biomarkers in Prostate Cancer
by Osama Hamzeh, Abedalrhman Alkhateeb, Julia Zhuoran Zheng, Srinath Kandalam, Crystal Leung, Govindaraja Atikukke, Dora Cavallo-Medved, Nallasivam Palanisamy and Luis Rueda
Diagnostics 2019, 9(4), 219; https://doi.org/10.3390/diagnostics9040219 - 11 Dec 2019
Cited by 27 | Viewed by 4351
Abstract
(1) Background:One of the most common cancers that affect North American men and men worldwide is prostate cancer. The Gleason score is a pathological grading system to examine the potential aggressiveness of the disease in the prostate tissue. Advancements in computing and next-generation [...] Read more.
(1) Background:One of the most common cancers that affect North American men and men worldwide is prostate cancer. The Gleason score is a pathological grading system to examine the potential aggressiveness of the disease in the prostate tissue. Advancements in computing and next-generation sequencing technology now allow us to study the genomic profiles of patients in association with their different Gleason scores more accurately and effectively. (2) Methods: In this study, we used a novel machine learning method to analyse gene expression of prostate tumours with different Gleason scores, and identify potential genetic biomarkers for each Gleason group. We obtained a publicly-available RNA-Seq dataset of a cohort of 104 prostate cancer patients from the National Center for Biotechnology Information’s (NCBI) Gene Expression Omnibus (GEO) repository, and categorised patients based on their Gleason scores to create a hierarchy of disease progression. A hierarchical model with standard classifiers in different Gleason groups, also known as nodes, was developed to identify and predict nodes based on their mRNA or gene expression. In each node, patient samples were analysed via class imbalance and hybrid feature selection techniques to build the prediction model. The outcome from analysis of each node was a set of genes that could differentiate each Gleason group from the remaining groups. To validate the proposed method, the set of identified genes were used to classify a second dataset of 499 prostate cancer patients collected from cBioportal. (3) Results: The overall accuracy of applying this novel method to the first dataset was 93.3%; the method was further validated to have 87% accuracy using the second dataset. This method also identified genes that were not previously reported as potential biomarkers for specific Gleason groups. In particular, PIAS3 was identified as a potential biomarker for Gleason score 4 + 3 = 7, and UBE2V2 for Gleason score 6. (4) Insight: Previous reports show that the genes predicted by this newly proposed method strongly correlate with prostate cancer development and progression. Furthermore, pathway analysis shows that both PIAS3 and UBE2V2 share similar protein interaction pathways, the JAK/STAT signaling process. Full article
(This article belongs to the Special Issue Next-Generation Sequencing in Tumor Diagnosis and Treatment)
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Other

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6 pages, 2305 KiB  
Brief Report
From Targeting Somatic Mutations to Finding Inherited Cancer Predispositions: The Other Side of the Coin
by Pascal Pujol, Thibault De La Motte Rouge and Frédérique Penault-Llorca
Diagnostics 2019, 9(3), 83; https://doi.org/10.3390/diagnostics9030083 - 26 Jul 2019
Cited by 6 | Viewed by 3775
Abstract
The expanding use of tumor genome analysis by next generation sequencing to drive target therapies has led to increased germline findings in genes predisposing to hereditary cancer. These putative germline findings obtained from theranostic analyses, such as BRCA1/2 gene testing, large panels, whole-exome, [...] Read more.
The expanding use of tumor genome analysis by next generation sequencing to drive target therapies has led to increased germline findings in genes predisposing to hereditary cancer. These putative germline findings obtained from theranostic analyses, such as BRCA1/2 gene testing, large panels, whole-exome, or whole-genome sequencing, need to be managed carefully and in an anticipated way with the patient. Before the genetic analysis of a tumor, specific information should be given to patients, who should be aware that the results may have extra-therapeutic medical issues for themselves and relatives. We previously published a list of 36 actionable genes predisposing to cancer for which informing the patient is recommended prior to pangenomic germline analysis because of available screening or preventive strategies. Here, we report clinical practice considerations and schemes for managing germline findings in tumor analyses, including written informed consent and a multidisciplinary approach involving an oncologist, molecular biologist/pathologist, and geneticist in case of germline findings. A somatic result showing a deleterious mutation in a known predisposing gene in a patient who has consented to this purpose should result in referral to a geneticist who is part of the multidisciplinary team. At any time of the somatic analysis process, the patient may have access to a geneticist consultation if additional information is required. This framework will optimally manage both personalized theranostic issues and specific preventive strategies for individuals and relatives; it will also simplify and accelerate the process of genetic testing. Full article
(This article belongs to the Special Issue Next-Generation Sequencing in Tumor Diagnosis and Treatment)
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