scholarly journals Genetic alterations of early-stage breast cancers by next-generation sequencing (NGS)

2018 ◽  
Vol 29 ◽  
pp. viii67
Author(s):  
Y. Xu ◽  
M. Zhang ◽  
R. Chen ◽  
X. Xia
Keyword(s):  
Next Generation Sequencing ◽  
Early Stage ◽  
Genetic Alterations ◽  
Breast Cancers ◽  
Next Generation ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

scholarly journals Microbiome Analysis of Biofilms of Silver Nanoparticle-Dispersed Silane-Based Coated Carbon Steel Using a Next-Generation Sequencing Technique

Antibiotics ◽  
2018 ◽  
Vol 7 (4) ◽  
pp. 91 ◽  
Author(s):  
Akiko Ogawa ◽  
Keito Takakura ◽  
Katsuhiko Sano ◽  
Hideyuki Kanematsu ◽  
Takehiko Yamano ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Silver Nanoparticle ◽  
Biofilm Formation ◽  
Early Stage ◽  
Biofilm Reactor ◽  
Next Generation ◽  
Microbiome Analysis ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Closed Laboratory

Previously, we demonstrated that silver nanoparticle-dispersed silane-based coating could inhibit biofilm formation in conditions where seawater was used as a bacterial source and circulated in a closed laboratory biofilm reactor. However, it is still unclear whether the microbiome of a biofilm of silver nanoparticle-dispersed silane-based coating samples (Ag) differs from that of a biofilm of non-dispersed silane-based coating samples (Non-Ag). This study aimed to perform a microbiome analysis of the biofilms grown on the aforementioned coatings using a next-generation sequencing (NGS) technique. For this, a biofilm formation test was conducted by allowing seawater to flow through a closed laboratory biofilm reactor; subsequently, DNAs extracted from the biofilms of Ag and Non-Ag were used to prepare 16S rRNA amplicon libraries to analyze the microbiomes by NGS. Results of the operational taxonomy unit indicated that the biofilms of Non-Ag and Ag comprised one and no phyla of archaea, respectively, whereas Proteobacteria was the dominant phylum for both biofilms. Additionally, in both biofilms, Non-Ag and Ag, Marinomonas was the primary bacterial group involved in early stage biofilm formation, whereas Anaerospora was primarily involved in late-stage biofilm formation. These results indicate that silver nanoparticles will be unrelated to the bacterial composition of biofilms on the surface of silane-based coatings, while they control biofilm formation there.

scholarly journals The Application of Next-Generation Sequencing to Define Factors Related to Oral Cancer and Discover Novel Biomarkers

Life ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 228
Author(s):  
Soyeon Kim ◽  
Joo Won Lee ◽  
Young-Seok Park
Keyword(s):  
Next Generation Sequencing ◽  
Oral Cancer ◽  
Genetic Alterations ◽  
Eligibility Criterion ◽  
Next Generation ◽  
Novel Biomarkers ◽  
Targeted Gene Therapy ◽  
Next Generation Sequencing Ngs ◽  
Potential Use ◽  
Generation Sequencing

Despite the introduction of next-generation sequencing in the realm of DNA sequencing technology, it is not often used in the investigation of oral squamous cell carcinoma (OSCC). Oral cancer is one of the most frequently occurring malignancies in some parts of the world and has a high mortality rate. Patients with this malignancy are likely to have a poor prognosis and may suffer from severe facial deformity or mastication problems even after successful treatment. Therefore, a thorough understanding of this malignancy is essential to prevent and treat it. This review sought to highlight the contributions of next-generation sequencing (NGS) in unveiling the genetic alterations and differential expressions of miRNAs involved in OSCC progression. By applying an appropriate eligibility criterion, we selected relevant studies for review. Frequently identified mutations in genes such as TP53, NOTCH1, and PIK3CA are discussed. The findings of existing miRNAs (e.g., miR-21) as well as novel discoveries pertaining to OSCC are also covered. Lastly, we briefly mention the latest findings in targeted gene therapy and the potential use of miRNAs as biomarkers. Our goal is to encourage researchers to further adopt NGS in their studies and give an overview of the latest findings of OSCC treatment.

scholarly journals Next-Generation Sequencing Improves Diagnosis, Prognosis and Clinical Management of Myeloid Neoplasms

Cancers ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 1364 ◽  
Author(s):  
Diego Carbonell ◽  
Julia Suárez-González ◽  
María Chicano ◽  
Cristina Andrés-Zayas ◽  
Juan Carlos Triviño ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Copy Number Variants ◽  
Genetic Alterations ◽  
Next Generation ◽  
Pathogenic Variants ◽  
Myeloid Neoplasms ◽  
Diagnostic Samples ◽  
Gene Panels ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Molecular diagnosis of myeloid neoplasms (MN) is based on the detection of multiple genetic alterations using various techniques. Next-generation sequencing (NGS) has been proved as a useful method for analyzing many genes simultaneously. In this context, we analyzed diagnostic samples from 121 patients affected by MN and ten relapse samples from a subset of acute myeloid leukemia patients using two enrichment-capture NGS gene panels. Pathogenicity classification of variants was enhanced by the development and application of a custom onco-hematology score. A total of 278 pathogenic variants were detected in 84% of patients. For structural alterations, 82% of those identified by cytogenetics were detected by NGS, 25 of 31 copy number variants and three out of three translocations. The detection of variants using NGS changed the diagnosis of seven patients and the prognosis of 15 patients and enabled us to identify 44 suitable candidates for clinical trials. Regarding AML, six of the ten relapsed patients lost or gained variants, comparing with diagnostic samples. In conclusion, the use of NGS panels in MN improves genetic characterization of the disease compared with conventional methods, thus demonstrating its potential clinical utility in routine clinical testing. This approach leads to better-adjusted treatments for each patient.

scholarly journals Targeted Next-Generation Sequencing Analysis for Recurrence in Early-Stage Lung Adenocarcinoma

2020 ◽  
Author(s):  
In Ae Kim ◽  
Jae Young Hur ◽  
Hee Joung Kim ◽  
Jung Hoon Park ◽  
Jae Joon Hwang ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Lung Adenocarcinoma ◽  
Egfr Mutation ◽  
Early Stage ◽  
Genetic Alterations ◽  
Smoking History ◽  
Next Generation ◽  
Targeted Next Generation Sequencing ◽  
Targeted Ngs ◽  
Generation Sequencing

Abstract Background Despite surgical resection, early lung adenocarcinoma has a recurrence rate of 20–50%. No clear predictive markers for recurrence of early lung adenocarcinoma are available. Targeted next-generation sequencing (NGS) is rarely used to identify recurrence-related genes. We aimed to identify genetic alterations that can predict recurrence, by comparing the molecular profiles of patient groups with and without recurrence. Methods Tissues from 230 patients with resected stage I–II lung adenocarcinoma (median follow-up: 49 months) were analyzed via targeted NGS for 207 cancer-related genes. The recurrence-free survival according to the number and type of mutation was estimated using the Kaplan–Meier method. Independent predictive biomarkers related to recurrence were identified using the Cox proportional hazards model. Results Recurrence was observed in 64 patients (27.8%). In multivariate analysis adjusted for age, sex, smoking history, stage, surgical mode, and visceral pleural invasion, the CTNNB1 mutation and fusion genes (ALK, ROS1, RET) were negative prognostic factors for recurrence in early-stage lung adenocarcinoma (HR 4.47, p = 0.001; HR 2.73, p = 0.009). EGFR mutation was a favorable factor (HR 0.51, p = 0.016), but the CTNNB1/EGFR co-mutations were negative predictors (HR 19.2, p < 0.001). TP53 mutation was a negative predictor compared with EGFR mutation for recurrence (HR 5.24, p = 0.02). Conclusions: Targeted NGS can provide valuable information to predict recurrence and identify patients at high recurrence risk, facilitating selection of the treatment strategy among close monitoring and adjuvant-targeted therapy. Larger datasets are required to validate these findings.

SWI/SNF complex subunit aberrations in diverse cancers: Next-generation sequencing of 539 patients.

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. 2588-2588 ◽  
Author(s):  
Roman Groisberg ◽  
David S. Hong ◽  
Filip Janku ◽  
Yunfang Jiang ◽  
ChongJuan Wei ◽  
...  
Keyword(s):  
Colon Cancer ◽  
Next Generation Sequencing ◽  
Early Stage ◽  
Phase 1 ◽  
Performance Status ◽  
Genetic Alterations ◽  
Age At Diagnosis ◽  
Targeted Agents ◽  
Next Generation ◽  
Generation Sequencing

2588 Background: The SWI/SNF complex is an ATP-dependent chromatin remodeler that is enriched at promoters and enhancers of active genes. It has been implicated as both an oncogene and tumor suppressor. Specific subunit mutations have even been associated with specific cancers with increased PRC2 component EZH2 activity. EZH2/ EED inhibitors are in early stage development to target SWI/SNF complex. Methods: We analyzed 539 consecutive patients with diverse malignancies who were referred for Phase 1 clinical trials and had CLIA certified targeted next-generation sequencing (Foundation one) for presence of aberrations in SWI/SNF complex genes (ARID1A, ARID2, PBRM1, SMARCA4, SMARCB1). Patient charts were reviewed for general demographics (sex, age at diagnosis and death, performance status), tumor histology, stage, metastatic sites, treatment history, outcomes and co-occurring alterations. Results: Fifty patients had mutations in SWI/SNF subunits. Median age at diagnosis was 56 (14-79 years) and M:F ratio 21:29. Kidney, colorectal, ovary and breast were the most common among 15 different cancers. Most were stage IV at diagnosis (68%), had a strong family history of cancer (80%) & were smokers (42%). The most common mutated subunit was ARID1A (50%) followed by PBRM1 (16%), ARID2 (12%), SMARCA4 (12%), and SMARCB1 (10%). All mutations were predicted to be inactivating. Actionable co-occurring pathway alterations were found in 58% of patients, most commonly PI3K (26%), FGFR(16%), and NOTCH1/2 (10%). The majority of patients (62%) were enrolled on a clinical trial. Best responses on other targeted agents included 1 CR (BRAFV600E colon), 4 PR (transformed teratoma, skin SCC, ovarian, NSCLC), 12 SD. Exceptional responders included BRAFV600E colon cancer on BRAFi based therapy for 66 cycles, NSCLC on Nivolumab for 34 cycles, and MSI-H colon cancer on regorafenib/cetuximab for 27 cycles. Conclusions: The role of SWI/SNF in patients with extended clinical benefit from other targeted agents should be explored. Co-occurring genetic alterations are observed in PI3K, FGFR, and NOTCH pathways. Future pre-clinical and/or clinical studies could target these pathways in combination with EZH2/EED inhibitors.

scholarly journals Moving Next-Generation Sequencing into the Clinic

2021 ◽  
Vol 42 (03) ◽  
pp. 221-228
Author(s):  
Omshree Shetty ◽  
Mamta Gurav ◽  
Prachi Bapat ◽  
Nupur Karnik ◽  
Gauri Wagh ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Molecular Diagnostics ◽  
Single Gene ◽  
Tertiary Care ◽  
Genetic Alterations ◽  
Next Generation ◽  
Pathology Laboratory ◽  
Set Up ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

AbstractWith an advancement in the field of molecular diagnostics, there has been a profound evolution in the testing modalities, especially in the field of oncology. In the past decade, sequencing technology has evolved drastically with the advent of high-throughput next-generation sequencing (NGS). Subsequently, the single-gene tests have been replaced by multigene panel-based assays, deep sequencing, massively parallel whole genome, whole-exome sequencing, and so on. NGS has provided molecular diagnostics professionals a wonderful tool to explore and unearth the genetic alterations, underpinning the pathophysiology of the disease. However, this development has posed new challenges which consist of the following; understanding the technology, types of platforms available, various sequencing strategies, bioinformatics and data analysis algorithm, reporting of various variants, and validation of assays and overall for developing NGS assay for clinical utility. The challenges involved sometimes impede development of these high-end assays in laboratories. The present article provides a broad overview of our journey in setting up the NGS assay in a molecular pathology laboratory at a tertiary care oncology center. We hereby describe various important points and steps to be followed while working on the NGS setup, right from its inception to final drafting of the reports, with inclusion of various validation steps. We aim at providing a beginner’s guide to set up NGS assays in the laboratory using recommended best practices and various international guidelines.

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