Next-generation sequencing of esophageal carcinosarcoma to reveal high frequency of actionable PIK3CA gene mutations.

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. e15503-e15503
Author(s):  
Hongyang Lu ◽  
Shifeng Yang ◽  
Zhiming Jiang ◽  
Fajun Xie ◽  
Jing Qin ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Gene Mutations ◽  
Single Copy ◽  
Next Generation ◽  
Old Patients ◽  
Molecular Alterations ◽  
Anaplastic Lymphoma ◽  
Esophageal Carcinosarcoma ◽  
Clinical Characteristic ◽  
Generation Sequencing

e15503 Background: Esophageal carcinosarcoma (ESC) is a rare malignant esophageal neoplasm consisting of both carcinomatous and sarcomatous components. Drive genes mutations may potentially serve as novel biomarkers to targeted therapy in ESC, and they also may explain the mechanisms of the unique dual-differentiation pattern. Actionable gene alterations with any significant frequency in ESC were unknown due to specimen numbers and limited studies. A comprehensive study of clinical characteristic and molecular alterations in ESC is needed to better understand biology and guide therapy. Methods: Fifteen cases of ESCs which received surgical resection were retrospectively collected from the Zhejiang Cancer Hospital in China between 2009 and 2016, next generation sequencing was performed to identify genotypic changes, and clinical characteristic of these patients was also collected and analyzed. Results: ESC patients are easily occurred in male, heavy smokers, and old patients. The mainly gross types were medullary and fungating type. Mutation of phosphatase and tensin homologue ( PTEN), MAP2K1(MEK1), anaplastic lymphoma kinase ( ALK), RET, and NF1 were detected in one patient respectively. Mutation of ERBB2(HER2), MET and single copy loss of Rb1 were detected in two patients respectively. Mutation of ROS1 and phosphoinositide-3-kinase catalytic alpha ( PIK3CA) were detected in three patients respectively. Conclusions:PIK/AKT pathway may be important in pathogenesis of ESCs, and it may be an ideal therapeutic target.

scholarly journals A systematic comparison of eight new plastome sequences from Ipomoea L

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6563
Author(s):  
Jianying Sun ◽  
Xiaofeng Dong ◽  
Qinghe Cao ◽  
Tao Xu ◽  
Mingku Zhu ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Next Generation Sequencing ◽  
Chloroplast Genome ◽  
Dna Sequences ◽  
Repetitive Sequences ◽  
Single Copy ◽  
Next Generation ◽  
Variable Regions ◽  
Chloroplast Genomes ◽  
Generation Sequencing

Background Ipomoea is the largest genus in the family Convolvulaceae. The species in this genus have been widely used in many fields, such as agriculture, nutrition, and medicine. With the development of next-generation sequencing, more than 50 chloroplast genomes of Ipomoea species have been sequenced. However, the repeats and divergence regions in Ipomoea have not been well investigated. In the present study, we sequenced and assembled eight chloroplast genomes from sweet potato’s close wild relatives. By combining these with 32 published chloroplast genomes, we conducted a detailed comparative analysis of a broad range of Ipomoea species. Methods Eight chloroplast genomes were assembled using short DNA sequences generated by next-generation sequencing technology. By combining these chloroplast genomes with 32 other published Ipomoea chloroplast genomes downloaded from GenBank and the Oxford Research Archive, we conducted a comparative analysis of the repeat sequences and divergence regions across the Ipomoea genus. In addition, separate analyses of the Batatas group and Quamoclit group were also performed. Results The eight newly sequenced chloroplast genomes ranged from 161,225 to 161,721 bp in length and displayed the typical circular quadripartite structure, consisting of a pair of inverted repeat (IR) regions (30,798–30,910 bp each) separated by a large single copy (LSC) region (87,575–88,004 bp) and a small single copy (SSC) region (12,018–12,051 bp). The average guanine-cytosine (GC) content was approximately 40.5% in the IR region, 36.1% in the LSC region, 32.2% in the SSC regions, and 37.5% in complete sequence for all the generated plastomes. The eight chloroplast genome sequences from this study included 80 protein-coding genes, four rRNAs (rrn23, rrn16, rrn5, and rrn4.5), and 37 tRNAs. The boundaries of single copy regions and IR regions were highly conserved in the eight chloroplast genomes. In Ipomoea, 57–89 pairs of repetitive sequences and 39–64 simple sequence repeats were found. By conducting a sliding window analysis, we found six relatively high variable regions (ndhA intron, ndhH-ndhF, ndhF-rpl32, rpl32-trnL, rps16-trnQ, and ndhF) in the Ipomoea genus, eight (trnG, rpl32-trnL, ndhA intron, ndhF-rpl32, ndhH-ndhF, ccsA-ndhD, trnG-trnR, and pasA-ycf3) in the Batatas group, and eight (ndhA intron, petN-psbM, rpl32-trnL, trnG-trnR, trnK-rps16, ndhC-trnV, rps16-trnQ, and trnG) in the Quamoclit group. Our maximum-likelihood tree based on whole chloroplast genomes confirmed the phylogenetic topology reported in previous studies. Conclusions The chloroplast genome sequence and structure were highly conserved in the eight newly-sequenced Ipomoea species. Our comparative analysis included a broad range of Ipomoea chloroplast genomes, providing valuable information for Ipomoea species identification and enhancing the understanding of Ipomoea genetic resources.

scholarly journals Next‐generation sequencing identifies novel CACNA 1A gene mutations in episodic ataxia type 2

2016 ◽  
Vol 4 (2) ◽  
pp. 211-222 ◽  
Author(s):  
Neven Maksemous ◽  
Bishakha Roy ◽  
Robert A. Smith ◽  
Lyn R. Griffiths
Keyword(s):  
Next Generation Sequencing ◽  
Gene Mutations ◽  
Episodic Ataxia ◽  
Next Generation ◽  
Episodic Ataxia Type 2 ◽  
Generation Sequencing ◽  
Episodic Ataxia Type

The long tail of molecular alterations in non-small cell lung cancer: a single-institution experience of next-generation sequencing in clinical molecular diagnostics

2018 ◽  
Vol 71 (9) ◽  
pp. 767-773 ◽  
Author(s):  
Caterina Fumagalli ◽  
Davide Vacirca ◽  
Alessandra Rappa ◽  
Antonio Passaro ◽  
Juliana Guarize ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Molecular Diagnostics ◽  
Small Cell ◽  
Next Generation ◽  
Small Cell Lung ◽  
Single Institution ◽  
Lung Cancers ◽  
Targeted Next Generation Sequencing ◽  
Molecular Alterations ◽  
Generation Sequencing

BackgroundMolecular profiling of advanced non-small cell lung cancers (NSCLC) is essential to identify patients who may benefit from targeted treatments. In the last years, the number of potentially actionable molecular alterations has rapidly increased. Next-generation sequencing allows for the analysis of multiple genes simultaneously.AimsTo evaluate the feasibility and the throughput of next-generation sequencing in clinical molecular diagnostics of advanced NSCLC.MethodsA single-institution cohort of 535 non-squamous NSCLC was profiled using a next-generation sequencing panel targeting 22 actionable and cancer-related genes.Results441 non-squamous NSCLC (82.4%) harboured at least one gene alteration, including 340 cases (63.6%) with clinically relevant molecular aberrations. Mutations have been detected in all but one gene (FGFR1) of the panel. Recurrent alterations were observed in KRAS, TP53, EGFR, STK11 and MET genes, whereas the remaining genes were mutated in <5% of the cases. Concurrent mutations were detected in 183 tumours (34.2%), mostly impairing KRAS or EGFR in association with TP53 alterations.ConclusionsThe study highlights the feasibility of targeted next-generation sequencing in clinical setting. The majority of NSCLC harboured mutations in clinically relevant genes, thus identifying patients who might benefit from different targeted therapies.

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