scholarly journals Whole-exome sequencing of duodenal adenocarcinoma identifies recurrent Wnt/β-catenin signaling pathway mutations

Cancer ◽  
2016 ◽  
Vol 122 (11) ◽  
pp. 1689-1696 ◽  
Author(s):  
Wei Yuan ◽  
Zhou Zhang ◽  
Binghua Dai ◽  
Qing Wei ◽  
Jinjin Liu ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Signaling Pathway ◽  
Whole Exome Sequencing ◽  
Duodenal Adenocarcinoma ◽  
Whole Exome

Whole-exome sequencing reveals novel candidate single nucleotide variations for preventing adverse effects of levonorgestrel implantation

2021 ◽  
Author(s):  
Weiqiang Zhu ◽  
Junxian Zhang ◽  
Xuelian Yuan ◽  
Xiaoli Liu ◽  
Zhaofeng Zhang ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Protein Structure ◽  
Adverse Effects ◽  
Exome Sequencing ◽  
Signaling Pathway ◽  
Whole Exome Sequencing ◽  
Physicochemical Parameters ◽  
Single Nucleotide ◽  
Whole Exome ◽  
Single Nucleotide Variations

Aim: To identify novel genes associated with adverse effects of levonorgestrel (LNG) implants based on comparative whole-exome sequencing. Materials & methods: A cohort comprising 104 participants, including 52 controls and 52 women with LNG-related adverse effects, was recruited. Seven cases and eight controls were selected for whole-exome sequencing. We verified 13 single nucleotide variations (SNVs) related with integrin-mediated signaling pathway and cell proliferation using the MassARRAY platform. Results: Finally, we screened 49 cases and 52 controls for analyses. Two SNVs (rs7255721 and rs1042522) were located in ADAMTS10 and TP53, respectively, and significantly different between two groups. These two SNVs lead to changes in protein structure and physicochemical parameters. Conclusion: Here, we defined two pathogenic mutations related to adverse LNG effects.

scholarly journals Novel candidate genes may be possible predisposing factors revealed by whole exome sequencing in familial esophageal squamous cell carcinoma

Tumor Biology ◽  
2017 ◽  
Vol 39 (5) ◽  
pp. 101042831769911 ◽  
Author(s):  
Narjes Forouzanfar ◽  
Ancha Baranova ◽  
Saman Milanizadeh ◽  
Alireza Heravi-Moussavi ◽  
Amir Jebelli ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
Esophageal Squamous Cell Carcinoma ◽  
Notch Signaling ◽  
Cell Carcinoma ◽  
Exome Sequencing ◽  
Signaling Pathway ◽  
Whole Exome Sequencing ◽  
Squamous Cell ◽  
Notch Signaling Pathway ◽  
Whole Exome

Esophageal squamous cell carcinoma is one of the deadliest of all the cancers. Its metastatic properties portend poor prognosis and high rate of recurrence. A more advanced method to identify new molecular biomarkers predicting disease prognosis can be whole exome sequencing. Here, we report the most effective genetic variants of the Notch signaling pathway in esophageal squamous cell carcinoma susceptibility by whole exome sequencing. We analyzed nine probands in unrelated familial esophageal squamous cell carcinoma pedigrees to identify candidate genes. Genomic DNA was extracted and whole exome sequencing performed to generate information about genetic variants in the coding regions. Bioinformatics software applications were utilized to exploit statistical algorithms to demonstrate protein structure and variants conservation. Polymorphic regions were excluded by false-positive investigations. Gene–gene interactions were analyzed for Notch signaling pathway candidates. We identified novel and damaging variants of the Notch signaling pathway through extensive pathway-oriented filtering and functional predictions, which led to the study of 27 candidate novel mutations in all nine patients. Detection of the trinucleotide repeat containing 6B gene mutation (a slice site alteration) in five of the nine probands, but not in any of the healthy samples, suggested that it may be a susceptibility factor for familial esophageal squamous cell carcinoma. Noticeably, 8 of 27 novel candidate gene mutations (e.g. epidermal growth factor, signal transducer and activator of transcription 3, MET) act in a cascade leading to cell survival and proliferation. Our results suggest that the trinucleotide repeat containing 6B mutation may be a candidate predisposing gene in esophageal squamous cell carcinoma. In addition, some of the Notch signaling pathway genetic mutations may act as key contributors to esophageal squamous cell carcinoma.

scholarly journals Tumor Mutational Burden and Genomic Alterations in Chinese Small Cell Lung Cancer Measured by Whole-Exome Sequencing

2019 ◽  
Vol 2019 ◽  
pp. 1-8 ◽  
Author(s):  
Shan Su ◽  
Jian-Jun Zou ◽  
Yun-Yun Zeng ◽  
Wen-Chang Cen ◽  
Wei Zhou ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Small Cell Lung Cancer ◽  
Signaling Pathways ◽  
Exome Sequencing ◽  
Signaling Pathway ◽  
Whole Exome Sequencing ◽  
Small Cell ◽  
Small Cell Lung ◽  
Genomic Alterations ◽  
Whole Exome

Purpose. Studies on genetic alterations of the heterogenous small cell lung cancer (SCLC) are rare. We carried out the present study to clarify the genomic alterations and TMB levels of Chinese SCLC patients by whole-exome sequencing. Materials and Methods. Whole-exome sequencing by next-generation sequencing technique was implemented on twenty SCLC samples. Significant somatic mutations and copy number variations were screened, followed by comparison with the data extracted from COSMIC. Besides, altered signaling pathways were examined in order to figure out actionable targets. Results. A total of 8,062 nonsynonymous mutations were defined. The number of mutations for each case ranged from 98 to 864. As for base substitutions, a total of 15,817 substitutions were detected with C > A conversion which was correlated to smoking occupying 25.57%. The TMB values ranged from 2.51/Mb to 22.1/Mb with a median value of 9.95/Mb. RB1 was the most frequently mutated gene altered in 18 (90%) cases, followed by TP53 altered in 17 (85%) cases. Other commonly changed genes were PTEN, and RBL1, with frequencies of 55% and 50%, respectively. SOX2 significantly amplified in 6 (30%) cases and MYCN amplified in 1 (5%) patient. Notch signaling pathway and PI3K/AKT/mTOR signaling pathway were universally and significantly changed. Major genomic alterations were in consistency with data from COSMIC, but frequencies of less common mutations were different. Conclusion. TP53 and RB1 inactivations were universally detected in SCLC. The Notch and PI3K/AKT/mTOR signaling pathways were both significantly altered, implying potential actionable targets.

Whole Exome Sequencing (WES) in Familien mit linksventrikulärer Ausfluβtraktobstruktion (LVOTO)

2014 ◽  
Vol 62 (S 02) ◽  
Author(s):  
M. Hitz ◽  
S. Al-Turki ◽  
A. Schalinski ◽  
U. Bauer ◽  
T. Pickardt ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Whole Exome

FV 1031. Whole Exome Sequencing for Children with Dyskinetic Movement Disorder

2018 ◽  
Author(s):  
Yasemin Dincer ◽  
Michael Zech ◽  
Matias Wagner ◽  
Nikolai Jung ◽  
Volker Mall ◽  
...  
Keyword(s):  
Movement Disorder ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Whole Exome ◽  
Dyskinetic Movement
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