Gene mutation and clinical analysis of nephronophthisis diagnosed using whole exome sequencing: Experience from China

2019 ◽  
Vol 92 (2) ◽  
pp. 89-94 ◽  
Author(s):  
Xiaoshan Tang ◽  
Hong Xu ◽  
Qian Shen ◽  
Guoming Li ◽  
Jia Rao ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Gene Mutation ◽  
Whole Exome Sequencing ◽  
Clinical Analysis ◽  
Whole Exome

scholarly journals Sequential filtering for clinically relevant variants as a method for clinical interpretation of whole exome sequencing findings in glioma

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Ege Ülgen ◽  
Özge Can ◽  
Kaya Bilguvar ◽  
Cemaliye Akyerli Boylu ◽  
Şirin Kılıçturgay Yüksel ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Clinical Analysis ◽  
Clinical Interpretation ◽  
Germline Variants ◽  
Whole Exome ◽  
Gene Level ◽  
Analysis Workflow ◽  
Tumor Mutational Burden ◽  
Diffuse Gliomas

Abstract Background In the clinical setting, workflows for analyzing individual genomics data should be both comprehensive and convenient for clinical interpretation. In an effort for comprehensiveness and practicality, we attempted to create a clinical individual whole exome sequencing (WES) analysis workflow, allowing identification of genomic alterations and presentation of neurooncologically-relevant findings. Methods The analysis workflow detects germline and somatic variants and presents: (1) germline variants, (2) somatic short variants, (3) tumor mutational burden (TMB), (4) microsatellite instability (MSI), (5) somatic copy number alterations (SCNA), (6) SCNA burden, (7) loss of heterozygosity, (8) genes with double-hit, (9) mutational signatures, and (10) pathway enrichment analyses. Using the workflow, 58 WES analyses from matched blood and tumor samples of 52 patients were analyzed: 47 primary and 11 recurrent diffuse gliomas. Results The median mean read depths were 199.88 for tumor and 110.955 for normal samples. For germline variants, a median of 22 (14–33) variants per patient was reported. There was a median of 6 (0–590) reported somatic short variants per tumor. A median of 19 (0–94) broad SCNAs and a median of 6 (0–12) gene-level SCNAs were reported per tumor. The gene with the most frequent somatic short variants was TP53 (41.38%). The most frequent chromosome-/arm-level SCNA events were chr7 amplification, chr22q loss, and chr10 loss. TMB in primary gliomas were significantly lower than in recurrent tumors (p = 0.002). MSI incidence was low (6.9%). Conclusions We demonstrate that WES can be practically and efficiently utilized for clinical analysis of individual brain tumors. The results display that NOTATES produces clinically relevant results in a concise but exhaustive manner.

scholarly journals The combination of whole‐exome sequencing and clinical analysis allows better diagnosis of rare syndromic retinal dystrophies

2019 ◽  
Vol 97 (6) ◽  
Author(s):  
Alaa Abu Diab ◽  
Ala'a AlTalbishi ◽  
Boris Rosin ◽  
Moien Kanaan ◽  
Lara Kamal ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Clinical Analysis ◽  
Retinal Dystrophies ◽  
Whole Exome

Gene mutation screening using whole exome sequencing in lipid storage myopathy

2015 ◽  
Vol 25 ◽  
pp. S204
Author(s):  
K. Takayama ◽  
S. Mitsuhashi ◽  
I. Nonaka ◽  
S. Noguchi ◽  
I. Nishino
Keyword(s):  
Exome Sequencing ◽  
Gene Mutation ◽  
Whole Exome Sequencing ◽  
Mutation Screening ◽  
Lipid Storage ◽  
Lipid Storage Myopathy ◽  
Whole Exome
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