scholarly journals Whole Exome Sequencing of Simultaneous Primary Multifocal Lung Cancer (SMPLC): Case Report and Bioinformatics Analysis

2020 ◽  
Author(s):  
Donglin Zhu ◽  
Minghong Shen ◽  
Jinghuan Lv
Keyword(s):  
Lung Cancer ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Bioinformatics Analysis ◽  
Clonal Evolution ◽  
Evolutionary Relationship ◽  
Primary Lung Cancer ◽  
The Cancer Genome Atlas ◽  
Control Group ◽  
Whole Exome

Abstract Background: To understand the molecular mechanism of synchronous multifocal lung cancer (SMLC) is of great significance for the differential diagnosis of intrapulmonary metastasis (IM) and synchronous multiple primary lung cancer (SMPLC). Recently, next-generation sequencing (NGS) has become a useful tool for understanding SMLC. Case presentation: In this study, two lesions of a 61-year-old man with lung cancer were detected by whole exome sequencing (WES) and the correlation between different lesions was analyzed at the molecular level. Lesion 1 was adenocarcinoma and lesion 2 was squamous cell carcinoma. Gene mutation and copy number variation (CNV) are different in the two lesions. The genome of lesion 2 is more unstable. The clonal evolution analysis showed that there was no obvious evolutionary relationship between the two lesions, and both lesions were independent double primary lesions. Bioinformatics analysis revealed that the alternate genes of the two lesions were inconsistent in function and pathway. PCA analysis was performed using the Cancer Genome Atlas (TCGA) database and the GTEx database, and it was found that the changed genes in these two lesions were significantly separated from the control group, and the changes of TP53 and EGFR genes in the TCGA database were further described. Conclusions: These results indicate that NGS may provide new ideas for SMLC classification.

P-047: Clonal evolution in multiple myeloma evaluated by Whole Exome Sequencing

2021 ◽  
Vol 21 ◽  
pp. S64
Author(s):  
Ritu Gupta ◽  
Gurvinder Kaur ◽  
Akanksha Farswan ◽  
Lingaraja Jena ◽  
Anubha Gupta ◽  
...  
Keyword(s):  
Multiple Myeloma ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Clonal Evolution ◽  
Whole Exome

scholarly journals Mutation Profile of Tibetan Lung Cancer Revealed by Whole Exome Sequencing

2020 ◽  
Vol 15 (1) ◽  
pp. e10-e13
Author(s):  
Xin Wang ◽  
Yutian Lai ◽  
Wei Dai ◽  
Jintao He ◽  
Guowei Che
Keyword(s):  
Lung Cancer ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Whole Exome ◽  
Mutation Profile

Abstract 3276: Whole exome sequencing identifies significantly linked regions on multiple chromosomes in families with a history of lung cancer

2018 ◽  
Author(s):  
Anthony M. Musolf ◽  
Haiming Sun ◽  
Bilal A. Moiz ◽  
Diptasri Mandal ◽  
Mariza de Andrade ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Whole Exome ◽  
History Of

scholarly journals Integrated Somatic and Germline Whole-Exome Sequencing Analysis in Women with Lung Cancer after a Previous Breast Cancer

Cancers ◽  
2019 ◽  
Vol 11 (4) ◽  
pp. 441 ◽  
Author(s):  
Simona Coco ◽  
Silvia Bonfiglio ◽  
Davide Cittaro ◽  
Irene Vanni ◽  
Marco Mora ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Lung Cancer ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Smoking Habit ◽  
Cancer Control ◽  
Sequencing Analysis ◽  
Multiple Cancer ◽  
Germline Variants ◽  
Whole Exome

Women treated for breast cancer (BC) are at risk of developing secondary tumors, such as lung cancer (LC). Since rare germline variants have been linked to multiple cancer development, we hypothesized that BC survivors might be prone to develop LC as a result of harboring rare variants. Sixty patients with LC with previous BC (the study population; SP) and 53 women with either BC or LC and no secondary cancer (control population; CP) were enrolled. Whole exome sequencing was performed in both tumors and unaffected tissues from 28/60 SP patients, and in germline DNA from 32/53 CP. Candidate genes were validated in the remaining individuals from both populations. We found two main mutational signature profiles: S1 (C>T) in all BCs and 16/28 LCs, and S2 (C>A) which is strongly associated with smoking, in 12/28 LCs. The burden test over rare germline variants in S1-LC vs CP identified 248 genes. Validation confirmed GSN as significantly associated with LC in never-smokers. In conclusion, our data suggest two signatures involved in LC onset in women with previous BC. One of these signatures is linked to smoking. Conversely, regardless of smoking habit, in a subgroup of BC survivors genetic susceptibility may contribute to LC risk.

scholarly journals Mutation profile of Tibetan lung cancer revealed by whole exome sequencing

2019 ◽  
Vol 30 ◽  
pp. v15
Author(s):  
X. Wang ◽  
Y. Lai ◽  
G. Che ◽  
F. Zhao ◽  
F. Yang
Keyword(s):  
Lung Cancer ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Whole Exome ◽  
Mutation Profile

scholarly journals Low Input Whole-Exome Sequencing to Determine the Representation of the Tumor Exome in Circulating DNA of Non-Small Cell Lung Cancer Patients

PLoS ONE ◽  
2016 ◽  
Vol 11 (8) ◽  
pp. e0161012 ◽  
Author(s):  
Steffen Dietz ◽  
Uwe Schirmer ◽  
Clémentine Mercé ◽  
Nikolas von Bubnoff ◽  
Edgar Dahl ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Small Cell Lung Cancer ◽  
Exome Sequencing ◽  
Cancer Patients ◽  
Whole Exome Sequencing ◽  
Small Cell ◽  
Circulating Dna ◽  
Small Cell Lung ◽  
Lung Cancer Patients ◽  
Whole Exome

scholarly journals Whole exome sequencing identified mutations causing hearing loss in five consanguineous Pakistan families

2019 ◽  
Author(s):  
Yingjie Zhou ◽  
Muhammad Tariq ◽  
Sijie He ◽  
Uzma Abdullah ◽  
Jianguo Zhang ◽  
...  
Keyword(s):  
Hearing Loss ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Sanger Sequencing ◽  
Bioinformatics Analysis ◽  
The Other ◽  
Whole Exome ◽  
Clinical Detection ◽  
Syndromic Hearing Loss ◽  
Sensory Defect

Abstract Background: Hearing loss is the most common sensory defect that affects over 6% of the population worldwide. About 50%-60% of hearing loss patients are attributed to genetic causes. Currently more than 100 genes have been reported to cause non-syndromic hearing loss. It’s possible and efficient to screen all potential disease-causing genes for hereditary hearing loss by whole exome sequencing (WES).Methods: We collected 5 consanguineous pedigrees with hearing loss from Pakistan and applied WES on selected patients for each pedigree, followed by bioinformatics analysis and Sanger validation to identify the causing genes for them.Results: Variants in 7 genes were identified and validated in these pedigrees. We identified single candidate for 3 pedigrees, which were GIPC3 (c.937T>C), LOXHD1 (c.2935G>A) and TMPRSS3 (c.941T>C). And the remaining 2 pedigrees each contained two candidates, which were TECTA (c.4045G>A) and MYO15A (c.3310G>T and c.1705G>C) for one pedigree and DFNB59 (c.494G>A) and TRIOBP (c.1952C>T) for the other pedigree. The candidates were validated in all available samples by Sanger sequencing.Conclusion: The candidate variants in hearing loss genes were validated to be co-segregated in the pedigrees, which may indicate the reasons for such patients. We also suggested that WES may be suitable strategy for hearing loss gene screening in clinical detection.

scholarly journals Reliable analysis of clinical tumor-only whole exome sequencing data

2019 ◽  
Author(s):  
Sehyun Oh ◽  
Ludwig Geistlinger ◽  
Marcel Ramos ◽  
Martin Morgan ◽  
Levi Waldron ◽  
...  
Keyword(s):  
Open Source ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Copy Number ◽  
High Accuracy ◽  
The Cancer Genome Atlas ◽  
Cancer Type ◽  
Mutational Signatures ◽  
Whole Exome ◽  
Allele Specific

AbstractBackgroundAllele-specific copy number alteration (CNA) analysis is essential to study the functional impact of single nucleotide variants (SNV) and the process of tumorigenesis. Most commonly used tools in the field rely on high quality genome-wide data with matched normal profiles, limiting their applicability in clinical settings.MethodsWe propose a workflow, based on the open-source PureCN R/Bioconductor package in conjunction with widely used variant-calling and copy number segmentation algorithms, for allele-specific CNA analysis from whole exome sequencing (WES) without matched normals. We use The Cancer Genome Atlas (TCGA) ovarian carcinoma (OV) and lung adenocarcinoma (LUAD) datasets to benchmark its performance against gold standard SNP6 microarray and WES datasets with matched normal samples. Our workflow further classifies SNVs by somatic status and then uses this information to infer somatic mutational signatures and tumor mutational burden (TMB).ResultsApplication of our workflow to tumor-only WES data produces tumor purity and ploidy estimates that are highly concordant with estimates from SNP6 microarray data and matched-normal WES data. The presence of cancer type-specific somatic mutational signatures was inferred with high accuracy. We also demonstrate high concordance of TMB between our tumor-only workflow and matched normal pipelines.ConclusionThe proposed workflow provides, to our knowledge, the only open-source option for comprehensive allele-specific CNA analysis and SNV classification of tumor-only WES with demonstrated high accuracy.

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