Analysis of genomic variation in lung adenocarcinoma patients revealed the critical role of PI3K complex

PeerJ
Zhao Min DengYun Hong Wu

Abstract

Molecularly targeted therapies improved survival status of some patients with lung adenocarcinoma, which accounts for 40% of all lung cancers, and in-depth study of gene alterations is important for the personalized treatment. The legacy archive data of clinical information and genomic variations under the project TCGA Lung Adenocarcinoma were downloaded from the GDC Data Portal using R package TCGAbiolinks. The significantly aberrant copy number variants segments were figured out using GAIA. After annotation, the genes involving CNV were used to get enriched pathways. Recurrent amplifications and deletions were identified and visualized by OncoPrint. Genomic alterations in cancer, including CNV and mutations, were represented in Circos. The significantly aberrant CNV segments were found, and the genes involved were associated with the immune system. In an analysis of 517 mutation annotated files, we highlighted 63 highly recurrent mutated genes which were associated with lung cancer signaling. These genes involved in important pathways related to cancer progression. The intersections between the genes involving in the significantly aberrant CNV and the genes harboring recurrent somatic SNP were extracted. The PI3K protein fami...Continue Reading

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Citations

Oct 11, 2017·Journal of Pediatric Hematology/oncology·Allison S BechtelScott Bradfield
Oct 2, 2020·BMC Bioinformatics·Talip Zengin, Tuğba Önal-Süzek
Aug 24, 2018··Talip ZenginTugba Onal-Suzek

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Methods Mentioned

BETA
surgical resection
genotyping
exome sequencing

Software Mentioned

R package qvalue
OncoPrint
GAIA
R package biomaRt
SummarizedExperiment
R package circlize
TCGAbiolinks
DAVID Bioinformatics Resources
R package complexHeatmap
biomaRt

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