Identification of genome variations in patients with lung adenocarcinoma using whole genome re‑sequencing

Li,Guiyuan; Mei,Yunqing; Yang,Fan; Yi,Shengming; Wang,Lemin

doi:10.3892/mmr.2017.7805

Identification of genome variations in patients with lung adenocarcinoma using whole genome re‑sequencing

Authors:
- Guiyuan Li
- Yunqing Mei
- Fan Yang
- Shengming Yi
- Lemin Wang
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Affiliations: Department of Oncology, Shanghai Tongji Hospital of Tongji University School of Medicine, Shanghai 200065, P.R. China, Department of Thoracic Cardiovascular Surgery, Shanghai Tongji Hospital of Tongji University School of Medicine, Shanghai 200065, P.R. China, Department of Clinical Laboratory Medicine, Shanghai Tongji Hospital of Tongji University School of Medicine, Shanghai 200065, P.R. China, Department of Cardiology, Shanghai Tongji Hospital of Tongji University School of Medicine, Shanghai 200065, P.R. China
Published online on: October 17, 2017 https://doi.org/10.3892/mmr.2017.7805
Pages: 9464-9472
Copyright: © Li et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

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Abstract

Lung adenocarcinoma is one of the types of non‑small cell lung carcinoma, which tends to be treated with surgical therapy rather than radiation therapy. It occurs in smokers and non‑smokers, and is the most common form of lung cancer among non‑smokers and women. Gene rearrangements, including ALK, ROS1 and RET, and gene mutations, including epidermal growth factor receptor (EGFR), HER2, Kristen rat sarcoma viral oncogene homolog, BRAF, phosphoinositide‑3‑kinase, catalytic, α polypeptide and MET, have been identified in lung adenocarcinoma, which enable targeted therapy in lung adenocarcinoma, for example erlotinib, gefitinib and afatinib, which are EGFR inhibitors. The aim of the present study was to further investigate genome variations in lung adenocarcinoma. Single nucleotide polymorphisms (SNPs), insertions and deletions (InDels), structural variations (SVs) and copy number variations (CNVs) were identified in the whole genome from four patients with adenocarcinoma using a whole genome re‑sequencing method performed on the Illumina HiSeq Xten platform. In total, ~415 GB of clean reads were obtained, the average sequencing depth was 31.10‑fold, and 99.29% of the reference genome was covered by the clean reads. An average of 3,364,270 SNPs was identified, 98.76% of which were matched to the SNP database (dbSNP), and an average of 453,547 InDels were identified, 28.28% of which were in the dbSNP. The present study also identified a total of 13,050 SVs and 886 CNVs. The majority of the SVs were deletions (74.25%) and the major CNVs were in intergenic regions and coding sequence regions. In conclusion, the results of the present study generated an output of the genome alterations in lung adenocarcinoma, and provided a foundation for further investigation of the pathogenesis of lung adenocarcinoma.

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