Open AccessTargeted deep sequencing from multiple sources demonstrates increased NOTCH1 alterations in lung cancer patient plasma
Author(s) -
Liao Yuwei,
Ma Zhaokui,
Zhang Yu,
Li Dan,
Lv Dekang,
Chen Zhisheng,
Li Peiying,
AIDherasi Aisha,
Zheng Feng,
Tian Jichao,
Zou Kun,
Wang Yue,
Wang Dongxia,
Cordova Miguel,
Zhou Huan,
Li Xiuhua,
Liu Dan,
Yu Ruofei,
Zhang Qingzheng,
Zhang Xiaolong,
Zhang Jian,
Zhang Xuehong,
Zhang Xia,
Li Yulong,
Shao Yanyan,
Song Luyao,
Liu Ruimei,
Wang Yichen,
Sufiyan Sufiyan,
Liu Quentin,
Owen Gareth I.,
Li Zhiguang,
Chen Jun
Publication year - 2019
Publication title -
cancer medicine
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.403
H-Index - 53
ISSN - 2045-7634
DOI - 10.1002/cam4.2458
Subject(s) - kras , lung cancer , copy number variation , cancer , pleural effusion , cancer research , gene , biology , lung , population , targeted therapy , mutation , medicine , oncology , pathology , genetics , environmental health , genome
Targeted therapies are based on specific gene alterations. Various specimen types have been used to determine gene alterations, however, no systemic comparisons have yet been made. Herein, we assessed alterations in selected cancer‐associated genes across varying sample sites in lung cancer patients. Materials and Methods Targeted deep sequencing for 48 tumor‐related genes was applied to 153 samples from 55 lung cancer patients obtained from six sources: Formalin‐fixed paraffin‐embedded (FFPE) tumor tissues, pleural effusion supernatant (PES) and pleural effusion cell sediments (PEC), white blood cells (WBCs), oral epithelial cells (OECs), and plasma. Results Mutations were detected in 96% (53/55) of the patients and in 83% (40/48) of the selected genes. Each sample type exhibited a characteristic mutational pattern. As anticipated, TP53 was the most affected sequence (54.5% patients), however this was followed by NOTCH1 (36%, across all sample types). EGFR was altered in patient samples at a frequency of 32.7% and KRAS 10.9%. This high EGFR/ low KRAS frequency is in accordance with other TCGA cohorts of Asian origin but differs from the Caucasian population where KRAS is the more dominant mutation. Additionally, 66% (31/47) of PEC samples had copy number variants (CNVs) in at least one gene. Unlike the concurrent loss and gain in most genes, herein NOTCH1 loss was identified in 21% patients, with no gain observed. Based on the relative prevalence of mutations and CNVs, we divided lung cancer patients into SNV‐dominated, CNV‐dominated, and codominated groups. Conclusions Our results confirm previous reports that EGFR mutations are more prevalent than KRAS in Chinese lung cancer patients. NOTCH1 gene alterations are more common than previously reported and reveals a role of NOTCH1 modifications in tumor metastasis. Furthermore, genetic material from malignant pleural effusion cell sediments may be a noninvasive manner to identify CNV and participate in treatment decisions.