Co-occurring genetic alterations and primary EGFR T790M mutations detected by NGS in pre-TKI-treated NSCLCs

  • Yuan Tang
  • Nanying Che
  • Yang Yu
  • Yun Gao
  • Huaiyin Shi
  • Qin Feng
  • Bing Wei
  • Liheng Ma
  • Min Gao
  • Jie MaEmail author
  • Dongmei LinEmail author
Original Article – Clinical Oncology



Next-generation sequencing (NGS)-based assays to understand various mutations and co-occurrence of genomic alterations in non-small cell lung cancer (NSCLC) have enabled understanding of treatment impact on clinical outcomes.


This retrospective study was conducted in 1353 formalin-fixed paraffin-embedded (FFPE) tissues from surgically resected, pre-TKI-treated NSCLC patients with identified gene alterations. Genomic DNA and RNA extraction was followed by NGS library preparation and sequencing using the Ion Ampliseq Colon and Lung Cancer Gene Panel V2 and the AmpliSeq RNA Lung Cancer Research Fusion Panel.


A total of 2328 alterations in 25 genes were detected from the 1293 patients. DNA mutations and RNA fusions co-occurred in 27 patients with TP53 being the most common co-occurring DNA mutation (43.8%) with concurrent ALK fusions. Analysis of the 975 patients with EGFR mutations revealed that the incidence of dual EGFR L858R/T790M mutations was higher compared to EGFR 19del/T790M, and the mean allele fraction (MAF) of T790M was lower compared to 19del in dual EGFR 19del/T790M patients.


NSCLC patients represented genetically heterogeneous subgroup with a high frequency of co-occurring mutations in cancer-associated pathways. This diverse mutational profile may have key clinical and research implications for understanding the variability of treatment outcome in pre-TKI-treated NSCLC population. The differences in the MAF of EGFR T790M may determine different responses to TKI therapy in patients harboring dual mutations.


Non-small cell lung cancer Co-occurring genetic alterations Next-generation sequencing 



Mutant allele frequency


Next-generation sequencing


Formalin-fixed paraffin-embedded


Non-small cell lung cancer


Tyrosine kinase inhibitors


Epidermal growth factor receptor


Anaplastic lymphoma kinase


Amplification refractory mutation system


Fluorescence in situ hybridization




Progression free survival


Overall survival



We acknowledge all other studies that support our work and were not cited due to length limitations. We would like to thank all the patients who have participated in this study. We are also thankful to the doctors from departments of oncology, doctors from departments of pathology for technics and staff of the Novogene Bioinformatics.

Compliance with ethical standards

Conflict of interest

The authors declare no potential conflicts of interest.

Ethics approval and consent to participate

This study was approved by the ethics committee of Peking University Cancer Hospital (2017TW06), and written informed consent was obtained from all patients.

Supplementary material

432_2019_3065_MOESM1_ESM.docx (22 kb)
Supplementary material 1 (DOCX 21 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Pathology, West China HospitalSichuan UniversityChengduChina
  2. 2.Department of Pathology, Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Research InstituteCapital Medical UniversityBeijingChina
  3. 3.Beijing Novogene Bioinformatics Technology Co., Ltd.BeijingChina
  4. 4.Department of PathologyChinese PLA General Hospital and Chinese PLA Medical SchoolBeijingChina
  5. 5.Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of PathologyPeking University Cancer Hospital and InstituteBeijingChina
  6. 6.Department of Molecular PathologyThe Affiliated Cancer Hospital of Zhengzhou UniversityZhengzhouChina
  7. 7.Medical Affairs DepartmentPfizer OncologyShanghaiChina

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