Validating a targeted next-generation sequencing assay and profiling somatic variants in Chinese non-small cell lung cancer patients

Abstract

Non-small cell lung cancer (NSCLC) is featured with complex genomic alterations. Molecular profiling of large cohort of NSCLC patients is thus a prerequisite for precision medicine. We first validated the detection performance of a next-generation sequencing (NGS) cancer hotspot panel, OncoAim, on formalin-fixed paraffin-embedded (FFPE) samples. We then utilized OncoAim to delineate the genomic aberrations in Chinese NSCLC patients. Overall detection performance was powerful for mutations with allele frequency (MAF) ≥ 5% at >500 × coverage depth, with >99% sensitivity, high specificity (positive predictive value > 99%), 94% accuracy and 96% repeatability. Profiling 422 NSCLC FFPE samples revealed that patient characteristics, including gender, age, lymphatic spread, histologic grade and histologic subtype were significantly associated with the mutation incidence of EGFR and TP53. Moreover, RTK signaling pathway activation was enriched in adenocarcinoma, while PI(3)K pathway activation, oxidative stress pathway activation, and TP53 pathway inhibition were more prevalent in squamous cell carcinoma. Additionally, novel co-existence (e.g., variants in BRAF and PTEN) and mutual-exclusiveness (e.g., alterations in EGFR and NFE2L2) were found. Finally, we revealed distinct mutation spectrum in TP53, as well as a previously undervalued PTEN aberration. Our findings could aid in improving diagnosis, prognosis and personalized therapeutic decisions of Chinese NSCLC patients.Lung cancer is the leading cause of cancer-associated mortality worldwide. Up to 90% lung cancer is non-small cell lung cancer (NSCLC) 1 . NSCLC is usually diagnosed at the advanced stage with limited therapeutic options (e.g., surgery, radiotherapy and chemotherapy) 1 .Conventional molecular detection techniques, such as fluorescence in situ hybridization and Sanger sequencing, only detect a limited number of biomarkers 2-4 . The advent of next-generation sequencing (NGS) has broadened the landscape of genetic aberrations 5-7 , making it possible to implement targeted treatment tailored for specific mutations in individual patients 1,8,9 . Lung cancer is characterized with complex genomic aberrations 10 . The most frequently mutated genes in NSCLC include EGFR (Epidermal growth factor receptor), TP53 (Tumor Protein p53), KRAS (Kirsten rat sarcoma viral oncogene) and PIK3CA (Phosphatidylinositol 3-kinase). In addition, Genetic mutations detected in NSCLC are complicated by patient demographic, racial, clinical and pathological characteristics 1,8,9,11 . For instance, the mutational frequency of EGFR can vary from 10% in Western populations to 30% in Asians, and KRAS mutation incidence in Western populations is approximately 18-26% versus 3.8-8% in Asians 12 , and within

Comprehensive genomic profile of Chinese lung cancer patients and mutation characteristics of individuals resistant to icotinib/gefitinib

“…Although the mutational frequencies of KRAS and TP53 were also higher in smoking than those in nonsmoking patients in this study, the statistical analysis showed no significant difference (17.1% vs. 7.3%, P = 0.052; and 62.9% vs. 52.7%, P = 0.22, respectively). In contrast to previous studies 43 , 44 , our results revealed a series of smoking-associated genes, including CDKN2A , CCND1 , SMARCA4 , CCNE1 , STK11 , KEAP1 , KMT2C , FAT1 , FGFR1 , and NFE2L2 . This discrepancy may be caused by regional differences among populations.…”

“…Sacher et al focused on the GAs of young lung cancer patients and identified that mutations in EGFR , ALK , and ERBB2 trend to occur in younger NSCLC patients 42 . According to different age groups, Jiang et al reported that mutations in EGFR and TP53 were associated with age in Chinese NSCLC patients 43 . In contrast to this study, we did not detect an association between age and TP53 and EGFR mutations.…”

Role of NRF2 in Lung Cancer

“…For NRF2 activation, it is important to consider that other mutated genes that contribute to NSCLC development (EGFR, TP53, KRAS, PTEN and PIK3CA) [135,148] correlate with particular NFE2L2/KEAP1 mutations. Mutations in NFE2L2 usually co-occur with PI3KCA and TP53 mutations [149,150]; meanwhile, KEAP1 mutations co-occur more frequently with mutations in K-RAS or STK11 [105,138].…”

“…Mutations in NFE2L2 usually co-occur with PI3KCA and TP53 mutations [149,150]; meanwhile, KEAP1 mutations co-occur more frequently with mutations in K-RAS or STK11 [105,138]. EGFR mutations can coexist with NFE2L2 mutations [148,151].…”

MET Amplification in Non-Small Cell Lung Cancer (NSCLC)—A Consecutive Evaluation Using Next-Generation Sequencing (NGS) in a Real-World Setting

“…According to various studies, multigene testing for nonsynonymous mutations, translocations and copy number variations of a variety of genes is recommended to identify optimal treatment options for patients with advanced tumors, including NSCLC [ 21 , 22 , 23 ]. Next-generation sequencing (NGS), which does not reveal genetic aberrations of only one but multiple genes at the same time, represents a tissue-sparing alternative for the detection of various genetic aberrations.…”