EGFR Gene Mutations Research Articles

Một số bất thường gen ở bệnh nhân ung thư phổi không tế bào nhỏ tại Bệnh viện Đại học Y Hà Nội phát hiện bằng phương pháp giải trình tự gen thế hệ mới

This study aimed to evaluate the rate of genetic mutations in patients with non- small-cell lung cancer by Next-Generation Sequencing at Hanoi Medical university hospital from 2022 to 2023 and to assess the relationship between genetic mutations and pathological characteristics in non-small-cell lung cancer. In 90 non-small-cell lung cancer patients in the study, we found EGFR gene mutations in 41.1% of cases; KRAS gene mutation in 11.1%; ALK gene fusion in 4.4%; PIK3CA gene mutation in 2.2%; BRAF gene mutation in 1.1%; MET gene mutation in 1.1% and ROS1 gene fusion in 1.1%. We found that EGFR mutations were more commonly detected in female, non-smokers and having adenocarcinoma while KRAS mutations were more commonly detected in male.

Amplifying mutational profiling of extracellular vesicle mRNA with SCOPE.

Sequencing of messenger RNA (mRNA) found in extracellular vesicles (EVs) in liquid biopsies can provide clinical information such as somatic mutations, resistance profiles and tumor recurrence. Despite this, EV mRNA remains underused due to its low abundance in liquid biopsies, and large sample volumes or specialized techniques for analysis are required. Here we introduce Self-amplified and CRISPR-aided Operation to Profile EVs (SCOPE), a platform for EV mRNA detection. SCOPE leverages CRISPR-mediated recognition of target RNA using Cas13 to initiate replication and signal amplification, achieving a sub-attomolar detection limit while maintaining single-nucleotide resolution. As a proof of concept, we designed probes for key mutations in KRAS, BRAF, EGFR and IDH1 genes, optimized protocols for single-pot assays and implemented an automated device for multi-sample detection. We validated SCOPE's ability to detect early-stage lung cancer in animal models, monitored tumor mutational burden in patients with colorectal cancer and stratified patients with glioblastoma. SCOPE can expedite readouts, augmenting the clinical use of EVs in precision oncology.

Follicular cell-derived thyroid carcinomas harboring novel genetic BRAFNON-V600E mutations: real-world data obtained using a multigene panel.

To assess the molecular profile of follicular cell-derived thyroid carcinomas (FCDTCs) and correlate the identified mutations with the clinical and pathological features of the affected patients. Cross-sectional study of tumor samples from 100 adult patients diagnosed with FCDTC between 2010 and 2019. The patients' clinical and pathological data were collected. Genomic DNA was extracted from formalin-fixed, paraffin-embedded (FFPE) tumors using the ReliaPrep FFPE gDNA Miniprep System. Genotyping of target genomic regions (KRAS, NRAS, BRAF, EGFR, and PIK3CA) was performed using the AmpliSeq panel, while sequencing was performed on the iSeq 100 platform. The patients' mean age was 39 years. In all, 82% of the tumors were classic papillary thyroid carcinomas. Overall, 54 (54%) tumor samples yielded satisfactory results on next-generation sequencing (NGS), of which 31 harbored mutations. BRAF gene mutations were the most frequent, with the BRAF V600E mutation present in 10 tumors. Seven tumors had BRAF NON-V600E mutations not previously described in FCDTCs (G464E, G464R, G466E, S467L, G469E, G596D, and the T599Ifs*10 deletion) but described in other types of cancer (i.e., skin/melanoma, lung, colorectal, and others). One tumor had a previously reported BRAF A598V mutation. EGFR gene mutations were found in 16 (29%) and KRAS or NRAS alterations in 8 (14%) of the 54 tumors analyzed. We described herein seven non-hotspot/novel variants in the BRAF gene, highlighting their potential role in expanding our understanding of FCDTC genetics.

Circulating tumor DNA predicts venous thromboembolism in patients with cancers

BackgroundDespite rapid advances in liquid biopsy for circulating tumor DNA (ctDNA), its prognostic value for venous thromboembolism (VTE) in patients with cancer is underexplored, particularly in underserved and minoritized populations. Objectives▪. MethodsWe analyzed data from 1038 cancer patients who underwent ctDNA measurement for oncologic care at a large safety-net hospital system in the United States. We investigated the association between ctDNA and VTE after adjusting for cancer type, stage, treatment, and time from initial diagnosis using Fine–Gray models. We further assessed the discrimination of the genetic, clinical-only, and combined models using the area under the time-dependent receiver operating characteristic curve (AUC). ResultsThe presence of pathogenic ctDNA was independently associated with VTE after adjusting for clinical variables. Independent of tumor type, the number of pathogenic ctDNA mutations was predictive of future VTE risk (adjusted subdistribution hazard ratios of 2.75, 1.94, and 1.38 for ≥3, 2, and 1 pathogenic mutation, respectively, compared with none; P < .0001). The association was primarily driven by mutations in KRAS, PTEN, CDKN2A, NF1, and EGFR genes. Compared with the clinical-only model (AUC, 0.71; 95% CI, 0.64-0.76), the combined clinical and ctDNA model had a numerically higher time-dependent AUC (AUC, 0.74; 95% CI, 0.67-0.80). ConclusionctDNA testing may serve as an adjunctive tool to clinical risk assessment models in cancer patients to improve personalized VTE risk assessment and management.

Prognostic genome and transcriptome signatures in colorectal cancers

Colorectal cancer is caused by a sequence of somatic genomic alterations affecting driver genes in core cancer pathways1. Here, to understand the functional and prognostic impact of cancer-causing somatic mutations, we analysed the whole genomes and transcriptomes of 1,063 primary colorectal cancers in a population-based cohort with long-term follow-up. From the 96 mutated driver genes, 9 were not previously implicated in colorectal cancer and 24 had not been linked to any cancer. Two distinct patterns of pathway co-mutations were observed, timing analyses identified nine early and three late driver gene mutations, and several signatures of colorectal-cancer-specific mutational processes were identified. Mutations in WNT, EGFR and TGFβ pathway genes, the mitochondrial CYB gene and 3 regulatory elements along with 21 copy-number variations and the COSMIC SBS44 signature correlated with survival. Gene expression classification yielded five prognostic subtypes with distinct molecular features, in part explained by underlying genomic alterations. Microsatellite-instable tumours divided into two classes with different levels of hypoxia and infiltration of immune and stromal cells. To our knowledge, this study constitutes the largest integrated genome and transcriptome analysis of colorectal cancer, and interlinks mutations, gene expression and patient outcomes. The identification of prognostic mutations and expression subtypes can guide future efforts to individualize colorectal cancer therapy.

Lung adenocarcinoma metastatic to the ovary: a retrospective clinicopathological analysis of 17 cases and literature review

Lung adenocarcinoma metastatic to the ovary is rarely detected in clinical practice, and only a few cases have been reported. Its clinicopathological features, molecular genetics, and prognosis have not been well characterised. The data of 17 patients diagnosed with this disease between 2013 and 2022 were analysed retrospectively. All patients were non-smokers, with a median age of 46 years (range 30-71 years). Unilateral ovarian involvement was more frequent than bilateral involvement (58.8% vs 41.2%). Lesions presented as solid ovarian or mixed cystic and solid masses, and nearly two-thirds of the tumours (11/17, 64.7%) had a diameter greater than 10 cm. Solid adenocarcinoma was the most common histological subtype (9/17, 52.9%), and three of the cases showed abundant intracellular mucin and signet ring cells. Acinar adenocarcinoma was the second most common type (6/17, 35.3%), usually of moderate to poor differentiation. The remaining two cases were identified as micropapillary adenocarcinoma and mucinous adenocarcinoma. Multinodular growth, necrosis, and lymphovascular invasion were observed in half of the cases, and most of them had a marked stromal response. The most prevalent molecular alteration was ALK-rearranged (8/17, 47.1%), followed by EGFR gene mutations (5/17, 29.4%). A total of 34 cases, comprising 17 from the cohort and 17 from the literature, were included in the survival analysis. Patients with ALK-rearranged genes demonstrated an 80.0% 2-year overall survival rate, whereas those without ALK rearrangement exhibited a lower rate of 33.7%. Although there appears to be a potentially better prognosis for patients with ALK-rearranged genes, further cases and an extended follow-up period are necessary to substantiate this observation.

The frequency of EGFR gene mutations in a cohort of Romanian patients with non-small cell lung cancer and their association with PD-L1 expression level and ALK rearrangements

Abstract Background The mortality rate linked to non-small cell lung cancer (NSCLC) has notably decreased in recent years, primarily due to refined diagnostic techniques. This retrospective study aims to offer new insights into the frequency of EGFR gene mutations in Romanian NSCLC patients, examining potential associations or exclusions with ALK rearrangements and elevated PD-L1 expression level and seeks to contribute crucial insights into molecular marker alterations associated with NSCLC, advancing our understanding of targeted therapy prospects for oncology patients diagnosed with NSCLC in Romania. Methods DNA was extracted from the FFPET sections using the DNA Sample Preparation kit from Roche Diagnostics while the EGFR mutation detection test was performed using Real-Time PCR methods. PD-L1 expression levels and ALK rearrangements were immunohistochemically assessed. Results Among the 453 patients, 42 displayed EGFR gene mutations. The most prevalent mutation was Ex19Del, observed in 3.5% of cases, followed by the L858R substitution (2.9%). A noticeable elevation of PD-L1 expression level was observed on average when comparing patients EGFR Wild-Type with patients with EGFR gene mutations (40.37% versus 26.13%). The association of the L858R mutation and positive ALK was observed in one patient in our study cohort. Conclusions The study reveals a significantly higher prevalence of EGFR gene mutations among females and non-smokers. EGFR mutations were exclusively identified in patients with lung adenocarcinoma. This study data act as a catalyst for future investigations into resistance mechanisms to anti-EGFR TKIs in NSCLC patients in Romania and the prevalence of EGFR gene mutations associated with this phenomenon.

EGFR and K-Ras Gene Mutations in the Diagnosis of Non-Small Cell Lung Cancer and their Pathological Correlation

EGFR and K-Ras Gene Mutations in the Diagnosis of Non-Small Cell Lung Cancer and their Pathological Correlation

Neoadjuvant camrelizumab combined with chemotherapy for resectable stage IIIA-IIIb non-small cell lung cancer: Single arm phase II study.

e20074 Background: This study aimed to evaluate the safety and efficacy of neoadjuvant camrelizumab combined with chemotherapy in patients with resectable non-small cell lung cancer (NSCLC). Methods: In this single-arm phase II clinical trial, patients aged 18-75 with pathologically confirmed resectable stage IIIA-IIIB (T3-4N2) NSCLC without EGFR, ALK, and ROS1 gene mutations were enrolled since December 2022. Patients were assigned to receive 3 cycles of camrelizumab (200 mg) plus chemotherapy (nab-paclitaxel, 130 mg/m2 or pemetrexed (for adenocarcinoma), 500mg/m2 plus platinum [cisplatin, 75 mg/m2; carboplatin, area under the curve, 5]). Radical surgery was performed within 4-6 weeks after neoadjuvant therapy. Patients undergo 18F-fluorodeoxyglucose (FDG) PET/CT scans within 1 week before treatment and surgery, respectively. The primary endpoints for follow-up are pathologic complete response (pCR) rate and major pathological response (MPR) rate, while secondary endpoints include safety and disease-free survival (DFS). Exploratory endpoints include molecular imaging research and biomarker analysis. Results: Up to December 2023, 30 patients (median age: 64 years) have been enrolled, including 22 cases of squamous carcinoma and 8 cases of adenocarcinoma. All patients received 3 cycles of neoadjuvant camrelizumab plus chemotherapy, and 27 patients underwent radical sugery. Three patients did not receive surgical treatment, 2 of whom refused surgery and 1 was unable to undergo surgery due to disease progression. Among patients received surgery, 27 (100%) achieved R0 resection, 10 (37.0%) achieved pCR, and 15 (55.6%) achieved MPR. For patients with squamous cell carcinoma, the MPR and pCR rates were 70% (14/20) and 45% (9/20), respectively, while for adenocarcinoma patients, the MPR and pCR rates were 14.3% (1/7) and 14.3% (1/7), respectively. There was no significant difference in pathological response rates between the PD-L1 tumor proportion score (TPS) ≥ 1% group and the PD-L1 TPS &lt; 1% group. Most of treatment-related adverse events (TRAEs) were grade 1-2, and the most common TRAEs was leukopenia (63.0%). Five patients (18.5%) developed grade ≥ 3 TRAEs, including 3 leukopenia, 1 neutropenia, and 1 pneumonia. Biomarker analysis showed that among patients with pCR, the proportion of increased circulating M1 macrophages and decreased mononuclear myeloid-derived suppressor cells (M-MDSCs) and M2 macrophages after treatment was higher than those in non-pCR patients. Circulating ctDNA analysis showed that the ctDNA concentration of patients with non-pCR after treatment was higher than that of patients with pCR. Patients with ctDNA remaining positive after treatment were all in the non-pCR group. Conclusions: Neoadjuvant camrelizumab combined with chemotherapy for NSCLC patients show promising pathological response rates and tolerable safety. Clinical trial information: NCT06241807 .

Real-world applications of the new grading system in lung adenocarcinoma: A study of 907 patients focusing on revealing the relationship between pathologic grade and genetic status

BackgroundThe status of the lung adenocarcinoma (LUAD) grading system and the association between LUAD differentiation, driver genes, and clinicopathological features remain to be elucidated. MethodsWe included patients with invasive non-mucinous LUAD, evaluated their differentiation, and collected available clinicopathological information, gene mutations, and analyzed clinical outcomes. ResultsAmong the 907 patients with invasive non-mucinous LUAD, 321 (35.4 %) were poorly differentiated, 422 (46.5 %) were moderately differentiated, and 164 (18.1 %) were well differentiated. EGFR mutation was more common in the LUADs accompanied without CGP (complex glandular pattern) than LUADs with CGP (p < 0.001). Correlation analysis between mutations and clinical characteristics showed that EGFR gene mutation (p < 0.001), KRAS gene mutation (p < 0.05), and ALK gene rearrangement (p < 0.001) were significantly related to the degree of tumor differentiation, and the KRAS and ALK gene mutation frequencies were higher in the low-differentiation group than in the high and medium differentiation groups. The EGFR mutation frequency was higher in the well/moderately differentiated adenocarcinoma group. ConclusionsOur study adds to the evidence regarding the role of the grading system in prognosis. EGFR, KRAS, and ALK are related to the degree of tumor differentiation.

Predictive value of spectral computed tomography parameters for EGFR gene mutation in non-small–cell lung cancer

To explore the predictive value of morphological signs and quantitative parameters from spectral CT for EGFR gene mutations in intermediate and advanced non-small-cell lung cancer (NSCLC). This retrospective observational study included patients with intermediate or advanced NSCLC at Xinjiang Medical University Affiliated Tumor Hospital between January 2017 and December 2019. The patients were divided into the EGFR gene mutation-positive and -negative groups. Seventy-nine patients aged 60.75±9.66 years old were included: 32 were EGFR mutation-positive, and 47 were negative. There were significant differences in pathological stage (P<0.001), tumor diameter (P=0.019), lobulation sign, intrapulmonary metastasis, mediastinal lymph node metastasis, distant metastasis (P<0.001), bone metastasis (P<0.001), arterial phase normalized iodine concentration (NIC) (P=0.001), venous phase NIC (P=0.001), slope of the energy spectrum curve (λ) (P<0.001), and CT value at 70 keV in arterial phase (P=0.004) and venous phase (P=0.003) between the EGFR mutation-positive and -negative patients. The multivariable logistic regression analysis showed that intrapulmonary metastasis, distant metastasis, venous phase NIC, venous phase λ, and pathological stage were independent factors predicting EGFR gene mutations, with high diagnostic power (AUC=0.975, 91.5% sensitivity, and 90.6% specificity). The pathological stage and the spectral CT parameters of intrapulmonary metastasis, distant metastasis, venous phase NIC, and venous phase λ might pre-operatively predict EGFR gene mutations in intermediate and advanced NSCLC.

EGFR gene mutation and association with carcinoembryonic antigen status in non-small cell lung cancer — a cross-sectional study

EGFR gene mutation and association with carcinoembryonic antigen status in non-small cell lung cancer — a cross-sectional study

Abstract 4242: Preserving lung cancer patient mutations in 3D organoid models: Advancing cancer research through innovative culture systems

Abstract Lung cancer is one of the most prevalent cancers worldwide. There are currently many anticancer drugs available, but they have numerous issues in terms of treatment, such as drug resistance and recurrence. Culturing systems that can replace a patient's cancer tissue are crucial, and the existing 2D culturing systems have many limitations. Patient-derived cancer organoid culture is the most advanced culture system for understanding mechanism of cancers. Using a 3D organoid culture system, we have successfully established a culture system for lung cancer using biopsy/surgical specimens and malignant effusions, including a long-term culture system. There are two critical indicators to determine the success of 3D organoid culture. One is whether the organoids retain their cancer-specific mutations from patient’s lung cancer tissue, and the second is whether the organoids grow well and can be maintained in long-term culture for more than 20-30 passages. We typically assess gene mutations in EGFR, ALK, ROS, and P53 when evaluating lung cancer organoids. We confirm these mutations when we establish organoids. and currently we have established a total of 127 patient-derived lung cancer organoids. Among the 127 organoids, we completed NGS analysis on 108 of them and validated that 86.5% exhibit similarity when compared to lung cancer tissues. Additionally, we achieved a 100% retention of mutations in the long-term culturing of these organoids. Our studies indicate that patient-derived lung cancer organoids represent a meaningful organoid system for cancer tissue replacement and treatment response in the context of precision cancer medicine. Citation Format: Ji-yeon Park, Seo Rin Gu, Jiyeon Lee, Na-Gyeong Lee, Dojin Choi, Sang Eun Park, Ji Min Kim, Jinguen Rheey. Preserving lung cancer patient mutations in 3D organoid models: Advancing cancer research through innovative culture systems [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4242.

Detection of EGFR gene mutations for prescription of targeted drugs for non-small cell lung cancer

Detection of EGFR gene mutations for prescription of targeted drugs for non-small cell lung cancer

EGFR amplification indicated poor prognosis in EGFR‐mutated lung cancer with leptomeningeal metastases

AbstractBackgroundLeptomeningeal metastasis (LM) is a lethal complication of advanced lung cancer, and due to limited access to the leptomeningeal lesion, we explored the potential role of cerebrospinal fluid (CSF) as a source for liquid biopsy in LM patients of lung cancer with EGFR mutation.Materials and MethodsFrom August 2018 to June 2021, we collected CSF samples of lung cancer patients at First Affiliated Hospital of Zhengzhou University. Next‐generation sequencing was performed to detect the mutations in EGFR genes, and 38 patients detected with EGFR mutations were finally enrolled in further clinical analyses.ResultsTP53 missense mutation (50%) was the most frequently detected concurrent gene in CSF. In those 10 patients whose CSF was obtained upon resistance to first TKI, TP53 missense mutation (40%, n = 4) and EGFR copy number amplification (40%, n = 4) was detected with high frequency; meanwhile, T790M mutation was found only in two patients. Known mechanisms of acquired resistance to third EGFR‐TKIs were found in 31.8% of cases. C797S or C797G mutation was identified in three patients. Possible EGFR‐independent resistant mechanism included MET amplification (4.5%), RET gene fusion (4.5%), PIK3CA missense mutation (4.5%) and CDK4 amplification (4.5%). The median OS was 55 months, the median OSLM was 38 months. EGFR amplification was associated with shortened OS in these EGFR‐mutated lung cancer with leptomeningeal metastases.ConclusionEGFR amplification indicated poor prognosis in EGFR‐mutated lung cancer with leptomeningeal metastases, providing a novel pathogenesis and treatment direction of these patients.

Association of mutation profiles with metastasis in patients with non-small cell lung cancer.

This study focused on the analysis of the correlation between common gene mutation types and metastatic sites in NSCLC patients. We retrospectively studied 1586 NSCLC patients and used fluorescence Polymerase chain reaction (PCR) to detect EGFR, ALK, ROS1, RET, MET, BRAF, HER2, KRAS, NRAS, and PIK3CA gene mutations, and also investigated sex, smoking status, age at diagnosis, histological type and TNM stage. In addition, we analyzed the site of metastasis in patients with stage IV NSCLC. The EGFR-mutation group more frequently metastasized to lung (18.9%, P = 0.004), brain (18.9%, P = 0.001) and bone (27.1%, P = 0.004) than wild-type patients. ALK-mutation group (71.0%, P < 0.001), BRAF-mutation group (82.4%, P = 0.005) and NRAS-mutation group (100%, P = 0.025) were more likely to metastasize than the wild-type group. In the ALK mutation, lung metastasis (24.2%, P = 0.013), brain (24.2%, P = 0.007), bone metastasis (32.3%, P = 0.024), liver metastasis (19.4%, P = 0.001), and pleural metastasis (29.0%, P = 0.021) were common. In the KRAS-mutation group, lung metastasis (21.7%, P = 0.012) and brain metastasis (23.3%, P = 0.001) were more common. Less metastasis occurred in the HER2-mutation group (28.3%, P = 0.014). There was no difference in the RET, MET and PIK3CA mutations. Patients with ALK mutant, BRAF mutant or NRAS mutant were more prone to metastasis, while the HER 2 mutation group was less metastatic. Patients with EGFR mutant NSCLC are more likely to develop bone, lung, or brain metastasis.

CT Image Diagnostic Support System for Predicting EGFR Gene Mutations in Lung Cancer

CT Image Diagnostic Support System for Predicting EGFR Gene Mutations in Lung Cancer

A Correlative Study on EGFR Gene Mutation Status of Primary Lung Tumor and Brain Metastases in NSCLC

Objective: This study aims to explore the predictive role of EGFR gene mutation in the primary lung tumor on brain metastases in Non-Small Cell Lung Cancer (NSCLC). Methods: Morphological differences between EGFR gene 19 exon deletion mutant HCC827 and wild-type EGFR gene A549 human lung adenocarcinoma cells were observed under a microscope. The MTT method was employed to detect the proliferation differences between HCC827 and A549 cells. The Transwell in vitro cell invasion experiment was used to compare the invasion capabilities of the two cell lines. Furthermore, the Χ2 test was applied to analyze the relationship between the EGFR mutation in the primary lung tumor and the occurrence of brain metastases in 253 NSCLC patients. Results: A549 cells were smaller in size, resembling paving stones, whereas HCC827 cells were larger and polygonal. MTT analysis revealed that wild-type EGFR A549 human lung adenocarcinoma cells proliferated faster than EGFR mutant HCC827 cells, with a significant difference (P&lt;0.05). The Transwell in vitro cell invasion experiment indicated that HCC827 cells were significantly stronger than A549 cells (P&lt;0.05). The incidence of brain metastases in 253 NSCLC patients was 12.3% (31/253), among which eight cases had EGFR gene mutations in primary lung tumor, with a mutation rate of only 25.81% (8/31). No significant correlation was found between the occurrence of brain metastases and the mutation in primary lung tumor. Conclusion: EGFR gene mutation in NSCLC cells can significantly enhance their invasive activity. However, the correlation between EGFR gene mutation in primary lung tumor and the occurrence of brain metastases warrants further study.

Comprehensive molecular analysis of driver mutations in non-small cell lung carcinomas and its correlation with PD-L1 expression, An Indian perspective

BackgroundThe understanding of molecular mechanisms involved in non-small cell lung carcinoma (NSCLC) has revolutionized significantly in the recent years. These have helped to develop personalized management strategies by identifying specific molecular alterations such as mutations in EGFR, ROS1, BRAF, ERBB2, MET, ALK, and KRAS genes. These mutations are targetable ensuring a better clinical outcome. Next-generation sequencing (NGS) methodology is the recommended technique for the identification of driver mutations in the five hot-spot genes (EGFR, ALK, ROS1, MET, and BRAF) involved in the NSCLC. NGS has numerous advantages including multiplexing, tissue conservation, identification of rare and novel variants, and reduced cost over the sequential single gene testing. Herein, we sought to demonstrate the mutational profile in NSCLC and their clinicopathologic correlation in a contemporary cohort of Indian NSCLC patients. Additionally, we studied the correlation of oncogenic driver mutations with PD-L1 status in these patients. Materials and MethodsFive fifty-two stage IV NSCLC patients (adenocarcinoma=490; squamous cell carcinoma=51; adenosquamous carcinoma=5; large cell carcinoma=2; sarcomatoid carcinoma=3; spindle cell carcinoma=1) underwent broad molecular profiling by a custom-made, targeted DNA- and RNA-based five hot-spot genes lung cancer panel (EGFR, ALK, ROS1, BRAF, and MET), compatible with the NGS Ion S5 system. The mutations were correlated with the clinicopathologic characteristics. Additionally, PD-L1 expression status, available on 252 tumors, was correlated with the oncogenic drivers. ResultsValidation of the 5 gene panel yielded the following results: a) specificity of 99.74%; b) sensitivity of 100% for single nucleotide variants (SNVs) (>5% variant allele frequency, VAF), indels (>10% VAF) and fusions; c) 100% intra- and inter-run reproducibility; d) 88% inter-laboratory agreement. Validated panel was then used to analyze clinical samples. Sixty percentage tumors harbored either one (54.71%) or multiple (3.26%) mutations. EGFR and BRAF V600E mutations, ALK and ROS1 rearrangements, and MET exon 14 skipping mutation were observed in 38.41% (n = 212) and 2.72% (n = 15) patients, 12.14% (n = 67) and 3.62% (n = 20) patients, and 1.09% (n = 6) patients, respectively. EGFR exon 19 deletion accounted for 52.83% of all mutations, followed by L858R (35.85%), T790M (5.19%), exon 20 insertions (6.6%), and other rare mutations (G719X, L861Q, S768I) (9.91%). Concurrent EGFR with ALK, EGFR with ROS1, EGFR with MET, and EGFR with BRAF were observed in 10, 4, 1, and 3 patients, respectively. PD-L1 was expressed in 134 patients (53.2%). Exon 19 deletion was more prevalent in PD-L1 negative tumors whereas exon 21 substitution (L858R) was seen more in PD-L1 positive tumors. ConclusionsThis is one of the largest cohorts of NSCLC for comprehensive targeted mutational profiling and correlation with the PD-L1 expression. The mutations are more prevalent in non-smoker females for all genes, except ALK (non-smoker males). MET and BRAF mutations are more common in elderly population whereas EGFR mutations, and ALK and ROS1 genes rearrangements are more prevalent in younger population. The most common histopathologic subtype/feature associated with various mutations was as follows: acinar with EGFR, solid with ALK, macronucleoli with ROS1, signet ring with MET, and micropapillary with BRAF.

Detection of EGFR gene polymorphisms in non-small cell lung cancer Egyptian patients: a case–control study

BackgroundNon-Small Cell Lung Cancer displays several genetic mutations including epidermal growth factor receptor. This study's objective was to determine if the EGFR exon19 rs121913438 and exon21 rs121434568 variations play a role in NSCLC susceptibility.MethodsCase–control research was done at the Mansoura university oncology center including 124 NSCLC patients, and 124 healthy volunteers. blood was used to obtain genomic DNA. ARMS-PCR was used to genotype single-nucleotide polymorphisms.ResultsMolecular study for EGFR exon 19 del. showed NSCLC cases were significantly associated with a higher proportion of heterozygous WD, WD + DD dominant genotypes, and mutant D allele, (p < 0.05 for each), with a risk to develop NSCLC. also, NSCLC cases were significantly associated with a higher proportion of heterozygous TG, TG + GG dominant genotype, G mutant allele, (p < 0.05 for each), with a risk to develop LC (OR > 1 for each). regarding the two EGFR mutations, TTF1 staining was significantly associated with WD + DD genotypes for EGFR exon 19 del But not EGFR exon 21. No substantial differences were found among all studied cases with CK7 or napsin A Tumor cytochemistry.ConclusionsThe WD heterozygous genotype and D allele in exon 19 del. mutation as well as the TG heterozygous and G allele in exon 21 substitution mutation in EGFR gene are strongly associated with the development of advanced-NSCLC in the Egyptians.