Exonic Mutation Rate Research Articles

Comprehensive analysis of NGS and ARMS-PCR for detecting EGFR mutations based on 4467 cases of NSCLC patients

BackgroundBy comparing the detection rate and type of targeted gene mutations in non-small cell lung cancer (NSCLC) between amplification refractory mutation system PCR (ARMS-PCR) and next-generation sequencing (NGS), the characteristics and application advantages of non-small cell lung cancer detection are explained, providing a basis for clinicians to effectively select the corresponding detection methods.Methods and materialsThe cases of targeted genes for lung cancer were selected from the First Affiliated Hospital of Chongqing Medical University from January 2016 to October 2020. A sample of 4467 cases was selected, and they were diagnosed with NSCLC by Pathological biopsy. Sample sources include surgical resection, bronchoscope biopsy, metastatic biopsy, blood, sputum, cytology of pleural effusion. Among them, 3665 cases were detected by ARMS-PCR technique, and 802 cases were detected by NGS technology. The detection rate and type of ARMS-PCR and NGS techniques for EGFR gene mutations (including exon 18, exon 19, exon 20, exon 21 and so on) in different NSCLC samples were compared, respectively.ResultsThe total mutation rate of EGFR gene detected by ARMS-PCR was 47.6% while 42.4% detected by NGS which indicated that there was a significant difference between the two methods in detecting total mutation of EGFR gene (P < 0.001). In different exons, the EGFR mutation rate detected by two methods is various. The mutation rate of exon 19 by ARMS-PCR detection was evidently higher than that of NGS detection, while the mutation rate of exons 20 and 21 by ARMS-PCR detection were statistically significantly lower than that of NGS detection. Moreover, the multiple mutation rate detected by NGS was 16.3% which was much higher than the 2.7% detected by ARMS-PCR with statistically different.ConclusionIt showed that NGS could direct the drug use for the resistant patients. However, some rare loci could be detected by NGS but the importance and directed meaning are still unknown and the number of rare mutations is rare too. Further research on new biomarkers and technique is still needed for early diagnosis, directing drug use and assessing the therapy prognosis.

Reconstructing tumor history in breast cancer: signatures of mutational processes and response to neoadjuvant chemotherapy⋆

Different endogenous and exogenous mutational processes act over the evolutionary history of a malignant tumor, driven by abnormal DNA editing, mutagens or age-related DNA alterations, among others, to generate the specific mutational landscape of each individual tumor. The signatures of these mutational processes can be identified in large genomic datasets. We investigated the hypothesis that genomic patterns of mutational signatures are associated with the clinical behavior of breast cancer, in particular chemotherapy response and survival, with a particular focus on therapy-resistant disease. Whole exome sequencing was carried out in 405 pretherapeutic samples from the prospective neoadjuvant multicenter GeparSepto study. We analyzed 11 mutational signatures including biological processes such as APOBEC-mutagenesis, homologous recombination deficiency (HRD), mismatch repair deficiency and also age-related or tobacco-induced alterations. Different subgroups of breast carcinomas were defined mainly by differences in HRD-related and APOBEC-related mutational signatures and significant differences between hormone-receptor (HR)-negative and HR-positive tumors as well as correlations with age, Ki-67 and immunological parameters were observed. We could identify mutational processes that were linked to increased pathological complete response rates to neoadjuvant chemotherapy with high significance. In univariate analyses for HR-positive tumors signatures, S3 (HRD, P < 0.001) and S13 (APOBEC, P= 0.001) as well as exonic mutation rate (P= 0.002) were significantly correlated with increased pathological complete response rates. The signatures S3 (HRD, P= 0.006) and S4 (tobacco, P= 0.011) were prognostic for reduced disease-free survival of patients with chemotherapy-resistant tumors. The results of this investigation suggest that the clinical behavior of a tumor, in particular, response to neoadjuvant chemotherapy and disease-free survival of therapy-resistant tumors, could be predicted by the composition of mutational signatures as an indicator of the individual genomic history of a tumor. After additional validations, mutational signatures might be used to identify tumors with an increased response rate to neoadjuvant chemotherapy and to define therapy-resistant subgroups for future therapeutic interventions.

Germline de novo mutation rates on exons versus introns in humans

A main assumption of molecular population genetics is that genomic mutation rate does not depend on sequence function. Challenging this assumption, a recent study has found a reduction in the mutation rate in exons compared to introns in somatic cells, ascribed to an enhanced exonic mismatch repair system activity. If this reduction happens also in the germline, it can compromise studies of population genomics, including the detection of selection when using introns as proxies for neutrality. Here we compile and analyze published germline de novo mutation data to test if the exonic mutation rate is also reduced in germ cells. After controlling for sampling bias in datasets with diseased probands and extended nucleotide context dependency, we find no reduction in the mutation rate in exons compared to introns in the germline. Therefore, there is no evidence that enhanced exonic mismatch repair activity determines the mutation rate in germline cells.

Author Correction: Reduced mutation rate in exons due to differential mismatch repair.

In the version of this article initially published, the x axis on the fourth plot in Fig. 2e was incorrectly labeled "H3K36me3 exon-to-intron ratio (lower to higher)." The x axis on this plot should read "Genic H3K36me3 coverage bins (higher to lower)".

Reduced mutation rate in exons due to differential mismatch repair.

While recent studies have revealed higher than anticipated heterogeneity of mutation rate across genomic regions, mutations in exons and introns are assumed to be generated at the same rate. Here we find fewer somatic mutations in exons than expected based on their sequence content, and demonstrate that this is not due to purifying selection. Moreover, we show that it is caused by higher mismatch repair activity in exonic than in intronic regions. Our findings have important implications for our understanding of mutational and DNA repair processes, our knowledge of the evolution of eukaryotic genes, and practical ramifications for the study of the evolution of both tumors and species.

Analysis of the EGFR gene mutation in patients with nonsmall cell lung cancer in a Chinese population

Purpose: To investigate the epidermal growth factor receptor (EGFR) gene mutations and analyze their clinical significance in patients with non-small cell lung cancer (NSCLC) in Hubei province of China. Methods: A total of 138 paraffin embedded tissues were taken from patients with NSCLC who were treated at Hubei Hospital from January 2014 to June 2015. The tissue DNA was extracted and EGFR mutation was evaluated by polymerase chain reaction (PCR) sequencing analysis of exons 18, 19, 20, and 21. Results: The overall mutation rate of EGFR gene was 30.43 % (42/138) in 138 NSCLC patients. The mutation rates of EGFR gene at exon 18, 19, 20, 21 were 0 %（0/138), 13.8 %（19/138), 0.7 % (1/138) and 15.9 % (22/138), respectively. The mutation rate of EGFR gene was higher in female patients than that in males (62.2 % (28/45) vs 15.1 % (14/93), p 0.05). EGFR mutation frequency in adenocarcinoma was higher than that in squamous cell carcinoma: 33.9 % (41/121) vs. 5.9 % (1/17, p < 0.05). Conclusion: EGFR mutations in NSCLC patients mainly exist in exons 19 and 21, and the mutation rate of exon 21 is higher than that of exon 19, which is more commonly found in female, adenocarcinoma and non-smoking patients. Keywords: Non-small cell lung cancer, Epidermal growth factor receptor (EGFR), Targeted therapy, Sequencing

The first PTPN1 1 mutations in hotspot exons reported in Moroccan children with Noonan syndrome and comparison of mutation rate to previous studies.

Noonan syndrome is an autosomal dominant disorder with an incidence of 1/1000-2500. It results from protein-tyrosine phosphatase, nonreceptor type 11 (PTPN11) mutations in roughly 50% of cases. Mutational screening of PTPN11 has been carried out in different populations. Thus, the aim of this study was to screen, for the first time, PTPN11 mutations in a series of Moroccan Noonan syndrome patients. We used bidirectional sequencing of exons 3 and 8, considered as PTPN11 mutation hot spots, and then compared the rate of mutational events of these exons between different populations using chi-square and Fisher's exact tests. We detected 3 heterozygous mutations (Asp6lGly, Tyr63Cys, and Asn308Ser) in 4 individuals of 16 sporadic patients (25%). The rate of mutation in our cohort did not differ from that of other populations. However, we found significant differences in the mutation rate of exon 8 between one Japanese cohort and some populations, which requires more investigations to be explained. The present study allowed identification of mutations clustered in exons 3 and 8 of the PTPN11 gene in a Moroccan Noonan syndrome cohort and enabled us to give appropriate genetic counseling to the mutation-positive patients.

Abstract 4669: EGFR gene mutation analysis in Chinese lung cancer patients: value for differentiation diagnostics and therapeutics

Abstract There have been a lot studies focusing on EGFR mutation analysis in the patients of lung cancer especially in the patients with adenocarcinoma, for EGFR mutation has shown helpful in patient prognosis and therapeutic selection. Erlotinib and Gefitinib are playing increasing role in late stage adenocarcinoma of lung although it has not been listed as a first line treatment for advanced patients of Asian ethnic yet. However, the fact of a better respond rate to Erlotinib and Gefitinib and longer survival related to the mutant status of EGFR gene among Asian patients is encouraging the use for routine test of this gene in clinical service for lung cancer patients. Ninety two Chinese cancer patients were included into the study, from which 60 were lung cancer. The other cases were 11 supraclavicular lymph node biopsies and 21 tumor masses of different sites with differentiation diagnosis needed. EGFR mutation analysis was performed in DNA extracted from tumor tissue or biopsy samples. Overall mutation rate of EGFR was 42.39% (39/92) in whole patient group. The mutation rate in lung cancer was 46.67% (28/60) whereas it turned to 58.14% (25/43) when only looking at adenocarcinoma (56.10%, 23/41) and adenosquamous carcinoma (100%, 2/2). No mutation was found in squamous carcinoma, large cell carcinoma and poorly differentiated carcinoma. EGFR mutation analysis in the samples from Endobronchila Ultrasound-Guided Transbronchial Needle Aspiration (EBUS-TBNA) for mediastinal masses revealed an EGFR mutation rate of 42.86% (3/7), mimicking the mutation rate of lung cancer in our study. Forty eight percent of the EGFR mutation was located in exon 19 and 36% of the mutation in exon 21. Mutation of exon 19 seemed to be lower in the patient group older (35.71%, 5/14) than 58 year old (median age) than that in the patient group younger than 58 year old (58.82%, 10/17) (P=0.0581). In opposition, mutation rate of exon 21 appeared higher in the older group (64.29%, 9/14) than that in the younger patient group (23.53%, 4/17) (P=0.0800). The mutations in male patients were mainly located in exon 19 (71.43%, 10/14). And the mutation rate of exon 19 and 21 in female patients showed very close (43.47%, 10/23 for exon 19 and 47.83%, 11/23 for exon 21). Mutation rate of exon 20 was generally low but showed a higher rate in younger and female patients (17.65% and 13.04%). Mutation of supraclavicular lymph node was quite high (36.37%, 4/11) while mutation rate from variant site was low (20.00%, 4/20). One adenocarcinoma located in uterus muscle layer was demonstrated to possess an exon 19 mutation. All follow up analysis is in process. In conclusion, EGFR mutation analysis is a useful tool in defining patients suitable for EGFR TKI treatment as well as helpful in differentiation diagnosis in metastasis lesion. Mutation analysis in the samples derived from EBUS-TBNA is especially of important with clinical value. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4669.