Sequencing by binding rivals SMOR error-corrected sequencing by synthesis technology for accurate detection and quantification of minor (< 0.1%) subpopulation variants.

BACKGROUND: Detecting very minor (< 1%) subpopulations using next-generation sequencing is a critical need for multiple applications, including the detection of drug resistant pathogens and somatic variant detection in oncology. A recently available sequencing approach termed 'sequencing by binding (SBB)' claims to have higher base calling accuracy data "out of the box." This paper evaluates the utility of using SBB for the detection of ultra-rare drug resistant subpopulations in Mycobacterium tuberculosis (Mtb) using a targeted amplicon assay and compares the performance of SBB to single molecule overlapping reads (SMOR) error corrected sequencing by synthesis (SBS) data. RESULTS: SBS displayed an elevated error rate when compared to SMOR error-corrected SBS and SBB techniques. SMOR error-corrected SBS and SBB technologies performed similarly within the linear range studies and error rate studies. CONCLUSIONS: With lower sequencing error rates within SBB sequencing, this technique looks promising for both targeted and unbiased whole genome sequencing, leading to the identification of minor (< 1%) subpopulations without the need for error correction methods.

Chasing Sequencing Perfection: Marching Toward Higher Accuracy and Lower Costs.

Next-generation sequencing (NGS), represented by Illumina platforms, has been an essential cornerstone of basic and applied research. However, the sequencing error rate of 1 per 1000 bp (10-3) represents a serious hurdle for research areas focusing on rare mutations, such as somatic mosaicism or microbe heterogeneity. By examining the high-fidelity sequencing methods developed in the past decade, we summarized three major factors underlying errors and the corresponding 12 strategies mitigating these errors. We then proposed a novel framework to classify 11 preexisting representative methods according to the corresponding combinatory strategies and identified three trends that emerged during methodological developments. We further extended this analysis to eight long-read sequencing methods, emphasizing error reduction strategies. Finally, we suggest two promising future directions that could achieve comparable or even higher accuracy with lower costs in both NGS and long-read sequencing.

Sequencing by Binding rivals error-corrected Sequencing by Synthesis technology for accurate detection and quantification of minor (<0.1%) subpopulation variants.

Detecting very minor (< 1%) subpopulations using next-generation sequencing is a critical need for multiple applications including detection of drug resistant pathogens and somatic variant detection in oncology. To enable these applications, wet lab enhancements and bioinformatic error correction methods have been developed for 'sequencing by synthesis' technology to reduce its inherent sequencing error rate. A recently available sequencing approach termed 'sequencing by binding' claims to have higher base calling accuracy data "out of the box." This paper evaluates the utility of using 'sequencing by binding' for the detection of ultra-rare subpopulations down to 0.001%.

Insensitivity of oncogenic EGFR R776L mutation to EGFR inhibitors in lung cancer.

Non-small cell lung cancers (NSCLC) account for 85 % of total lung cancers. Mutation in EGFRdrives the progress of NSCLSs with high mortality rate. Besides the common mutations in EGFR, which together comprise of 85 % of all EGFR mutations and respond to the targeted therapy of EGFR tyrosine kinase inhibitors (TKIs), many other low-frequency mutations of EGFR are existed in patients. The oncogenic roles and sensitivity of these mutations to EGFR TKIs are not fully understood yet. Here we described two cases of lung adenocarcinoma patients harboring EGFR R776L missense mutation, showed PD and SD after treatment with third-generation EGFR inhibitor, Almonertinib. Chemotherapy afterward showed PR effect in one patient with PSF of 10 months. We also explored the oncogenic feature of single R776L mutation by Ba/F3 isogenic cells and found that, EGFR R776L mutation activates EGFR-related survival signaling pathway in Ba/F3 cells, and they are insensitive to gefitinib, afatinib, and Almonertinib, which consistent with our clinical observation.

Progress of osimertinib in epidermal growth factor receptor mutant non-small cell lung cancer / 肿瘤研究与临床

As an important tumor driver gene, epidermal growth factor receptor (EGFR) gene plays an important role in the development and progression of non-small cell lung cancer (NSCLC). As the latest generation of EGFR-tyrosine kinase inhibitor (TKI) drugs, osimertinib has brought significant therapeutic efficacies and encouraging results both in patients with sensitive EGFR mutations and patients with rare EGFR mutations. Compared with previous EGFR-TKI drugs, osimertinib has strong blood-brain barrier penetration, which can effectively prevent the occurrence of lung cancer brain metastasis. After the resistance of first and second generation of targeted drugs, osimertinib is still effective in the follow-up treatment process. This article reviews the characteristics of EGFR mutation, the action mechanism of osimertinib, and the latest progress of osimertinib in treatment of EGFR mutations in NSCLC.

Efficacy of Immune Checkpoint Inhibitors for Non-small Cell Lung Cancer with Rare Mutation / 中国肺癌杂志

Over the past several decades, advances in driven targeted therapy has revolutionized the management of oncogene-driven non-small cell lung cancer (NSCLC). However, there are only a few targeted drugs available for patients with rare mutations, such as BRAF, HER2, MET, RET, etc. In recent years, immune checkpoint inhibitors (ICIs) have demonstrated promising benefit in NSCLC. Till now, efficacy of ICIs for NSCLC with rare mutation is largely unknown. It is fairly difficult to conduct a large formal prospective controlled trials because of the rarity of these mutation. In this article, currently available real world studies based on convincing clinical evidence will be reviewed, which will ultimately facilitate our rational use of ICIs for NSCLC with rare mutation.
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Non-small cell lung cancer with both EGFR gene L861Q mutation and the first symptom of perforation due to small bowel metastasis: A case report / 肿瘤

Objective: To explore the treatment strategy for non-small cell lung cancer patients with both rare mutation (L861Q) of epidermal growth factor receptor (EGFR) gene and the first symptom of perforation due to small bowel metastasis. Methods: The medical records as well as the diagnosis and treatment process of a case of non-small cell lung cancer with both rare EGFR mutation and the first symptom of perforation due to small bowel metastasis were reviewed restropectively, to explore the treatment strategy. Results: The perforation was the first symptom in this non-small cell lung cancer patient with both rare EGFR mutation (L861Q) and small bowel metastasis. After the laparotomy and partial small intestine resection, afatinib was administered orally for 16 days according to the genetic test results until peritoneal effusion and enlarged lesions in the right lung was found, as well as liver, bilateral adrenal, brain parenchymal, vertebral and retroperitoneal lymph node metastases were assessed by CT and MR scan. Progressive disease with eventual death of vomiting occured, and the rescue is invalid. The overall survival time was 110 days after surgery. Conclusion: For non-small cell lung cancer patients with both rare EGFR mutation (L861Q) and small bowel metastasis, the prompt diagnosis and treatment against primary tumor are the keys to improve their prognosis. Rare EGFR mutations are heterogeneous and lack of standard treatment due to the low incidence. Further large-scale prospective randomized controlled studies are needed.

Recent advances in genome-wide association study and rare variants of late-onset Alzheimer's disease in different populations / 中华神经医学杂志

Alzheimer's disease is a neurodegenerative disease of the central nervous system. With the aging of the population, the prevalence of AD is increasing, which seriously affects the society and family. The etiology of AD is influenced by many factors, such as genetic factors and environmental factors. Among them, the influence of genetic factors accounted for dominant position. Therefore, the study of genetic factors plays an important role in the prevention and treatment of AD. In this paper, we reviewed the recent studies on genome-wide association study and rare variants of late-onset AD in different population.