Sensitive detection of trace amounts of KRAS codon 12 mutations by a fast and novel one-step technique

Xie, Feifei; Huang, Jie; Qu, Su; Wu, Weili; Jiang, Jun; Wang, Huagui; Wang, Shujuan; Liu, Qi; Zhang, Senlin; Xu, Lizhi; Gao, Shangxian; Zhang, Yunqing; Zhao, Jinyin; Chen, Weijun

doi:10.1016/j.clinbiochem.2014.08.015

Cited by 7 publications

(4 citation statements)

References 27 publications

(23 reference statements)

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“…Indeed, probe-blocking methods have been engineered to block amplification of wild-type templates and thus, to increase detection sensitivity of mutant alleles. Therefore, minor groove binder (MGB) blocker oligonucleotide [37] and modified non-extendable primer blocker (NEPB) [36] have been developed and demonstrated the detection of mutation present at 0.1% in a background of wild-type DNA. Scorpion probes, for which higher sensitivity compared to Taqman probes has been demonstrated, also enable the detection of rare mutations [58,59,60,61,62].…”

Section: Technical Approaches For Ctdna Detection and Analysismentioning

confidence: 99%

Circulating Cell Free Tumor DNA Detection as a Routine Tool forLung Cancer Patient Management

Vendrell

Mau-Them

Béganton

et al. 2017

IJMS

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Circulating tumoral DNA (ctDNA), commonly named “liquid biopsy”, has emerged as a new promising noninvasive tool to detect biomarker in several cancers including lung cancer. Applications involving molecular analysis of ctDNA in lung cancer have increased and encompass diagnosis, response to treatment, acquired resistance and prognosis prediction, while bypassing the problem of tumor heterogeneity. ctDNA may then help perform dynamic genetic surveillance in the era of precision medicine through indirect tumoral genomic information determination. The aims of this review were to examine the recent technical developments that allowed the detection of genetic alterations of ctDNA in lung cancer. Furthermore, we explored clinical applications in patients with lung cancer including treatment efficiency monitoring, acquired therapy resistance mechanisms and prognosis value.

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Section: Technical Approaches For Ctdna Detection and Analysismentioning

confidence: 99%

Circulating Cell Free Tumor DNA Detection as a Routine Tool forLung Cancer Patient Management

Vendrell

Mau-Them

Béganton

et al. 2017

IJMS

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“…On gene analysis, the MassARRAY (Agena Bioscience) platform based on PCR and MALDI-TOF MS has been used in various genetics and epigenetics research, and in clinical diagnosis of genetic disorders, including the quantitative analysis of gene expression, analysis of gene copy number variation (CNV), single nucleotide polymorphism (SNP) genotyping, DNA methylation identification, etc. [ [22] , [23] , [24] , [25] , [26] ].…”

Section: Introductionmentioning

confidence: 99%

Isothermal gene amplification coupled MALDI-TOF MS for SARS-CoV-2 detection

Han

Lin

et al. 2022

Talanta

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The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been spreading worldwide for more than a year and has undergone several mutations and evolutions. Due to the lack of effective therapeutics and long-active vaccines, accurate and large-scale screening and early diagnosis of infected individuals are crucial to control the pandemic. Nevertheless, the current widely used RT-qPCR-based methods suffer from complicated temperature control, long processing time and the risk of false-negative results. Herein, we present a three-way junction induced exponential rolling circle amplification (3WJ-eRCA) combined MALDI-TOF MS assay for SARS-CoV-2 detection. The assay can detect simultaneously the target nucleocapsid (N) and open reading frame 1 ab (orf1ab) genes of SARS-CoV-2 in a single test within 30 min, with an isothermal process (55 °C). High specificity to discriminate SARS-CoV-2 from other coronaviruses, like SARS-CoV, MERS-CoV and bat SARS-like coronavirus (bat-SL-CoVZC45), was observed. We have further used the method to detect pseudovirus of SARS-CoV-2 in various matrices, e.g. water, saliva and urine. The results demonstrated a great potential of the method for large scale screening of COVID-19, which is an important part of the pandemic control.

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Section: Introductionmentioning

confidence: 99%

“…Selectivity, which refers to the abilities to detect mutant (MT) alleles selectively among an excess of WT-alleles, is one of the most important methodological parameters in mutation analysis 8 – 10 . Selectivity is defined as the ratio of copy number between minimum detectable MT-alleles and the total inputted alleles, including both WT- and MT-alleles 8 – 10 . Among various methods targeting BRAF V600E, allele-specific PCR (AS-PCR) is the most common but always has a limited selectivity of 1–5%, i.e., it can only detect around 1–5% of MT-alleles except for one publication reported higher selectivity up to 0.3% using TaqMan-based AS-PCR system 11 – 13 .…”

Section: Introductionmentioning

confidence: 99%

Improved detection of BRAF V600E using allele-specific PCR coupled with external and internal controllers

Yang

Zhao

Chen³

et al. 2017

Sci Rep

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Although traditional allele-specific PCR (tAS-PCR) is a common screening method for BRAF V600E mutations, its lower amplification specificity and mutation selectivity have limited its clinical applications. We hypothesize that these limitations are associated with the weaker specificities of allele-specific primers and the thermodynamic driving forces of DNA polymerase. We used three strategies to circumvent these limitations, namely, modifying allele-specific primers, introducing a competitive external allele-specific controller (i.e., cAS-PCR), and introducing a referenced internal positive controller in the cAS-PCR (i.e., rcAS-PCR). The amplification sensitivities and specificities were influenced by the position of the artificially introduced mismatched nucleotide in the allele-specific primers. Moreover, both cAS-PCR and rcAS-PCR could detect single-copy BRAF V600E alleles with higher mutation selectivity (0.1%) than tAS-PCR. In addition, cAS-PCR eliminated false-negative results caused by various PCR inhibitors that might be present in the DNA solutions. The rcAS-PCR could also be employed to avoid the false-negative results caused by low-abundance input templates in cAS-PCR. In conclusion, rcAS-PCR provides a rapid, simple, and low-cost method for detecting low levels of the mutated BRAF V600E gene.

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Sensitive detection of trace amounts of KRAS codon 12 mutations by a fast and novel one-step technique

Cited by 7 publications

References 27 publications

Circulating Cell Free Tumor DNA Detection as a Routine Tool forLung Cancer Patient Management

Circulating Cell Free Tumor DNA Detection as a Routine Tool forLung Cancer Patient Management

Isothermal gene amplification coupled MALDI-TOF MS for SARS-CoV-2 detection

Improved detection of BRAF V600E using allele-specific PCR coupled with external and internal controllers

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