A novel liquidchip platform for simultaneous detection of 70 alleles of DNA somatic mutations on <i>EGFR, KRAS, BRAF</i> and <i>PIK3CA</i> from formalin-fixed and paraffin-embedded slides containing tumor tissue

Li, Guoqiang; Luo, Xiaodi; He, Jinzhi; Zhu, Zhengyan; Yu, Gang; Qin, Hongwu; Zeng, Tao; Liu, Zhiming; Wu, Shiyang; Xu, Jianbing; Ren-Heidenreich, Lifen

doi:10.1515/cclm.2011.040

Cited by 18 publications

(19 citation statements)

References 14 publications

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“…Tumor genomic DNA from each formalin fixed tissue was extracted by the Maxwell system (Promega, GA, USA) and the concentration determined using the Nanodrop 1000 spectrophotometer (Thermo Scientific, USA). The mutation status of exons 18 to 21 of EGFR, exons 2 and 3 of KRAS, exon 15 of BRAF and exons 9 and 20 of PIK3CA were analyzed simultaneously by xTAG liquidchip technology (SurExam, Guangzhou, China) [20]. Gene mRNA expression levels were analyzed simultaneously by multiplex branched DNA liquidchip (MBL) technology (SurExam, Guangzhou, China), a sandwich nucleic acid hybridization plat form in which targets are captured through cooperative hybridization of multiple probes in conjunction with a fluorescence signal amplification system, which has previously been shown to be a sufficient mRNA detection technology for FFPE specimens [21].…”

Section: Methodsmentioning

confidence: 99%

PIK3CA mutations are a predictor of docetaxel plus epirubicin neoadjuvant chemotherapy clinical efficacy in breast cancer

ZHANG¹,

LIU²,

Yang³

et al. 2014

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This study proposed to investigate the relationship of PIK3CA somatic mutations, the most common activating mutations in human breast cancer (BC), and the efficacy of neoadjuvant chemotherapy (NCT).Using a novel liquidchip technology, PIK3CA DNA somat ic mutations and HER2, PTEN, EGFR mRNA expression profiles were analyzed in formalin fixed paraffin embedded samples of 93 BC patients treated with epirubicin plus docetaxel NCT.PIK3CA mutations were found in 30 patients (32.3%), in which the point mutations of E542K, E545K, H1047L and H1047R were 4.3, 9.7, 4.3 and 14.0% respectively. The PIK3CA mutations were significantly associated with patients' clinical response; 27 of 30 PIK3CA mutated patients had either a partial or complete response (p=0.002). Multivariate analysis further confirmed that, after adjustments for age, disease stages and NCT cycles, PIK3CA was associated with clinical response (Odds Ration 0.126, 95% CI [0.029, 0.691]). However, there was no significant difference between PIK3CA mutations in pathological complete response (pCR, 7/92) and non-pCR group. Furthermore, no EGFR, KRAS and BRAF mutations were detected in any of the 93 samples.Our data for the first time suggested that PIK3CA mutation status may be a predictor for better understanding clinical response to the combination of epirubicin and docetaxel NCT in patients with BC.

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Section: Methodsmentioning

confidence: 99%

PIK3CA mutations are a predictor of docetaxel plus epirubicin neoadjuvant chemotherapy clinical efficacy in breast cancer

ZHANG¹,

LIU²,

Yang³

et al. 2014

neo

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“…The AR is equal to the net MFI for an allele divided by the sum of the net MFIs for all alleles tested for a given mutation site, which represents the fraction of the total net MFI signal for the mutation site attributed to the presence of a particular allele. Threshold values were determined according to procedures described in previous studies (35,36); an AR of Ն0.10 indicated the presence of a particular allele, and if more than one allele had an AR of Ն0.10, a mixture was called. Figure 1 is a schematic illustration of the mASPE and suspension array analysis processes.…”

Section: Methodsmentioning

confidence: 99%

Simultaneous Detection of Major Drug Resistance Mutations in the Protease and Reverse Transcriptase Genes for HIV-1 Subtype C by Use of a Multiplex Allele-Specific Assay

Zhang¹,

Cai

Zhou³

et al. 2013

J Clin Microbiol

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High-throughput, sensitive, and cost-effective HIV drug resistance (HIVDR) detection assays are needed for large-scale monitoring of the emergence and transmission of HIVDR in resource-limited settings. Using suspension array technology, we have developed a multiplex allele-specific (MAS) assay that can simultaneously detect major HIVDR mutations at 20 loci. Forty-five allele-specific primers tagged with unique 24-base oligonucleotides at the 5= end were designed to detect wild-type and mutant alleles at the 20 loci of HIV-1 subtype C. The MAS assay was first established and optimized with three plasmid templates (C-wt, C-mut1, and C-mut2) and then evaluated using 148 plasma specimens from HIV-1 subtype C-infected individuals. All the wild-type and mutant alleles were unequivocally distinguished with plasmid templates, and the limits of detection were 1.56% for K219Q and K219E, 3.13% for L76V, 6.25% for K65R, K70R, L74V, L100I, K103N, K103R, Q151M, Y181C, and I47V, and 12.5% for M41L, K101P, K101E, V106A, V106M, Y115F, M184V, Y188L, G190A, V32I, I47A, I84V, and L90M. Analyses of 148 plasma specimens revealed that the MAS assay gave 100% concordance with conventional sequencing at eight loci and >95% (range, 95.21% to 99.32%) concordance at the remaining 12 loci. The differences observed were caused mainly by 24 additional low-abundance alleles detected by the MAS assay. Ultradeep sequencing analysis confirmed 15 of the 16 low-abundance alleles. This multiplex, sensitive, and straightforward result-reporting assay represents a new efficient genotyping tool for HIVDR surveillance and monitoring.

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“…EGFR exons 18, 19 and 21 were screened using SurPlex®-xTAG70plex (SurExam, GZ, China). The method includes five steps published in ref [31].…”

Section: Methodsmentioning

confidence: 99%

Individualized treatment of NSCLC: From research to clinical practice

Zd²,

Lm³

et al. 2013

neo

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The exact clinical significance of EGFR mutation status in NSCLC at the time of initial diagnosis remains disputable. The gene expression module in NSCLC for chemotherapy outcome prediction needs to be developed. We analyzed 56 patients with NSCLC received chemotherapy either with (n=20) or without EGFR-TKIs (n=36) between 2008 and 2012 in China. EGFR mutation test and gene expression profiling were performed in samples obtained before medication treatment by liquidchip platform. Significant association (P = 0.028) was seen between EGFR mutation status before first-line chemotherapy and EGFR-TKIs treatment outcomes, which even can be found from the status before second-or third-line treatment. A 14-gene expression profiling had been studied. Patients with low mRNA expression of ERCC1 or TYMS preferred higher DCR to cisplatin and pemetrexed than those with high expression (P = 0.39 and P = 0.11). Highly co-expression of TUBB3 and STMN1 gene has associated with the resistance to antimicrotubule drugs (P = 0.03). Our data suggest the EGFR mutations status, even at the time of initial diagnosis, is predictive of outcomes of TKIs treatment after chemotherapy. The mRNA expression profiling investigated in this study has a predictive value in NSCLC treatment, but further research with expanded samples is still required.

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A novel liquidchip platform for simultaneous detection of 70 alleles of DNA somatic mutations on EGFR, KRAS, BRAF and PIK3CA from formalin-fixed and paraffin-embedded slides containing tumor tissue

Abstract: A simple, accurate, sensitive HTP technology was developed and standardized for detecting simultaneously 70 different alleles of EGFR, KRAS, BRAF and PIK3CA gene mutations from FFPE tumor slides.

Cited by 18 publications

References 14 publications

PIK3CA mutations are a predictor of docetaxel plus epirubicin neoadjuvant chemotherapy clinical efficacy in breast cancer

PIK3CA mutations are a predictor of docetaxel plus epirubicin neoadjuvant chemotherapy clinical efficacy in breast cancer

Simultaneous Detection of Major Drug Resistance Mutations in the Protease and Reverse Transcriptase Genes for HIV-1 Subtype C by Use of a Multiplex Allele-Specific Assay

Individualized treatment of NSCLC: From research to clinical practice

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A novel liquidchip platform for simultaneous detection of 70 alleles of DNA somatic mutations on EGFR, KRAS, BRAF and PIK3CA from formalin-fixed and paraffin-embedded slides containing tumor tissue

Abstract: A simple, accurate, sensitive HTP technology was developed and standardized for detecting simultaneously 70 different alleles of EGFR, KRAS, BRAF and PIK3CA gene mutations from FFPE tumor slides.

Cited by 18 publications

References 14 publications

PIK3CA mutations are a predictor of docetaxel plus epirubicin neoadjuvant chemotherapy clinical efficacy in breast cancer

PIK3CA mutations are a predictor of docetaxel plus epirubicin neoadjuvant chemotherapy clinical efficacy in breast cancer

Simultaneous Detection of Major Drug Resistance Mutations in the Protease and Reverse Transcriptase Genes for HIV-1 Subtype C by Use of a Multiplex Allele-Specific Assay

Individualized treatment of NSCLC: From research to clinical practice

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PIK3CA mutations are a predictor of docetaxel plus epirubicin neoadjuvant chemotherapy clinical efficacy in breast cancer

PIK3CA mutations are a predictor of docetaxel plus epirubicin neoadjuvant chemotherapy clinical efficacy in breast cancer