Probe-free allele-specific copy number detection and analysis of tumors

Zhu, Ailin; Guan, Xiaowei; Gu, Xing; Xie, Guiqin

doi:10.1016/j.ab.2015.12.012

Cited by 3 publications

(2 citation statements)

References 25 publications

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“…And mutations can be genotyped using the threshold cycle (C t ) value. 27,28 Thus, in this study, we developed a genotype assay method based on AS-qPCR in the presence of SYBR green I and validated the accuracy of the method by conventional DNA sequencing, which is a highly sensitive, time-saving, and cost-effective method.…”

mentioning

confidence: 94%

“…If SYBR green I DNA‐binding dye‐based quantitative real‐time PCR (Q‐PCR) is combined with AS‐PCR, the assay can be performed in one step without post‐PCR processing. And mutations can be genotyped using the threshold cycle ( C t ) value 27,28 . Thus, in this study, we developed a genotype assay method based on AS‐qPCR in the presence of SYBR green I and validated the accuracy of the method by conventional DNA sequencing, which is a highly sensitive, time‐saving, and cost‐effective method.…”

Section: Introductionmentioning

confidence: 99%

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An AS‐qPCR‐based method for the detection of Alzheimer's disease‐related SNPs

Chen

Shi

et al. 2022

J of Cellular Biochemistry

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Alzheimer's disease (AD) is one of the most serious neurodegenerative diseases in the world and has a strong genetic predisposition. At present, there is still no effective method for the early diagnosis and prevention of AD. Accumulating evidence shows the association of several loci with AD risk, such as apolipoprotein E (APOE) and translocase of outer mitochondrial membrane 40 (TOMM40). However, for routine disease diagnosis in clinics, genotype detection methods based on gene sequencing technology are time-consuming and excessively costly. Thus, in this study, we developed a high-sensitivity, low-cost, and convenient single nucleotide polymorphism (SNP) detection assay method based on allele-specific quantitative polymerase chain reaction (AS-qPCR) technology, which can be used to determine the SNP genotype in APOE and TOMM40. A total of 40 patients were recruited from the outpatient department of the memory clinic of Dongzhimen Hospital, Beijing University of Chinese Medicine. The SNP detection assay method includes three steps. First, positive plasmids with different genotypes (TT/CC/TC) in APOE rs429358, rs7412, and TOMM40 rs11556505 were prepared. Second, 3′-T/3′-C primers were designed to amplify these positive plasmids for each SNP site. Finally, we calculated the log10 of the copy number ratio for each positive plasmid, and the genotype interpretation interval was established. Based on this method, we investigated whether the SNPs in 40 patients could be accurately calculated using AS-qPCR technology. The accuracy of SNP detection was verified by PCR-Pooling sequencing. The results showed that SNP genotypes assessed by AS-qPCR technology corresponded perfectly to the results obtained by conventional DNA sequencing. We have developed a genotype detection method for AD based on AS-qPCR, which can be performed easily, rapidly, accurately, and at low cost. The method will contribute to the early diagnosis of patients with late-onset Alzheimer's and the detection of large clinical samples in the future. K E Y W O R D Sallele-specific quantitative polymerase chain reaction (AS-qPCR), Alzheimer's disease (AD), apolipoprotein E (APOE), single nucleotide polymorphism (SNP), translocase of outer mitochondrial membrane 40 (TOMM40)

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confidence: 94%

Section: Introductionmentioning

confidence: 99%

An AS‐qPCR‐based method for the detection of Alzheimer's disease‐related SNPs

Chen

Shi

et al. 2022

J of Cellular Biochemistry

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Simple quantitative PCR analysis for allelic Pten loss in tumor progression

Zhu

Pang

et al. 2017

Analytical Biochemistry

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Antitumor Efficacy of EGFR-Targeted Recombinant Immunotoxin in Human Head and Neck Squamous Cell Carcinoma

Xie

Shan

Liu

et al. 2022

Biology

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Over 90% of head and neck squamous cell carcinoma (HNSCC) overexpresses the epidermal growth factor receptor (EGFR). However, the EGFR-targeted monotherapy response rate only achieves 10–30% in HNSCC. Recombinant immunotoxin (RIT) often consists of an antibody targeting a tumor antigen and a toxin (e.g., diphtheria toxin [DT]) that kills cancer cells. We produced a humanized RIT, designated as hDT806, targeting overexpressed EGFR and investigated its effects in HNSCC. Distinct from the EGFR-targeted tyrosine kinase inhibitor erlotinib or antibody cetuximab, hDT806 effectively suppressed cell proliferation in the four HNSCC lines tested (JHU-011, -013, -022, and -029). In JHU-029 mouse xenograft models, hDT806 substantially reduced tumor growth. hDT806 decreased EGFR protein levels and disrupted the EGFR signaling downstream effectors, including MAPK/ERK1/2 and AKT, while increased proapoptotic proteins, such as p53, caspase-9, caspase-3, and the cleaved PAPR. The hDT806-induced apoptosis of HNSCC cells was corroborated by flow cytometric analysis. Furthermore, hDT806 resulted in a drastic inhibition in RNA polymerase II carboxy-terminal domain phosphorylation critical for transcription and a significant increase in the γH2A.X level, a DNA damage marker. Thus, the direct disruption of EGFR signaling, transcription inhibition, DNA damage, as well as apoptosis induced by hDT806 may contribute to its antitumor efficacy in HNSCC.

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Probe-free allele-specific copy number detection and analysis of tumors

Cited by 3 publications

References 25 publications

An AS‐qPCR‐based method for the detection of Alzheimer's disease‐related SNPs

An AS‐qPCR‐based method for the detection of Alzheimer's disease‐related SNPs

Simple quantitative PCR analysis for allelic Pten loss in tumor progression

Antitumor Efficacy of EGFR-Targeted Recombinant Immunotoxin in Human Head and Neck Squamous Cell Carcinoma

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