Microarray-based detection of Korean-specific BRCA1 mutations

Jung, Cheulhee; Yim, Seong Chun; Cho, Dae Yeon; Chang, Ho Nam; Park, Hyun Gyu

doi:10.1007/s00216-008-1988-x

Cited by 8 publications

(3 citation statements)

References 19 publications

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“…To show that two-step PCR is possible with SD polymerase, we used human genomic DNA as the template and a primer set that amplified a BRCA -related gene (Online Resource Table 1) [ 5 ]. To compare the sensitivity of the three-step qPCR and two-step qPCR processes, serial dilutions of the DNA template with 300, 30, 3, and 0 copies were tested in duplicate assays .…”

Section: Resultsmentioning

confidence: 99%

“…DNA targets are mainly used for cancer diagnosis, such as the BRCA1 and BRCA2 genes, which are associated with breast, ovarian, pancreatic, and prostate cancers [ 3 , 4 ]. Accurate BRCA testing is essential for early detection, identifying gene mutations, and selection of treatments [ 5 , 6 ]. RNA viruses include Zika [ 7 ], Ebola [ 8 ], and influenza [ 9 , 10 ], as well as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) [ 11 ], first identified in December 2019.…”

Section: Introductionmentioning

confidence: 99%

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SF-qPCR: Strand Displacement-Based Fast Quantitative Polymerase Chain Reaction

Kim

Jung

2022

BioChip J

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Nucleic acid testing (NAT) is important for the identification and quantification of specific nucleic acid targets, both DNA and RNA, in life sciences and clinical diagnostics. Nucleic acid amplification can be a time-consuming step in NAT using the polymerase chain reaction (PCR) assay. Therefore, this study aimed to develop a simple method to reduce the amplification time while maintaining the PCR system. The three-step process of a general qPCR was reduced to a two-step process. The annealing/extension temperatures were increased to minimize the differences between the denaturation temperature and the annealing/extension temperatures. Subsequently, the time for each of these steps was reduced and, finally, the denaturation temperature was lowered. Taq polymerase was replaced with SD polymerase because it has strand displacement activity and is efficient in amplifying partial dsDNA at lower denaturation temperatures. In the two-step qPCR of genomic DNA using SD polymerase, the final conditions included an initial denaturation at 92 °C for 2 min, and 1 s at each cycling step with a denaturation temperature of 87 °C and an annealing/extension temperature of 72 °C. Amplification of the nucleocapsid ( N ) gene of SARS-CoV-2 RNA virus was evaluated at a template concentration as low as 10 copies. This method, named SF-qPCR (strand displacement-based fast quantitative polymerase chain reaction), can stably detect less than 10 copies of DNA and RNA within 25–40 min. This new protocol allows for sensitive and rapid detection of important DNA and RNA targets in clinical diagnosis. Supplementary Information The online version contains supplementary material available at 10.1007/s13206-021-00044-x.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

SF-qPCR: Strand Displacement-Based Fast Quantitative Polymerase Chain Reaction

Kim

Jung

2022

BioChip J

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“…The invention of the PCR technique has made a tremendous impact on the areas of biological research and diagnostics since it can be used to generate quantities of nucleic acids needed for detection and measurements. − However, the need for a temperature cycling instrument limits applications of PCR in point-of-care testing (POCT) environments . In order to overcome this limitation, several isothermal nucleic acid amplification methods have been developed.…”

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confidence: 99%

Isothermal Target and Signaling Probe Amplification Method, Based on a Combination of an Isothermal Chain Amplification Technique and a Fluorescence Resonance Energy Transfer Cycling Probe Technology

et al. 2010

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An iTPA (isothermal target and signaling probe amplification) method for the quantitative detection of nucleic acids, based on a combination of novel ICA (isothermal chain amplification) and fluorescence resonance energy transfer cycling probe technology (FRET CPT), is described. In the new ICA method, which relies on the strand displacement activity of DNA polymerase and the RNA degrading activity of RNase H, two displacement events occur in the presence of four specially designed primers. This phenomenon leads to powerful amplification of target DNA. Since the amplification is initiated only after hybridization of the four primers, the ICA method leads to high specificity for the target sequence. As part of the new ICA method, iTPA is achieved by incorporating FRET CPT to generate multiple fluorescence signals from a single target molecule. Using the resulting dual target and signaling probe amplification system, even a single copy level of a target gene can be successfully detected and quantified under isothermal conditions.

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Biochips as Novel Bioassays

Rudolph

Weber

Möller

2012

Handbook of Biophotonics

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The sections in this article are Introduction Types of Microarrays DNA Microarrays Protein Microarrays Tissue Microarrays Cell‐Based Microarrays (Transfection Microarrays) Principle Steps of an Experimental Microarray Process Basics Surface Biofunctionalization Preparation of Biomolecules (Sample Preparation) DNA RNA Proteins Target Amplification and Labeling PCR – Polymerase Chain Reaction In Vitro Transcription – c DNA / IVT Bio‐Barcode Amplification of Nucleic Acids and Proteins Radioactive and Fluorophore Labeling Enzymes Nanoparticles Readout/Detection Radioactivity Fluorescence/Absorbance Surface Plasmon Resonance Examples of Biochip Applications in Biology and Medicine Genomic Research SNP Detection Gene Expression Profile Analysis Pharmacogenomics and Toxicogenomics Pathogen Detection and Clinical Diagnosis Pathogen Detection Clinical Diagnosis Trends in Biochip Research Metal Nanoparticles Quantum Dots Enzymes Conclusion

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Microarray-based detection of Korean-specific BRCA1 mutations

Cited by 8 publications

References 19 publications

SF-qPCR: Strand Displacement-Based Fast Quantitative Polymerase Chain Reaction

SF-qPCR: Strand Displacement-Based Fast Quantitative Polymerase Chain Reaction

Isothermal Target and Signaling Probe Amplification Method, Based on a Combination of an Isothermal Chain Amplification Technique and a Fluorescence Resonance Energy Transfer Cycling Probe Technology

Biochips as Novel Bioassays

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