A mass spectrometry-based multiplex SNP genotyping by utilizing allele-specific ligation and strand displacement amplification

Park, Jung Hun; Jang, Hyowon; Jung, Yun Kyung; Jung, Ye Lim; Shin, Insik; Cho, Daeyeon; Park, Hyun Gyu

doi:10.1016/j.bios.2016.10.065

Cited by 26 publications

(10 citation statements)

References 54 publications

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“…have proved reliable application for this purpose. Nevertheless, SDA has poorly achieved longer sequence amplification and a comparable amplification as for LAMP toward turbidity measurement, but under stringent conditions, possesses higher sensitivity, specificity, and cost-efficiency, and can be multiplexed and reprogrammed for various targets [58,[93][94][95][96]. But also, other isothermal amplification methods such as LAMP have hardly shown multiplexing capacity [97][98][99] and are solely dye dependent for colorimetric detection and quantification, which are target independent and nonspecific.…”

Section: Discussion Conclusion and Future Perspectivesmentioning

confidence: 99%

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Strand Displacement Amplification for Multiplex Detection of Nucleic Acids

Zeng¹,

Mukama²,

Lu³

et al. 2019

Modulating Gene Expression - Abridging the RNAi and CRISPR-Cas9 Technologies

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The identification of various targets such as bacteria, viruses, and other cells remains a prerequisite for point-of-care diagnostics and biotechnological applications. Nucleic acids, as encoding information for all forms of life, are excellent biomarkers for detecting pathogens, hereditary diseases, and cancers. To date, many techniques have been developed to detect nucleic acids. However, most of them are based on polymerase chain reaction (PCR) technology. These methods are sensitive and robust, but they require expensive instruments and trained personnel. DNA strand displacement amplification is carried out under isothermal conditions and therefore does not need expensive instruments. It is simple, fast, sensitive, specific, and inexpensive. In this chapter, we introduce the principles, methods, and updated applications of DNA strand displacement technology in the detection of infectious diseases. We also discuss how robust, sensitive, and specific nucleic acid detection could be obtained when combined with the novel CRISPR/Cas system.

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Section: Discussion Conclusion and Future Perspectivesmentioning

confidence: 99%

“…Allele-specific regions were amplified and then ligated to adapters by DNA ligase, and the ligated products were SDA amplified with universal primers. The resulting fragments were analyzed and confirmed using mass spectrometry [58]. Though, this SDA method required complex equipment, it was able to detect hundreds of mutations.…”

Section: Multiplex Sda Reactionmentioning

confidence: 99%

Strand Displacement Amplification for Multiplex Detection of Nucleic Acids

Zeng¹,

Mukama²,

Lu³

et al. 2019

Modulating Gene Expression - Abridging the RNAi and CRISPR-Cas9 Technologies

View full text Add to dashboard Cite

show abstract

“…Several methods were reported in the detection of SNP markers, including SSCP (Kozlowski and Krzyzosiak, 2001), DGGE (Guldberg et al 1993), CAPS (Li et al 2012), DNA-chip (Singh et al 2015), DHPLC (Wolford et al 2000;Colasuonno et al 2016), mass spectrometric detection (Park et al 2017), and HRM (high-resolution melting) (Villano et al 2016;Kim et al 2016). The recently developed HRM analysis method provided us a novel, quick, and close-tube PCR approach to analyze SNPs (Nguyen et al 2012).…”

Section: Introductionmentioning

confidence: 99%

DNA Fingerprinting of Vegetable Soybean Cultivar ‘Zhexian No.9’ Using 101 New Developed HRM-Based SNP Markers

Pei

Zheng

et al. 2019

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Single nucleotide polymorphisms (SNPs) have been proved to be powerful markers in genetic analysis due to their high abundance and polymorphism in plant genomes. The recently developed high-resolution melting (HRM) analysis method provides a novel, quick, and close-tube PCR approach to analyze SNP variations. In present study, 101 HRM-based SNP markers from 20 soybean chromosomes were developed for genotyping vegetable soybean cultivar 'Zhexian No.9' with 'Williams 82' as reference. 33.7% of these markers were polymorphic between 'Zhexian No.9' and 'Williams 82'. Polymorphic markers were found on 85% (17 of 20) of the soybean chromosomes when comparing 'Zhexian No.9' and 'Williams 82'. Finally, an array of 101 in-sequence nucleotide letters was generated as the first precise SNP fingerprint of 'Zhexian No.9'. The described marker-developing methodology could be used in other crops with known genomic information.

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“…Recently, several technologies have been developed that can simplify experimental process by using hybridization with fluorescence resonance energy transfer probes, high‐resolution melting curves, TaqMan probes, MS, or next generation sequencing (NGS) . The disadvantages of real‐time PCR methods include expensive instruments, and the cost to design and synthesize new TaqMan probe for each SNP.…”

Section: Introductionmentioning

confidence: 99%

A multiplex SNP genotyping by allele‐specificspecific PCR based on stem‐loop and universal fluorescent primers of Chr1^daxin mice

Wang

Chen

et al. 2019

Electrophoresis

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Single nucleotide polymorphisms (SNPs) are one of the most common markers in mammals. Rapid, accurate, and multiplex typing of SNPs is critical for subsequent biological and genetic research. In this study, we have developed a novel method for multiplex genotyping SNPs in mice. The method involves allele‐specific PCR amplification of genomic DNA with two stem‐loop primers accompanied by two different universal fluorescent primers. Blue and green fluorescent signals were conveniently detected on a DNA sequencer. We verified four SNPs of 65 mice based on the novel method, and it is well suited for multiplex genotyping as it requires only one reaction per sample in a single tube with multiplex PCR. The use of universal fluorescent primers greatly reduces the cost of designing different fluorescent probes for each SNP. Therefore, this method can be applied to many biological and genetic studies, such as multiple candidate gene testing, genome‐wide association study, pharmacogenetics, and medical diagnostics.

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A mass spectrometry-based multiplex SNP genotyping by utilizing allele-specific ligation and strand displacement amplification

Cited by 26 publications

References 54 publications

Strand Displacement Amplification for Multiplex Detection of Nucleic Acids

Strand Displacement Amplification for Multiplex Detection of Nucleic Acids

DNA Fingerprinting of Vegetable Soybean Cultivar ‘Zhexian No.9’ Using 101 New Developed HRM-Based SNP Markers

A multiplex SNP genotyping by allele‐specificspecific PCR based on stem‐loop and universal fluorescent primers of Chr1^daxin mice

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A mass spectrometry-based multiplex SNP genotyping by utilizing allele-specific ligation and strand displacement amplification

Cited by 26 publications

References 54 publications

Strand Displacement Amplification for Multiplex Detection of Nucleic Acids

Strand Displacement Amplification for Multiplex Detection of Nucleic Acids

DNA Fingerprinting of Vegetable Soybean Cultivar ‘Zhexian No.9’ Using 101 New Developed HRM-Based SNP Markers

A multiplex SNP genotyping by allele‐specificspecific PCR based on stem‐loop and universal fluorescent primers of Chr1daxin mice

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Product

Resources

About

A multiplex SNP genotyping by allele‐specificspecific PCR based on stem‐loop and universal fluorescent primers of Chr1^daxin mice