A multiplex single nucleotide polymorphism genotyping method using ligase‐based mismatch discrimination and <scp>CE‐SSCP</scp>

Choi, Woong; Shin, Gi Won; Hwang, Hee Sung; Pack, Seung Pil; Jung, Gyu Yong; Jung, Gyoo Yeol

doi:10.1002/elps.201300486

Cited by 13 publications

(10 citation statements)

References 19 publications

(18 reference statements)

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“…The main drawback for fluorescent detection is photo-bleaching. Fluorescent detection has been successfully applied in multiplex detection of various SNPs and mutations using various fluorescent probes or the same fluorescent label but with different sized LCR amplicons [53,57].…”

Section: Fluorescent Methodsmentioning

confidence: 99%

“…This universal chip platform has also been microfabricated with polycarbonate and poly(methyl methacrylate) for the detection of K-ras oncogene SNPs [56]. Choi et al reported a multiplex SNP genotyping assay consisting of multiplex PCR pre-amplification, ligation with DNA ligase and CE-fSSCP to increase resolving power for similar sized probes [57]. This assay was able to accurately discriminate SNPs in the tp53 gene.…”

Section: Ligase Detection Reaction (Ldr)mentioning

confidence: 99%

“…LCR was used in multiplex SNP genotyping of nine SNP in p53 gene. It has advantages over conventional PCR in lack of constraints over primer size as well as the use of primers of similar sizes to facilitate optimization of ligation conditions [57].…”

Section: Detection Of Genetic Diseasesmentioning

confidence: 99%

“…Nested LCR is not common at all and is considered to be more expensive than conventional LCR as it requires more reagents and reactions. LDR is one of the most widely used versions of LCR that has overcome several drawbacks reported earlier on for conventional LCR [51][52][53][54][55][56][57][149][150][151][152][153][154][155]. In this technique, only two oligonucleotides are used for linear amplification of samples and this in turn preserves the ratio for the two alleles and also reduces background signal for target independent ligation.…”

Section: Comparative Evaluation For Various Versions Of Lcr and Ligatmentioning

confidence: 99%

“…In this technique, only two oligonucleotides are used for linear amplification of samples and this in turn preserves the ratio for the two alleles and also reduces background signal for target independent ligation. Various detection methods such as microarray, SERS, FRET, capillary electrophoresis and magnetic beads have been integrated with LDR for improved sensitivity, multiplexing potential and high-throughput applications [51][52][53][54][55][56][57]101,[105][106][107][108]119]. LDR can detect as low as 1 mutant allele in 1000 copies of wild type sample with a detection limit of 0.4-1fM [101,[106][107].…”

Section: Comparative Evaluation For Various Versions Of Lcr and Ligatmentioning

confidence: 99%

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Advances in ligase chain reaction and ligation-based amplifications for genotyping assays: Detection and applications

Gibriel

Adel

2017

Mutation Research/Reviews in Mutation Research

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Genetic variants have been reported to cause several genetic diseases. Various genotyping assays have been developed for diagnostic and screening purposes but with certain limitations in sensitivity, specificity, cost effectiveness and/or time savings. Since the discovery of ligase chain reaction (LCR) in the late nineties, it became one of the most favored platforms for detecting these variants and also for genotyping low abundant contaminants. Recent and powerful modifications with the integration of various detection strategies such as electrochemical and magnetic biosensors, nanoparticles (NPs), quantum dots, quartz crystal and leaky surface acoustic surface biosensors, DNAzyme, rolling circle amplification (RCA), strand displacement amplification (SDA), surface enhanced raman scattering (SERS), chemiluminescence and fluorescence resonance energy transfer have been introduced to both LCR and ligation based amplifications to enable high-throughput and inexpensive multiplex genotyping with improved robustness, simplicity, sensitivity and specificity. In this article, classical and up to date modifications in LCR and ligation based amplifications are critically evaluated and compared with emphasis on points of strength and weakness, sensitivity, cost, running time, equipment needed, applications and multiplexing potential. Versatile genotyping applications such as genetic diseases detection, bacterial and viral pathogens detection are also detailed. Ligation based gold NPs biosensor, ligation based RCA and ligation mediated SDA assays enhanced detection limit tremendously with a discrimination power approaching 1.5aM, 2aM and 0.1fM respectively. MLPA (multiplexed ligation dependent probe amplification) and SNPlex assays have been commercialized for multiplex detection of at least 48 SNPs at a time. MOL-PCR (multiplex oligonucleotide ligation) has high-throughput capability with multiplex detection of 50 SNPs/well in a 96 well plate. Ligase detection reaction (LDR) is one of the most widely used LCR versions that have been successfully integrated with several detection strategies with improved sensitivity down to 0.4fM.

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Section: Fluorescent Methodsmentioning

confidence: 99%

Section: Ligase Detection Reaction (Ldr)mentioning

confidence: 99%

Section: Detection Of Genetic Diseasesmentioning

confidence: 99%

Section: Comparative Evaluation For Various Versions Of Lcr and Ligatmentioning

confidence: 99%

Section: Comparative Evaluation For Various Versions Of Lcr and Ligatmentioning

confidence: 99%

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Advances in ligase chain reaction and ligation-based amplifications for genotyping assays: Detection and applications

Gibriel

Adel

2017

Mutation Research/Reviews in Mutation Research

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F‐108 polymer and capillary electrophoresis easily resolves complex environmental DNA mixtures and SNPs

et al. 2014

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Ecological studies of microbial communities often use profiling methods but the true community diversity can be underestimated in methods that separate amplicons based on sequence length using performance optimized polymer 4. Taxonomically, unrelated organisms can produce the same length amplicon even though the amplicons have different sequences. F-108 polymer has previously been shown to resolve same length amplicons by sequence polymorphisms. In this study, we showed F-108 polymer, using the ABI Prism 310 Genetic Analyzer and CE, resolved four bacteria that produced the same length amplicon for the 16S rRNA domain V3 but have variable nucleotide content. Second, a microbial mat community profile was resolved and supported by NextGen sequencing where the number of peaks in the F-108 profile was in concordance with the confirmed species numbers in the mat. Third, equine DNA was analyzed for SNPs. The F-108 polymer was able to distinguish heterozygous and homozygous individuals for the melanocortin 1 receptor coat color gene. The method proved to be rapid, inexpensive, reproducible, and uses common CE instruments. The potential for F-108 to resolve DNA mixtures or SNPs can be applied to various sample types-from SNPs to forensic mixtures to ecological communities.

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High‐resolution pluronic‐filled microchip CE‐SSCP analysis system via channel width control

et al. 2015

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Although the resolution of CE-SSCP has been significantly improved by using a poly(ethyleneoxide)-poly(propyleneoxide)-poly(ethyleneoxide) (PEO-PPO-PEO; Pluronic(®)) triblock copolymer as a separation medium, CE-SSCP on a microchip format is not widely applicable because their resolution is limited by short channel length. Therefore, a strategy to improve the resolution in channels of limited lengths is highly required for enabling microchip-based CE-SSCP. In this study, we developed a high-resolution CE-SSCP microchip system by controlling the width of the pluronic-filled channel. We tested four different channel widths of 180, 240, 300, and 400 μm, and found that 300 μm showed the highest resolution in the separation of two pathogen specific markers. Potential applications of our method in various genetic analyses were also shown by using SNP markers for spinal muscular atrophy.

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A multiplex single nucleotide polymorphism genotyping method using ligase‐based mismatch discrimination and CE‐SSCP

Cited by 13 publications

References 19 publications

Advances in ligase chain reaction and ligation-based amplifications for genotyping assays: Detection and applications

Advances in ligase chain reaction and ligation-based amplifications for genotyping assays: Detection and applications

F‐108 polymer and capillary electrophoresis easily resolves complex environmental DNA mixtures and SNPs

High‐resolution pluronic‐filled microchip CE‐SSCP analysis system via channel width control

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