Robust SNP genotyping by multiplex PCR and arrayed primer extension

Podder, Mohua; Ruan, Jian; Tripp, Ben W.; Chu, Zane E.; Tebbutt, Scott J.

doi:10.1186/1755-8794-1-5

Cited by 19 publications

(26 citation statements)

References 31 publications

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“…SNPs are single base change in DNA sequences and although biallelic, they show some advantages over microsatellites, mainly because they overtake the major problem of microsatellites, consisting in the lack of unicity in determining their size, when genotyping is performed on different analyzers and/or at different times. SNPs are highly abundant in the genome, i.e., averagely one SNP every 100-500 base pairs (Heaton et al, 2001) and several technologies are now well established for SNPs genotyping (MALDI TOF assay, primer extension, TaqMan, and several microchip technologies) (Bray, Boerwinkle, & Doris, 2001;Dearlove, 2002;Syvanen, 2005;Podder, Ruan, Tripp, Chu & Tebbutt, 2008). These technologies allow high throughput automated analysis and the SNPs databases so obtained are comparable even when changing genotyping platform.…”

Section: Introductionmentioning

confidence: 99%

Characterization of a SNPs panel for meat traceability in six cattle breeds

Orrù¹,

Catillo²,

Napolitano³

et al. 2009

Food Control

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Section: Introductionmentioning

confidence: 99%

Characterization of a SNPs panel for meat traceability in six cattle breeds

Orrù¹,

Catillo²,

Napolitano³

et al. 2009

Food Control

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“…small slides. The main principle of APEX is that oligonucleotides are placed on the microarray glass slide through their 5' end and complementary PCR amplified fragment from DNA sample is annealed to the oligonucleotides [39].…”

Section: Array Primer Extension (Apex) Assaymentioning

confidence: 99%

“…After signal detection, the nucleotide being typed is the dye tagged nucleotide (e.g. T) bound to the oligonucleotide on the microarray slide [3,39].…”

Section: Array Primer Extension (Apex) Assaymentioning

confidence: 99%

DNA Microarray and Bioinformatics Technologies: A mini-review

Missoum¹

2018

Proc. Nat. Res. Soc.

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This bibliographic review gives a concise overview of how DNA microarrays became one of the most important recent technologies. In brief, DNA sequences acting as probes are fixed on tiny slides in arrays to identify the presence of tagged fluorescently nucleic acids from a certain sample. The nucleic acids having complementary sequences with probes will hybridize on the array slides and because they are labeled, they are detected easily using specialized scanner and software. According to the way DNA microarrays are manufactured, there are three main types including spotted arrays, in situ synthesized arrays, and self-assembled arrays. Bioinformatics, which is the use of mathematical and computational methods, plays a crucial role in this technology as it is used for designing specific primers and probes suitable for each sample that is investigated. Moreover, although DNA microarrays are widely used to determine gene expression levels, they are also used in single nucleotide polymorphism (SNP) genotyping. For this application itself, more than one approach can be used including allele discrimination using hybridization, array primer extension assay (APEX), and Illumina infinium assay. The APEX approach was discussed in more detail as it was found that to be useful in screening for inherited genetic diseases such as Stargardt disease. Finally, this review was ended with short discussion of some DNA microarray limitations arising hybridization kinetics as well as difficulties in designing arrays for highly variable genomes.

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“…Minisequencing [1] is probably the SNP detection principle with the highest signal to noise ratio. Minisequencing, however, is limited by a linear signal amplification, [2] making it difficult with direct genomic SNP detection.…”

Section: Introductionmentioning

confidence: 99%

DIRECT DETECTION OF SINGLE-NUCLEOTIDE POLYMORPHISMS IN BACTERIAL DNA BY SNPtrap

Grønlund

Moen

Hoorfar

et al. 2011

Preparative Biochemistry and Biotechnology

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A major challenge with single-nucleotide polymorphism (SNP) fingerprinting of bacteria and higher organisms is the combination of genome-wide screenings with the potential of multiplexing and accurate SNP detection. Single-nucleotide extension by the minisequencing principle represents a technology that both is highly accurate and enables multiplexing. A current bottleneck for direct genome analyses by minisequencing, however, is the sensitivity, since minisequencing relies on linear signal amplification. Here, we present SNPtrap, which is a novel approach that combines the specificity and possibility of multiplexing by minisequencing with the sensitivity obtained by logarithmic signal amplification by polymerase chain reaction (PCR). We show a SNPtrap proof of principle in a model system for two polymorphic SNP sites in the Salmonella tetrathionate reductase gene (ttrC).

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Robust SNP genotyping by multiplex PCR and arrayed primer extension

Cited by 19 publications

References 31 publications

Characterization of a SNPs panel for meat traceability in six cattle breeds

Characterization of a SNPs panel for meat traceability in six cattle breeds

DNA Microarray and Bioinformatics Technologies: A mini-review

DIRECT DETECTION OF SINGLE-NUCLEOTIDE POLYMORPHISMS IN BACTERIAL DNA BY SNPtrap

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