Enhanced allele-specific PCR discrimination in SNP genotyping using 3? locked nucleic acid (LNA) primers

2003 ◽  
Vol 22 (1) ◽  
pp. 79-85 ◽  
Author(s):  
David Latorra ◽  
Krista Campbell ◽  
Andreas Wolter ◽  
J. Michael Hurley
Keyword(s):  
Nucleic Acid ◽  
Snp Genotyping ◽  
Locked Nucleic Acid ◽  
Specific Pcr ◽  
Allele Specific ◽  
Allele Specific Pcr

scholarly journals Multiplex Allele-Specific PCR with Optimized Locked Nucleic Acid Primers

BioTechniques ◽  
2003 ◽  
Vol 34 (6) ◽  
pp. 1150-1158 ◽  
Author(s):  
David Latorra ◽  
Deborah Hopkins ◽  
Krista Campbell ◽  
J. Michael Hurley
Keyword(s):  
Nucleic Acid ◽  
Locked Nucleic Acid ◽  
Specific Pcr ◽  
Allele Specific ◽  
Allele Specific Pcr

scholarly journals SNP genotyping by allele-specific PCR using ENA® primers

2005 ◽  
Vol 49 (1) ◽  
pp. 47-48 ◽  
Author(s):  
Makoto Koizumi ◽  
Koji Morita ◽  
Miho Takagi ◽  
Hiroaki Yasumo ◽  
Atsushi Kasuya
Keyword(s):  
Snp Genotyping ◽  
Specific Pcr ◽  
Allele Specific ◽  
Allele Specific Pcr

Colorimetric SNP Genotyping Based on Allele-Specific PCR by Using a Thiol-Labeled Primer

ChemBioChem ◽  
2011 ◽  
Vol 12 (9) ◽  
pp. 1387-1390 ◽  
Author(s):  
Ye Lim Jung ◽  
Cheulhee Jung ◽  
Harshala Parab ◽  
Dae-Yeon Cho ◽  
Hyun Gyu Park
Keyword(s):  
Snp Genotyping ◽  
Specific Pcr ◽  
Allele Specific ◽  
Allele Specific Pcr

scholarly journals Modified “Allele-Specific qPCR” Method for SNP Genotyping Based on FRET

2022 ◽  
Vol 12 ◽  
Author(s):  
Ruslan Kalendar ◽  
Akmaral Baidyussen ◽  
Dauren Serikbay ◽  
Lyudmila Zotova ◽  
Gulmira Khassanova ◽  
...  
Keyword(s):  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Snp Genotyping ◽  
Single Nucleotide ◽  
Specific Pcr ◽  
Reaction Specificity ◽  
Qpcr Method ◽  
Associated Proteins ◽  
Allele Specific ◽  
Allele Specific Pcr

The proposed method is a modified and improved version of the existing “Allele-specific q-PCR” (ASQ) method for genotyping of single nucleotide polymorphism (SNP) based on fluorescence resonance energy transfer (FRET). This method is similar to frequently used techniques like Amplifluor and Kompetitive allele specific PCR (KASP), as well as others employing common universal probes (UPs) for SNP analyses. In the proposed ASQ method, the fluorophores and quencher are located in separate complementary oligonucleotides. The ASQ method is based on the simultaneous presence in PCR of the following two components: an allele-specific mixture (allele-specific and common primers) and a template-independent detector mixture that contains two or more (up to four) universal probes (UP-1 to 4) and a single universal quencher oligonucleotide (Uni-Q). The SNP site is positioned preferably at a penultimate base in each allele-specific primer, which increases the reaction specificity and allele discrimination. The proposed ASQ method is advanced in providing a very clear and effective measurement of the fluorescence emitted, with very low signal background-noise, and simple procedures convenient for customized modifications and adjustments. Importantly, this ASQ method is estimated as two- to ten-fold cheaper than Amplifluor and KASP, and much cheaper than all those methods that rely on dual-labeled probes without universal components, like TaqMan and Molecular Beacons. Results for SNP genotyping in the barley genes HvSAP16 and HvSAP8, in which stress-associated proteins are controlled, are presented as proven and validated examples. This method is suitable for bi-allelic uniplex reactions but it can potentially be used for 3- or 4-allelic variants or different SNPs in a multiplex format in a range of applications including medical, forensic, or others involving SNP genotyping.

scholarly journals Introduction of High Throughput and Cost Effective SNP Genotyping Platforms in Soybean

2017 ◽  
Vol 2 (1) ◽  
pp. 90-94 ◽  
Author(s):  
Jiazheng Yuan ◽  
Zixiang Wen ◽  
Cuihua Gu ◽  
Dechun Wang
Keyword(s):  
Cost Effective ◽  
Snp Genotyping ◽  
Large Sample Size ◽  
Specific Pcr ◽  
Assay Optimization ◽  
Wide Range ◽  
Two Systems ◽  
Allele Specific ◽  
Soybean Plants ◽  
Allele Specific Pcr

We presented here the application of two in-plate SNP (single nucleotide polymorphism) genotyping platforms for soybean plants [Glycine max (L.) Merr.], KASP® (Kompetitive Allele Specific PCR genotyping, LGC Genomics) and TaqMan® (Life Technologies) respectively. These two systems offer us an ability to determine the genotypes of 384 individual samples accurately and efficiently by allele specific PCR in a single plate using typical PCR conditions. Both of the systems require small quantity of genomic DNA obtained from a simple DNA extraction. The genomic sequences containing target SNPs can easily be used as a basic blueprint to design the probes and primers of KASP® and TaqMan® assays whether the sequences are obtained from the genome sequence of soybean William 82 (Wm82.a2.v1), Illumina Soy50k SNPs, or parallel resequencing. Moreover, we listed the pros and cons of the two systems and explained the principles behind the platforms. The high call rate and clear clustering separation of the SNPs can be readily obtained from these platforms without conducting any assay optimization processes. These platforms can routinely be performed on 96/384-well plate format with or without an automation procedure. Therefore, these platforms are especially suitable for the SNP genotyping on a particular trait with a large sample size, gene fine mapping, and marker assisted selection. Further, they require little hands-on experience and achieve per-site and per-individual costs below that of current SSR, AFLP, RFLP, and SNP chip technologies. The platforms can be used for genotyping on a wide range of organisms due to their simplicity and flexibility of handling. Meanwhile, we also especially presented some of the advantages using KASP® SNP genotyping pipeline, which was cost effective in the selection of allele specific assay and therefore, efficiently facilitated the soybean genotyping across large numbers (thousands or more) of individual lines for a great range of markers (hundreds to thousands) in our laboratory.

Single-reaction for SNP Genotyping on Agarose Gel by Allele-specific PCR in Black Poplar (Populus nigra L.)

2007 ◽  
Vol 25 (1-2) ◽  
pp. 1-9 ◽  
Author(s):  
Muriel Gaudet ◽  
Anna-Giulia Fara ◽  
Maurizio Sabatti ◽  
Elena Kuzminsky ◽  
Giuseppe Scarascia Mugnozza
Keyword(s):  
Populus Nigra ◽  
Snp Genotyping ◽  
Agarose Gel ◽  
Specific Pcr ◽  
Black Poplar ◽  
Allele Specific ◽  
Allele Specific Pcr ◽  
Single Reaction

Allele-Specific PCR in SNP Genotyping

2009 ◽  
pp. 415-424 ◽  
Author(s):  
Muriel Gaudet ◽  
Anna-Giulia Fara ◽  
Isacco Beritognolo ◽  
Maurizio Sabatti
Keyword(s):  
Snp Genotyping ◽  
Specific Pcr ◽  
Allele Specific ◽  
Allele Specific Pcr
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