Visual SNP genotyping using asymmetric PCR and split DNA enzymes

The Analyst ◽  
2011 ◽  
Vol 136 (8) ◽  
pp. 1569 ◽  
Author(s):  
Jia Ling Neo ◽  
Kanglie Darius Aw ◽  
Mahesh Uttamchandani
Keyword(s):  
Snp Genotyping ◽  
Asymmetric Pcr ◽  
Dna Enzymes

scholarly journals Simple and reliable detection of CRISPR-induced on-target effects by qgPCR and SNP genotyping

2021 ◽  
Vol 16 (3) ◽  
pp. 1714-1739
Author(s):  
Isabel Weisheit ◽  
Joseph A. Kroeger ◽  
Rainer Malik ◽  
Benedikt Wefers ◽  
Peter Lichtner ◽  
...  
Keyword(s):  
Snp Genotyping ◽  
Reliable Detection ◽  
Target Effects

scholarly journals Allele frequencies of single nucleotide polymorphisms of clinically important drug-metabolizing enzymes CYP2C9, CYP2C19, and CYP3A4 in a Thai population

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Rattanaporn Sukprasong ◽  
Sumonrat Chuwongwattana ◽  
Napatrupron Koomdee ◽  
Thawinee Jantararoungtong ◽  
Santirhat Prommas ◽  
...  
Keyword(s):  
Snp Genotyping ◽  
Allele Frequencies ◽  
Nucleotide Polymorphisms ◽  
Poor Metabolizer ◽  
Thai Population ◽  
Metabolizing Enzymes ◽  
Single Nucleotide ◽  
Genotyping Assay ◽  
Intermediate Metabolizer ◽  
Important Drug

AbstractPrior knowledge of allele frequencies of cytochrome P450 polymorphisms in a population is crucial for the revision and optimization of existing medication choices and doses. In the current study, the frequency of the CYP2C9*2, CYP2C9*3, CYP2C19*2, CYP2C19*3, CYP2C19*6, CYP2C19*17, and CYP3A4 (rs4646437) alleles in a Thai population across different regions of Thailand was examined. Tests for polymorphisms of CYP2C9 and CYP3A4 were performed using TaqMan SNP genotyping assay and CYP2C19 was performed using two different methods; TaqMan SNP genotyping assay and Luminex x Tag V3. The blood samples were collected from 1205 unrelated healthy individuals across different regions within Thailand. Polymorphisms of CYP2C9 and CYP2C19 were transformed into phenotypes, which included normal metabolizer (NM), intermediate metabolizer (IM), poor metabolizer (PM), and rapid metabolizers (RM). The CYP2C9 allele frequencies among the Thai population were 0.08% and 5.27% for the CYP2C9*2 and CYP2C9*3 alleles, respectively. The CYP2C19 allele frequencies among the Thai population were 25.60%, 2.50%, 0.10%, and 1.80% for the CYP2C19*2, CYP2C19*3, CYP2C19*6, and CYP2C19*17 alleles, respectively. The allele frequency of the CYP3A4 (rs4646437) variant allele was 28.50% in the Thai population. The frequency of the CYP2C9*3 allele was significantly lower among the Northern Thai population (P < 0.001). The frequency of the CYP2C19*17 allele was significantly higher in the Southern Thai population (P < 0.001). Our results may provide an understanding of the ethnic differences in drug responses and support for the utilization of pharmacogenomics testing in clinical practice.

scholarly journals Development and validation of SNP genotyping assays to identify genetic sex in the swimming crab Portunus trituberculatus

2021 ◽  
Vol 20 ◽  
pp. 100731
Author(s):  
Junkai Lu ◽  
Ronghua Li ◽  
Michaël Bekaert ◽  
Herve Migaud ◽  
Xiao Liu ◽  
...  
Keyword(s):  
Snp Genotyping ◽  
Portunus Trituberculatus ◽  
Swimming Crab ◽  
Development And Validation

scholarly journals A powerful tool for genome analysis in maize: development and evaluation of the high density 600 k SNP genotyping array

BMC Genomics ◽  
2014 ◽  
Vol 15 (1) ◽  
pp. 823 ◽  
Author(s):  
Sandra Unterseer ◽  
Eva Bauer ◽  
Georg Haberer ◽  
Michael Seidel ◽  
Carsten Knaak ◽  
...  
Keyword(s):  
Genome Analysis ◽  
High Density ◽  
Snp Genotyping ◽  
Genotyping Array

In Vitro Selection of Oligonucleotide Acid Aptamers against Pathogenic Vibrio Alginolyticus by SELEX

2010 ◽  
Vol 439-440 ◽  
pp. 1456-1462 ◽  
Author(s):  
Jiang Zheng ◽  
Yu Bao Li ◽  
Jia Xiang Li ◽  
Jun Wang ◽  
Yong Quan Su
Keyword(s):  
Secondary Structures ◽  
Magnetic Bead ◽  
Vibrio Alginolyticus ◽  
Pathogenic Microorganism ◽  
Asymmetric Pcr ◽  
High Affinity ◽  
Amplification Method ◽  
Pathogenic Vibrio ◽  
Selection Of

Detection of pathogenic microorganism is very necessary in the control of infectious disease prevailing in aquiculture animals. However, most of the present techniques can not meet the need of the quick field inspection. Systematic evolution of ligands by exponential enrichment (SELEX) is a new molecular recognition way for generating high affinity oligonucleotide acid aptamers, a new nucleotide acid material, which have been widely used in the detections of proteins, cells and so on. In the present paper, the technology was applied to select the high affinity aptamers against pathogenic microorganism Vibrio alginolyticus, which could be used for the rapid field detection of the microorganism. Based on the designment of the ssDNA library of 76 nucleotide acids with 35-base random region, the SELEX system for the selection of the high affinity aptamers against Vibrio alginolyticus was established. In the SELEX system, asymmetric PCR was proved to be a better amplification method for the ssDNA library than the reported affinity magnetic bead method, and the corresponding parameters of the asymmetric PCR were also studied and optimized. The affinity of the final ssDNA library increased by nearly 200% compared with the original library. Cloning and sequencing of the final ssDNA library showed that there were at least two kinds of ssDNAs with different length in the affinity ssDNA library: one was 76 bases, another was 149 bases. Simulation of the secondary structures showed that the secondary structures of the two fragments were different greatly, suggesting that the two fragments could bind to different sites of V. alginolyticus surface.

High Microsatellite and SNP Genotyping Success Rates Established in a Large Number of Genomic DNA Samples Extracted From Mouth Swabs and Genotypes

2006 ◽  
Vol 9 (4) ◽  
pp. 501-506 ◽  
Author(s):  
Josine L. Min ◽  
Nico Lakenberg ◽  
Margreet Bakker-Verweij ◽  
Eka Suchiman ◽  
Dorret I. Boomsma ◽  
...  
Keyword(s):  
Success Rate ◽  
Genomic Dna ◽  
Snp Genotyping ◽  
High Yield ◽  
Success Rates ◽  
Nucleotide Polymorphism ◽  
High Quality ◽  
Single Nucleotide ◽  
Dna Yield ◽  
Yield And Quality

AbstractIn this article, we present the genomic DNA yield and the microsatellite and single nucleotide polymorphism (SNP) genotyping success rates of genomic DNA extracted from a large number of mouth swab samples. In total, the median yield and quality was determined in 714 individuals and the success rates in 378,480 genotypings of 915 individuals. The median yield of genomic DNA per mouth swab was 4.1 μg (range 0.1–42.2 μg) and was not reduced when mouth swabs were stored for at least 21 months prior to extraction. A maximum of 20 mouth swabs is collected per participant. Mouth swab samples showed in, respectively, 89% for 390 microsatellites and 99% for 24 SNPs a genotyping success rate higher than 75%. A very low success rate of genotyping (0%–10%) was obtained for 3.2% of the 915 mouth swab samples using microsatellite markers. Only 0.005% of the mouth swab samples showed a geno-typing success rate lower than 75% (range 58%–71%) using SNPs. Our results show that mouth swabs can be easily collected, stored by our conditions for months prior to DNA extraction and result in high yield and high-quality DNA appropriate for genotyping with high success rate including whole genome searches using microsatellites or SNPs.

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