Design of allele-specific primers and detection of the human ABO genotyping to avoid the pseudopositive problem

2008 ◽  
Vol 29 (20) ◽  
pp. 4130-4140 ◽  
Author(s):  
Hidenobu Yaku ◽  
Tetsuo Yukimasa ◽  
Shu-ichi Nakano ◽  
Naoki Sugimoto ◽  
Hiroaki Oka
Keyword(s):  
Specific Primers ◽  
Allele Specific

A Hemi-nested, Allele Specific, Whole Blood PCR Assay for the Detection of the Factor V Leiden Mutation

1997 ◽  
Vol 77 (06) ◽  
pp. 1154-1155 ◽  
Author(s):  
Gary D Sinclair ◽  
Sandra Low ◽  
Man-Chiu Poon
Keyword(s):  
Whole Blood ◽  
Protein C ◽  
Activated Protein C ◽  
Factor V Leiden ◽  
Restriction Enzyme Digestion ◽  
Factor V ◽  
Pcr Assay ◽  
Specific Primers ◽  
Factor V Leiden Mutation ◽  
Allele Specific

SummaryWe describe a novel hemi-nested, allele specific whole blood PCR assay for detection of the factor V Leiden mutation associated with the plasma defect, activated protein C resistance. This assay utilizes 5 μl of whole blood without prior DNA extraction. The hemi-nested design, employing an outer primer pair in combination with nested, allele specific primers obviates the need for restriction enzyme digestion. PCR reactions are analysed directly on agarose or polyacrylamide minigels. The assay confirmed the genotypes of 50 individuals previously categorized by PCR and Mnll digestion, and has been subsequently utilized in the genotyping of 445 individuals referred for thrombosis studies.

scholarly journals Association of ACE DD Genotype with Hypertension among the Tribal Populations of South India

2016 ◽  
Vol 52 ◽  
pp. 1-8 ◽  
Author(s):  
Raghu Paramasivam ◽  
Nandhakumar Rengasamy ◽  
Deva Arumugam ◽  
Prabhakaran Krishnan
Keyword(s):  
South India ◽  
Renin Angiotensin System ◽  
Chain Reaction ◽  
Specific Primers ◽  
Angiotensin System ◽  
Allele Specific ◽  
Tribal Populations ◽  
Important Regulator ◽  
Polymerase Chain ◽  
Vasoactive Peptide

The Renin-Angiotensin System (RAS) is an important regulator of the blood pressure (BP). The level of the vasoactive peptide Angiotensin-II, is mainly determined by the RAS enzyme, angiotensin converting enzyme-1 (ACE-1). Polymorphisms in ACE gene is reported to be associated with hypertension in various populations worldwide. We investigated the association of ACE I/D polymorphisms with hypertension among the tribal populations of South India. Samples were collected from hypertensive patients (n = 33) and healthy controls (n = 37). Genotyping was performed using Polymerase chain reaction (PCR) with allele specific primers. The DD genotype is significantly observed among the cases (OR = 1.0). Specifically, the DD genotype is more evident among the females (OR = 0 .705) than males (OR = 1.22) and is analysed to be associated with hypertension among the tribal populations of South India.

PCR analysis of the wheat varieties and near-isogenic wheat lines with the use of allele-specific primers for the Gli-1 and Glu-3 loci

2010 ◽  
Vol 44 (6) ◽  
pp. 345-353
Author(s):  
A. M. Polishchuk ◽  
S. V. Chebotar ◽  
E. M. Blagodarova ◽  
N. A. Kozub ◽  
I. A. Sozinov ◽  
...  
Keyword(s):  
Pcr Analysis ◽  
Specific Primers ◽  
Wheat Varieties ◽  
Allele Specific ◽  
Gli 1 ◽  
Wheat Lines

Sequence diversity analysis of dihydroflavonol 4-reductase intron 1 in common bean

Genome ◽  
2004 ◽  
Vol 47 (2) ◽  
pp. 266-280 ◽  
Author(s):  
Phillip E McClean ◽  
Rian K Lee ◽  
Phillip N Miklas
Keyword(s):  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Sequence Data ◽  
Gene Pools ◽  
Specific Primers ◽  
Drift Model ◽  
Intron 1 ◽  
Allele Specific ◽  
Sufficient Variation ◽  
Diversity Studies

Variation in common bean (Phaseolus vulgaris L.) was investigated by sequencing intron 1 of the dihydroflavonol 4-reductase (DFR) gene for 92 genotypes that represent both landraces and cultivars. We were also interested in determining if introns provide sufficient variation for genetic diversity studies and if the sequence data could be used to develop allele-specific primers that could differentiate genotypes using a standard PCR assay. Sixty-nine polymorphic sites were observed. Nucleotide variation (π/bp) was 0.0481, a value higher than that reported for introns from other plant species. Tests for significant deviation from the mutation drift model were positive for the population as a whole, the cultivar and landrace subsets, and the Middle American landrace set. Significant linkage disequilibrium extended about 300 nucleotides. Twenty haplotypes were detected among the cultivated genotypes. Seven recombination events were detected for the whole population, and six events for the landraces. Recombination was not observed among the landraces within either the Middle American or Andean gene pools. Evidence for hybridization between the two gene pools was discovered. Five allele-specific primers were developed that could distinguish 56 additional genotypes. The allele-specific primers were used to map duplicate DFR genes on linkage group B8.Key words: Phaseolus vulgaris, intron, diversity, evolution.

Rapid determination of platelet alloantigen genotypes by polymerase chain reaction using allele-specific primers

Transfusion ◽  
1994 ◽  
Vol 34 (11) ◽  
pp. 955-960 ◽  
Author(s):  
B Skogen ◽  
DB Bellissimo ◽  
MJ Hessner ◽  
S Santoso ◽  
RH Aster ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Rapid Determination ◽  
Chain Reaction ◽  
Specific Primers ◽  
Allele Specific ◽  
Polymerase Chain

scholarly journals Short Communication: Genotyping of kdr allele in insecticide resistant-Aedes aegypti populations from West Sumatra, Indonesia

2018 ◽  
Vol 19 (2) ◽  
pp. 502-508
Author(s):  
HASMIWATI HASMIWATI ◽  
SUPARGIYONO SUPARGIYONO
Keyword(s):  
Aedes Aegypti ◽  
Dengue Fever ◽  
Short Communication ◽  
Point Mutations ◽  
Pcr Analysis ◽  
Chemical Insecticide ◽  
Paper Test ◽  
Specific Primers ◽  
West Sumatra ◽  
Allele Specific

Hasmiwati, Supargiyono. 2018. Short Communication: Genotyping of kdr allele in insecticide resistant-Aedes aegypti populations from West Sumatra, Indonesia. Biodiversitas 19: 502-508. Aedes aegypti, the primary vector of Dengue fever, is widely distributed in Indonesia including in West Sumatra. Chemical insecticide is an effective way of shedding the chain of Dengue fever transmission. Long-term applications of insecticides have resulted in the development of resistance in Ae. aegypti populations. Knockdown resistance (kdr) allele as a result of point mutations has been found in Voltage-Gated Sodium Channel (VGSC) gene. This study aimed to design allele-specific primers to detect the kdr allele mutations. Ae aegypti samples were collected from several dengue endemic areas in West Sumatra. The susceptibility of adult mosquitos to insecticides was determined by bioassays using impregnation paper test with 0.18% malathion and 0.75% permethrin. In this study, we successfully confirmed that the A. populations have point mutations in the VGSC gene corresponding to S989P and V1016G amino acid substitutions. To genotype S989P and V1016G alleles, we designed kdr allele-specific primers based on the sequence of VGSC gene (NCBI Accession number No. EU399179.1. PCR analysis using the kdr allele-specific primers successfully identified the genotype of Ae. aegypti populations resistant to malathion and permethrin in West Sumatra.

The Polymerase Chain Reaction with Sequence Specific Primers for the Detection of the Factor V Mutation Associated with Activated Protein C Resistance

1995 ◽  
Vol 74 (03) ◽  
pp. 874-878 ◽  
Author(s):  
Nancy E Kirschbaum ◽  
Paul A Foster
Keyword(s):  
Protein C ◽  
Activated Protein C ◽  
Pcr Amplification ◽  
Factor V ◽  
Activated Protein C Resistance ◽  
Chain Reaction ◽  
Specific Primers ◽  
Allele Specific ◽  
Fv Leiden ◽  
Polymerase Chain

SummaryThe prevalence of the Factor V (FV) mutation associated with activated protein C resistance (FV Leiden) and its significance as a genetic risk factor for venous thrombosis have necessitated the development of a simple, rapid, and accurate assay for its detection. The polymerase chain reaction with sequence specific primers (PCR-SSP) provides a powerful technique for the discrimination of alleles resulting from single base substitutions. PCR amplification was performed using a sense primer complementary to both FV alleles coupled with either of two antisense allele specific primers, one complementary to the normal FV allele and one complementary to the FV Leiden allele. PCR conditions were developed that favored amplification only in the case of perfect complementation between template DNA and allele specific primer. The FV genotype was assigned based on whether or not each allele specific primer set produced an amplified product. Assignment of genotypes correlated 100% with those determined by the method of PCR amplification followed by MnII digestion. PCR-SSP allows the rapid and accurate identification of carriers of the Factor V Leiden mutation by a simple PCR reaction without the need for the usual post-amplification specificity step.

Determination of ABO genotypes by real-time PCR using allele-specific primers

2012 ◽  
Vol 14 (1) ◽  
pp. 47-50 ◽  
Author(s):  
Tomonori Muro ◽  
Junko Fujihara ◽  
Shinji Imamura ◽  
Hiroaki Nakamura ◽  
Kaori Kimura-Kataoka ◽  
...  
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Specific Primers ◽  
Allele Specific ◽  
Abo Genotypes
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