Tetra-primer ARMS-PCR is an efficient SNP genotyping method: An example from SIRT2

2014 ◽  
Vol 6 (6) ◽  
pp. 1835-1840 ◽  
Author(s):  
Mingxun Li ◽  
Xiaomei Sun ◽  
Jing Jiang ◽  
Yujia Sun ◽  
Xianyong Lan ◽  
...  
Keyword(s):  
Snp Genotyping ◽  
Genotyping Method ◽  
Arms Pcr ◽  
Pcr Rflp ◽  
Pcr Method ◽  
Rflp Assay

We have successfully genotyped a new identified bovine SIRT2 SNP g.4140A > G by T-ARMS-PCR method and validated the accuracy by PCR-RFLP assay using 1255 animals representing the five main Chinese breeds.

scholarly journals Identification of Eutypa lata by PCR-RFLP

Plant Disease ◽  
2004 ◽  
Vol 88 (9) ◽  
pp. 925-929 ◽  
Author(s):  
P. E. Rolshausen ◽  
F. Trouillas ◽  
W. D. Gubler
Keyword(s):  
Universal Primers ◽  
Phaeomoniella Chlamydospora ◽  
Phomopsis Viticola ◽  
Eutypa Lata ◽  
Incorrect Diagnosis ◽  
Pcr Rflp ◽  
Pcr Method ◽  
Polymerase Chain ◽  
Rflp Assay

Eutypa lata is a vascular canker pathogen of woody plants commonly diagnosed by isolating the pathogen from infected tissue. Related fungi from the same family, the Diatrypaceae, also have been found in association with grapevine in Californian vineyards. An in situ polymerase chain reaction (PCR) method has been developed for detection of E. lata in infected wood tissue. However, our results indicate that this method also would amplify other Diatrypaceous fungi, which could potentially lead to an incorrect diagnosis. Therefore, we developed a PCR-restriction fragment length polymorphism (PCR-RFLP) assay. The internal transcribed spacer (ITS)1/5.8S/ITS2 ribosomal DNA region was amplified by PCR using universal primers, and RFLP patterns were determined after digestion with AluI. The restriction profiles obtained served to distinguish E. lata from wood trunk pathogens of grapevine (Phomopsis viticola, Botryodiplodia sp., Phaeoacremonium aleophilum, and Phaeomoniella chlamydospora), Diatrypaceous fungi (Diatrype sp., Diatrypella sp., Eutypella vitis, and Eutypa leptoplaca), and Cryptovalsa sp. found on dead wood of grapevine, and other Eutypa spp. (E.petrakii var. hederae, E. astroidea, E. crustata, and E. lejoplaca), with the exception of E. armeniacae, which we regard as a synonym for E. lata, and E. laevata, which has not been found on grapevine.

scholarly journals CYP2C19*2, CYP2C19*17 and ITGB3 (PlA1/A2) polymorphisms and resulting therapeutic alterations of clopidogrel and aspirin: A clinical screening among CVD patients who undergone PCI

2020 ◽  
Author(s):  
Tasnova Tasnim Nova ◽  
Ishrat Jahan ◽  
N.A.M. Momenuzzaman ◽  
Sikder Nahidul Islam Rabbi ◽  
Thomas M.C. Binder ◽  
...  
Keyword(s):  
Coronary Intervention ◽  
Agarose Gel Electrophoresis ◽  
Loss Of Function ◽  
Arms Pcr ◽  
Pcr Product ◽  
Cardiovascular Patients ◽  
Percutaneous Coronary ◽  
Pcr Rflp ◽  
Pcr Products ◽  
Pcr Method

AbstractIntroductionClopidogrel and aspirin are at the base of treatment in conditions like arterial thrombosis and after patients have undergone percutaneous coronary intervention. But frequently found CYP2C19*2 and CYP2C19*17 polymorphisms and some variants of the ITGB3 gene cause alteration in the therapeutic effectiveness of this drug.MethodsOne thousand cardiovascular patients were recruited for each drug under study. Their blood was collected to analyze the genotype using PCR-RFLP and T-ARMS-PCR method for clopidogrel and aspirin respectively. The PCR products for clopidogrel were screened with agarose gel electrophoresis and then digested with SmaIfor CYP2C19*2 and Nsil-HF for CYP2C19*17. The digested products of clopidogrel and the ARMS-PCR product of aspirin were run on 2% AGE to analyze the polymorphisms.ResultsIn our outcome, the percentage of hetero and mutant homozygous people in CYP2C19*2 polymorphism (loss-of-function allele) was 64.1% and for CYP2C19*17 (gain-of-function allele) was 22.3%. For ITGB3 polymorphism, it was found that 84.1% of them belonged to the homozygous group while 15.6% was heterozygous and only 0.3% were mutant homozygous patients.ConclusionOur study findings were quite compatible with the results of some other studies in other ethnic groups. This phenomenon suggested for modification of dose or application of alternative generics in patients who are under the risk of therapeutic failure or toxicity produced by these drugs.

scholarly journals Tetra-primer ARMS-PCR identified a missense mutation of the bovine <i>NRIP1</i> gene associated with growth traits

2015 ◽  
Vol 58 (1) ◽  
pp. 165-169
Author(s):  
D. Liu ◽  
Z. Wang ◽  
W. Ma ◽  
Y. Gao ◽  
A. Li ◽  
...  
Keyword(s):  
Growth Traits ◽  
Average Daily Gain ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Interacting Protein ◽  
Association Analyses ◽  
Arms Pcr ◽  
Pcr Rflp ◽  
Cheap Method ◽  
Pcr Method

Abstract. Nuclear receptor-interacting protein 1 (NRIP1) specifically interacts with the hormone-dependent activation domain AF2 of nuclear receptors to inhibit transcription. Previous work has demonstrated this protein to be a key regulator in modulating transcriptional activity of many transcription factors, some of which are closely related to development and growth. In this study, we have successfully genotyped two newly identified bovine NRIP1 single-nucleotide polymorphisms (SNPs) (c.605A > G and c.1301G > A) using the T-ARMS-PCR method and validated the accuracy by means of PCR-RFLP assay using 1809 individuals of 9 different cattle breeds. The association analyses results indicated that c.605A > G locus was significantly associated with body weight and average daily gain in Nanyang cattle at 18 months (P < 0.05). Thus it can be inferred that T-ARMS-PCR is a rapid, reliable, and cheap method for SNP genotyping and that c.605A > G polymorphism in bovine NRIP1 is associated with growth traits. These findings will be of benefit for the application of DNA markers related to growth traits in marker-assisted selection (MAS), and will improve the promotion of beef cattle.

PCR-RFLP Detection od PAI-2 Gene Variants: Prevelence in Ethnic Groups and Disease Relationship in patients Undergoing corony Angiography

1997 ◽  
Vol 77 (05) ◽  
pp. 0955-0958 ◽  
Author(s):  
Carole A Foy ◽  
Peter J Grant
Keyword(s):  
Gene Variants ◽  
Genotype Distribution ◽  
Pima Indians ◽  
Significant Difference ◽  
Pcr Rflp ◽  
History Of ◽  
Caucasian Patients ◽  
Clinical Conditions ◽  
Rflp Assay ◽  
Coronary Atheroma

SummaryPAI-2 is a fibrinolytic inhibitor produced predominantly by monocytes. Most PAI-2 is intracellular making study in clinical conditions difficult. Abnormalities in production may be associated with inflammation and fibrinolysis at sites of tissue damage such as the atherosclerotic plaque.PAI-2 gene variants have been described: variant A consists of Asn120, Asn404 and Ser413 and variant B consists of Asp120, Lys404 and Cys413. We designed a PCR-RFLP assay using primers spanning the region containing Asn/Lys404 and Ser/Cys413. Variant B contains an Mwol restriction site. We analysed 302 Pima Indians and 286 healthy Caucasian volunteers. To investigate relationships between genotype and vascular disease we analysed 333 Caucasian patients undergoing coronary angiography.Gene variant B was more common in the Pimas than in Caucasians (p <0.0001). There was no significant difference in genotype distribution between the volunteers and patients. In the patients there was no association between genotype and either a history of MI or extent of coronary atheroma.

PCR‐RFLP assay confirms the existence of different mitochondrial lineages of Taenia hydatigena including a possible geographically restricted group

2021 ◽  
Author(s):  
John Asekhaen Ohiolei ◽  
Hong‐Bin Yan ◽  
Li Li ◽  
Mughees Aizaz Alvi ◽  
Rosline James Muku ◽  
...  
Keyword(s):  
Taenia Hydatigena ◽  
Pcr Rflp ◽  
Restricted Group ◽  
Rflp Assay

Sex identification PCR–RFLP assay tested in eight species of Sebastes rockfish

2020 ◽  
Vol 12 (4) ◽  
pp. 541-544
Author(s):  
Felix Vaux ◽  
Hannah M. Aycock ◽  
Sandra Bohn ◽  
Leif K. Rasmuson ◽  
Kathleen G. O’Malley
Keyword(s):  
Sex Identification ◽  
Pcr Rflp ◽  
Rflp Assay

scholarly journals PCR-based genotyping assays to detect germline APC variant associated with hereditary gastrointestinal polyposis in Jack Russell terriers

2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Kyoko Yoshizaki ◽  
Akihiro Hirata ◽  
Hiroyuki Matsushita ◽  
Naohito Nishii ◽  
Mifumi Kawabe ◽  
...  
Keyword(s):  
Mutant Allele ◽  
False Negative ◽  
Disease Onset ◽  
Pcr Amplification ◽  
Buccal Swab ◽  
Wild Type ◽  
Gastrointestinal Polyposis ◽  
Pcr Rflp ◽  
Formalin Fixed Paraffin Embedded ◽  
Rflp Assay

Abstract Background The prevalence of gastrointestinal (GI) neoplastic polyps in Jack Russell terriers (JRTs) has increased in Japan since the late 2000s. Recently, we demonstrated that JRTs with GI polyps harbor identical germline variant in the APC gene (c.[462_463delinsTT]) in the heterozygous state. Thus, this disease is an autosomal dominant hereditary disorder. Although the affected JRTs have distinct features, such as the development of multiple GI polyps and an early age of disease onset, genetic testing is indispensable for a definitive diagnosis. Here, polymerase chain reaction (PCR)-based assays capable of detecting germline APC variant were designed and validated using synthetic wild-type and mutant DNAs and genomic DNAs from carrier and non-carrier dogs. Result First, the PCR-restriction fragment length polymorphism (PCR-RFLP) assay was developed by taking advantage of the germline APC variant creating a new restriction site for MseI. In the PCR-RFLP assay, the 156-bp region containing the variant site was amplified by PCR and subsequently digested with MseI, yielding diagnostic 51 and 58 bp fragments from the mutant allele and allowing determination of the APC genotypes. It was possible to determine the genotypes using genomic DNA extracted from the peripheral blood, buccal swab, or formalin-fixed paraffin-embedded tissue. Next, a TaqMan duplex real-time PCR assay was developed, where a 78-bp region flanking the variant was amplified in the presence of wild-type allele- and mutant allele-specific fluorescent probes. Using blood-derived DNA, altogether 40 cycles of PCR amplification determined the APC genotypes of all examined samples by measuring the fluorescence intensities. Importantly, false-positive and false-negative errors were never detected in both assays. Conclusion In this study, we developed highly reliable genetic tests for hereditary GI polyposis in JRTs, providing accurate assessment of the presence of the causative germline APC variant. The genotyping assays could contribute to the diagnosis and prevention of hereditary GI polyposis in dogs.

scholarly journals A rapid and cost‐effective multiplex ARMS‐PCR method for the simultaneous genotyping of the circulating SARS‐CoV‐2 phylogenetic clades

2021 ◽  
Author(s):  
Mohammad Tanvir Islam ◽  
ASM Rubayet Ul Alam ◽  
Najmuj Sakib ◽  
Mohammad Shazid Hasan ◽  
Tanay Chakrovarty ◽  
...  
Keyword(s):  
Cost Effective ◽  
Arms Pcr ◽  
Pcr Method
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