scholarly journals Exploring the Potential and Limitations of PCR-RFLP and PCR-SSCP for SNP Detection: A Review

2019 ◽  
Vol 6 (4) ◽  
pp. 137-144 ◽  
Author(s):  
Hayder O. Hashim ◽  
Mohammed Baqur Al-Shuhaib
Keyword(s):  
Snp Detection ◽  
Pcr Rflp

scholarly journals Nucleotide Sequencing and SNP Detection of Toll-Like Receptor-4 Gene in Murrah Buffalo (Bubalus bubalis)

2012 ◽  
Vol 2012 ◽  
pp. 1-7 ◽  
Author(s):  
M. Mitra ◽  
S. Taraphder ◽  
G. S. Sonawane ◽  
A. Verma
Keyword(s):  
Rflp Analysis ◽  
Ovis Aries ◽  
Capra Hircus ◽  
Nucleotide Sequencing ◽  
Toll Like Receptor ◽  
Snp Detection ◽  
Toll Like Receptor 4 ◽  
Exon 2 ◽  
Murrah Buffalo ◽  
Pcr Rflp

Toll-like receptor-4 (TLR-4) has an important pattern recognition receptor that recognizes endotoxins associated with gram negative bacterial infections. The present investigation was carried out to study nucleotide sequencing and SNP detection by PCR-RFLP analysis of the TLR-4 gene in Murrah buffalo. Genomic DNA was isolated from 102 lactating Murrah buffalo from NDRI herd. The amplified PCR fragments of TLR-4 comprised of exon 1, exon 2, exon 3.1, and exon 3.2 were examined to RFLP. PCR products were obtained with sizes of 165, 300, 478, and 409 bp. TLR-4 gene of investigated Murrah buffaloes was highly polymorphic with AA, AB, and BB genotypes as revealed by PCR-RFLP analysis using Dra I, Hae III, and Hinf I REs. Nucleotide sequencing of the amplified fragment of TLR-4 gene of Murrah buffalo was done. Twelve SNPs were identified. Six SNPs were nonsynonymous resulting in change in amino acids. Murrah is an indigenous Buffalo breed and the presence of the nonsynonymous SNP is indicative of its unique genomic architecture. Sequence alignment and homology across species using BLAST analysis revealed 97%, 97%, 99%, 98%, and 80% sequence homology with Bos taurus, Bos indicus, Ovis aries, Capra hircus, and Homo sapiens, respectively.

Molecular authentication of Thai medicinal plant Khamin khruea by PCR-RFLP analysis

Planta Medica ◽  
2008 ◽  
Vol 74 (09) ◽  
Author(s):  
P Rojsanga ◽  
W Gritsanapan ◽  
W Leelamanit ◽  
S Sukrong
Keyword(s):  
Medicinal Plant ◽  
Rflp Analysis ◽  
Molecular Authentication ◽  
Pcr Rflp

Simple and Rapid Detection of Factor V Leiden by Allele-specific PCR Amplification

1996 ◽  
Vol 75 (05) ◽  
pp. 757-759 ◽  
Author(s):  
Rainer Blasczyk ◽  
Markus Ritter ◽  
Christian Thiede ◽  
Jenny Wehling ◽  
Günter Hintz ◽  
...  
Keyword(s):  
Direct Sequencing ◽  
Activated Protein C ◽  
Factor V Leiden ◽  
Pcr Amplification ◽  
Factor V ◽  
Specific Pcr ◽  
Pcr Rflp ◽  
Allele Specific ◽  
Specific Amplification ◽  
Allele Specific Pcr

SummaryResistance to activated protein C is the most common hereditary cause for thrombosis and significantly linked to factor V Leiden. In this study, primers were designed to identify the factor V mutation by allele-specific PCR amplification. 126 patients with thromboembolic events were analysed using this technique, PCR-RFLP and direct sequencing. The concordance between these techniques was 100%. In 27 patients a heterozygous factor VGln506 mutation was detected, whereas one patient with recurrent thromboembolism was homozygous for the point mutation. Due to its time- and cost-saving features allele-specific amplification should be considered for screening of factor VGln506.

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.

Differentiation Of Clarias Batrachus, C. Gariepinus And Heteropneustes Fossilis By Pcr-Sequencing Of Mitochondrial 16s Rrna Gene

2015 ◽  
Vol 41 (1) ◽  
pp. 51-58
Author(s):  
Mohammad Shamimul Alam ◽  
Hawa Jahan ◽  
Rowshan Ara Begum ◽  
Reza M Shahjahan
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Fish Larva ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Valuable Insight ◽  
Multiple Sequence ◽  
Pcr Rflp ◽  
Alternative Means

Heteropneustesfossilis, Clariasbatrachus and C. gariepinus are three major catfishes ofecological and economic importance. Identification of these fish species becomes aproblem when the usual external morphological features of the fish are lost or removed,such as in canned fish. Also, newly hatched fish larva is often difficult to identify. PCRsequencingprovides accurate alternative means of identification of individuals at specieslevel. So, 16S rRNA genes of three locally collected catfishes were sequenced after PCRamplification and compared with the same gene sequences available from othergeographical regions. Multiple sequence alignment of the 16S rRNA gene fragments ofthe catfish species has revealed polymorphic sites which can be used to differentiate thesethree species from one another and will provide valuable insight in choosing appropriaterestriction enzymes for PCR-RFLP based identification in future. Asiat. Soc. Bangladesh, Sci. 41(1): 51-58, June 2015

Genetic polymorphism in patients with colorectal and with head and neck cancer

2009 ◽  
Vol 150 (33) ◽  
pp. 1545-1549 ◽  
Author(s):  
András Csejtei ◽  
Antal Tibold ◽  
István Ember ◽  
István Kiss
Keyword(s):  
Head And Neck Cancer ◽  
Genetic Polymorphism ◽  
Head And Neck ◽  
Neck Cancer ◽  
Pcr Rflp ◽  
Xrcc1 Arg194trp

A colorectalis rákok a második leggyakoribb halálokként szerepelnek a rosszindulatú betegségek között. A fej-nyak táji daganatok halálozása Magyarországon 265%-kal emelkedett az utóbbi 30 évben. Nem lehet eléggé hangsúlyozni e két daganatcsoport közegészségügyi jelentőségét. A colorectalis daganatok esetén a GSTM1, GSTT1 enzimek, valamint a p53 72-es kodonjának, fej-nyak táji tumorok esetén az XRCC1 Arg194Trp és Arg399Gln polimorfizmusainak hatását elemeztük. Intraoperatíve eltávolított daganatos és megfelelően illesztett daganatmentes mintákat válogattunk. A formalinban fixált mintákat deparaffinizáltuk és proteináz-K-emésztésnek vetettük alá. A genotipizálást PCR, illetve a fej-nyak táji tumorok esetén PCR-RFLP módszerrel végeztük. A vizsgált allélek gyakoriságában nem volt különbség a daganatos és a kontrollcsoport között. Túlélés tekintetében szignifikáns különbséget találtunk a GSTM1 és a p53 allélek között Dukes B stádiumú colorectalis daganatok esetén és az XRCC1 194 allélek között III-as stádiumú fej-nyak táji tumorokban. A fenti típusú genetikai különbségek szisztematikus vizsgálata a jövőben hozzájárulhat az egyéni rizikóbecslés és az individualizált kezelések megalapozásához.

POLYMORPHISMS OF ENDOTHELIAL DYSFUNCTION GENES NOS3 AND CYBA IN YAKUT POPULATION

2020 ◽  
pp. 20-25
Author(s):  
Soloveva Yu.A. ◽  
Borisova N.V.
Keyword(s):  
Endothelial Dysfunction ◽  
Coronary Syndrome ◽  
Pathological Conditions ◽  
Nos3 Gene ◽  
Yakut Population ◽  
Length Polymorphisms ◽  
Pcr Rflp ◽  
Polymerase Chain ◽  
The Republic ◽  
Cyba Gene

Polymorphisms of different genes can predispose people to various diseases. They can influence the body's physiological response to exogenous risk factors. Polymorphisms of the endothelial dysfunction genes NOS3 and CYBA contribute to the development of socially significant diseases, such as acute coronary syndrome, stroke, as well as diseases accompanied by fibrotic changes (cirrhosis of the liver, pulmonary fibrosis, etc.). Therefore, the study of these genes in the Yakut population seems relevant. The present study involved 124 healthy volunteers, their ethnicity is Yakuts (including Yakuts in the third generation, living in the Republic of Sakha (Yakutia)). Genetic analysis of polymorphisms was performed by the method of polymerase chain reaction of restriction fragment length polymorphisms (PCR-RFLP). The study found that healthy Yakuts have GG homozygote of rs1799983 of the NOS3 gene in 83.87%, GT - 15.32%, TT - 0.81%. The frequency of the G allele was 91.53%, the T allele - 8.47%. The study found that healthy Yakuts have CC homozygote of rs4673 of the CYBA gene in 75.0%, CT - 21.77%, TT - 3.23%. The frequency of C allele was 91.44%, T - 8.56%. These results are consistent with the literature data. Thus, the research of the polymorphism rs1799983 of the NOS3 gene and rs4673 of the CYBA gene in various ethnic groups could have encouraging prospects in the personalized medicine for predicting pathological conditions associated with endothelial dysfunction: liver fibrosis, cardiovascular diseases, obstetric and gynecological pathologies, dysfunctions of various organs and systems.

IDENTIFYING THE C677T POLYMORPHISM OF MTHFR GENE BY PCR-RFLP TECHNIQUE

2011 ◽  
pp. 28-35
Author(s):  
Keyword(s):  
Internal Control ◽  
Restriction Site ◽  
Mthfr Gene ◽  
C677t Polymorphism ◽  
Mthfr Genotype ◽  
Restriction Digest ◽  
Genotype Frequencies ◽  
Pcr Rflp ◽  
Sequencing Technique ◽  
Volunteer Group

Background: The C677T polymorphism of MTHFR gene is a risk factor of many diseases. This study is aimed at: (1) Improving a PCR-RFLP process with the own designed primers to identify the C677T polymorphism of MTHFR gene. (2) Evaluating the prevalence of the C677T polymorphism of MTHFR gene in volunteer group. Materials and method: DNA samples was extracted from peripheral blood of 60 volunteers. Designing primers by using FastPCR software, then improving PCR technique. Standardizing the optimal conditions of restriction digest by HinfI. Confirming the results of polymorphism by DNA sequencing technique. Results: We designed successfully primers to amplify fragment of MTHFR gene including C677T polymorphism and an obligatory restriction site of HinfI (as internal control). 0.5 µl of HinfI enzyme (10 U/µl) is enough for restriction digest. The MTHFR genotype frequencies were: 71.67 % (677CC); 25% (677CT); and 3.33 % (677TT). Conclusion: We standardized successfully PCR-RFLP technique to identifying C677T polymorphism of MTHFR gene. Keywords: C677T polymorphism, MTHFR gene, PCR-RFLP

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