scholarly journals Rapid determination of clonality by detection of two closely-linked X chromosome exonic polymorphisms using allele-specific PCR.

1997 ◽  
Vol 99 (8) ◽  
pp. 1984-1990 ◽  
Author(s):  
Y Liu ◽  
J Phelan ◽  
R C Go ◽  
J F Prchal ◽  
J T Prchal
Keyword(s):  
X Chromosome ◽  
Rapid Determination ◽  
Specific Pcr ◽  
Allele Specific ◽  
Allele Specific Pcr

Determination of cis/trans phase of variations in the MC1R gene with allele-specific PCR and single base extension

2008 ◽  
Vol 29 (23) ◽  
pp. 4780-4787 ◽  
Author(s):  
Jonas Mengel-From ◽  
Claus Børsting ◽  
Juan J. Sanchez ◽  
Hans Eiberg ◽  
Niels Morling
Keyword(s):  
Single Base Extension ◽  
Mc1r Gene ◽  
Single Base ◽  
Specific Pcr ◽  
Base Extension ◽  
Allele Specific ◽  
Allele Specific Pcr

Quantitative determination of the ratio of mutated to normal ras genes in the blood of leukemia patients by allele-specific PCR

1994 ◽  
Vol 18 (9) ◽  
pp. 693-702 ◽  
Author(s):  
Tetsuro Horikoshi ◽  
Heinz-Josef Lenz ◽  
Kathleen Danenberg ◽  
Olaf M. Koch ◽  
Joseph R. Bertino ◽  
...  
Keyword(s):  
Quantitative Determination ◽  
Ras Genes ◽  
Specific Pcr ◽  
Allele Specific ◽  
Allele Specific Pcr

scholarly journals Update on and Review of the Incompatibility (S-) Genotypes of Apple Cultivars

HortScience ◽  
2004 ◽  
Vol 39 (5) ◽  
pp. 943-947 ◽  
Author(s):  
Wim Broothaerts ◽  
Ilse Van Nerum ◽  
Johan Keulemans
Keyword(s):  
Identification System ◽  
Published Data ◽  
Specific Pcr ◽  
S Alleles ◽  
Allele Specific ◽  
Self Fertilization ◽  
Apple Cultivars ◽  
S Allele ◽  
Allele Specific Pcr

Apple cultivars display a self-incompatibility system that restricts self-fertilization and fertilization between cultivars bearing identical S-alleles. There has been considerable progress in identification of S-alleles in apple in recent years and methods are now available for the accurate S-genotyping of cultivars. Following a recently revised numerical identification system for apple S-alleles, we present the first extensive compilation of apple cultivars with their S-genotypes. This list contains data from our own investigations using S-allele-specific PCR methodology, including a number of new data, as well as published data from various other sources. Eighteen different S-alleles are discriminated, which allowed the determination of the S-genotypes for 150 diploid or triploid European, American, and Japanese cultivars. Many of these cultivars are cultivated worldwide for their fruit. Also included are a number of old, obsolete cultivars and a few nondomestic genotypes. We observed a wide variation in the frequency of S-alleles in the apple germplasm. Three S-alleles (S2, S3, and S9) are very common in the cultivars evaluated, presumably as a result of the widespread use of the same breeding parents, and seven alleles are very rare (S4, S6, S8, S16, S22, S23, S26).

scholarly journals Allele-Specific PCR for Determination of IL28B Genotype

2012 ◽  
Vol 50 (12) ◽  
pp. 4144-4146 ◽  
Author(s):  
L. Cook ◽  
K. Diem ◽  
W. Kim ◽  
J. D. Scott ◽  
K. R. Jerome
Keyword(s):  
Il28b Genotype ◽  
Specific Pcr ◽  
Allele Specific ◽  
Allele Specific Pcr

A Novel and Quantitative Assay To Detect JAK2 V617F Allele by Real-Time AS-PCR and Its Applicability to PV Initiating Mutation.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 4915-4915
Author(s):  
Roberto H. Nussenzveig ◽  
Sabina Swierczek ◽  
Jaroslav Jelinek ◽  
Srdan Verstovsek ◽  
Jaroslav Prchal ◽  
...  
Keyword(s):  
Real Time ◽  
Allele Frequency ◽  
Somatic Mutation ◽  
Mutant Allele ◽  
Jak2 V617f ◽  
Allele Frequencies ◽  
Specific Pcr ◽  
Allele Specific ◽  
Allele Specific Pcr

Abstract Polycythemia vera (PV) arises due to a somatic mutation(s) of a single hematopoietic stem cell leading to clonal hematopoiesis. Greater than 80% of PV patients carry a somatic mutation in JAK2 (V617F). Growing evidence suggests that increased frequency of the JAK2V617F allele may have a prognostic impact on certain clinical aspects of PV, and, possibly, in other myeloproliferative disorders associated with this mutation. We have developed a novel approach to primer design for Real-Time quantitative allele-specific PCR. Allelic discrimination is enhanced by the combined synergistic effects of an artificial mismatch introduced in the −1 position, starting from the 3′ end of the primer, and the use of a locked nucleic acid (LNA) modified nucleoside placed at the −2 position. We provide evidence that the −2 LNA assists in stabilizing the 3′ end, while the −1 mismatch provides specificity but not stability. The difference in cycle number between the two allele-specific reactions is used to calculate the relative allele frequencies. We demonstrate the robustness, sensitivity and reproducibility of our design. The proportion of mutant JAK2 allele determined by pyrosequencing and kinetic allele-specific PCR was highly concordant with an average allele frequency deviation of 2.6%. Repeated determination of allelic ratios in multiple patient samples was highly reproducible with a standard deviation of 1.5%. We have also determined that the design and assay is highly sensitive; as little as 0.1% mutant allele in 40–50 ng of genomic DNA can be detected. We further tested the applicability of this technique to the analysis of individual BFU-E colonies in order to address the question whether the JAK2V617F is the disease initiating mutation. Less than 10% of a single isolated BFU-E colony, originating from a single progenitor, is sufficient for determination of allele frequency. The remainder of the colony may be used for other analyses. A proportion of 0 or 50 or 100 percent JAK2 mutant allele is expected from each individual BFU-E colony, which was indeed observed. However, when we tested granulocytes from PV females, wherein the granulocytes were found to be clonal by the X-chromosome transcriptionally based clonality assay, we found 3 females <50 (27.5 ±11) and 7 females >50 (75 ±10.5)percent mutant JAK2 allele frequencies. This result suggests the presence of a heterogeneous population of cells with differing genotypes regarding the JAK2 mutant allele, and is further supported by our genotyping results with individual BFU-E colonies as described above. Our PV data suggest that the JAK2V617F may not be the PV initiating mutation. This novel primer design is simple, does not require tedious optimization of reaction conditions, and can be applied to any kinetic PCR platform for reliable and sensitive determination of allele frequencies. Potential applications are varied, such as, quantitative determination of mosaicism, proportion of fetal cells in maternal circulation, detection of minimal residual disease associated with known somatic mutation (such as reduction of malignant cells by chemotherapy or reappearance of resistant clone), rapid monitoring of efficacy of new drugs in both “in vitro” systems as well as clinical trials, and many others that require quantitation of allele frequencies.

scholarly journals Development of cost-effective and accurate allele-specific PCR for determination of M2/ANXA5 haplotype in recurrent pregnancy loss

2021 ◽  
pp. 1-9
Author(s):  
Kai-Cheen Ang ◽  
Timofey S. Rozhdestvensky ◽  
Arseni Markoff ◽  
Nadja Bogdanova ◽  
Ewe Seng Ch'ng ◽  
...  
Keyword(s):  
Pregnancy Loss ◽  
Direct Sequencing ◽  
Meta Analysis ◽  
Working Hours ◽  
Cost Effective ◽  
Specific Pcr ◽  
Pcr Products ◽  
Allele Specific ◽  
Allele Specific Pcr

Repeated Pregnancy Loss (RPL) affects approximately 1 out of 20 pregnant women globally; it is traumatic for parents seeking parenthood with ensuing anxieties for the next pregnancy. M2/ANXA5 haplotype is a hereditary predisposition gene for thrombophilia-associated RPL; the association between M2/ANXA5 haplotype and RPL is further ascertained in a recent meta-analysis. Precision treatments have been proposed for RPL women with M2/ANXA5 haplotype. Therefore, screening for M2/ANXA5 haplotype is highly recommended as a panel of laboratory investigations for idiopathic RPL. To date, direct sequencing of PCR products is the most common method for the determination of M2/ANXA5 haplotype; this method is however tedious, expensive and time- consuming. Hereby, we demonstrate a simple and robust allele-specific PCR (AS-PCR) that detects two inherent SNPs in a single tube, which could serve as a routine genotyping tool for M2/ANXA5 haplotype. This test is rapid, only taking maximum 4 working hours to complete the analysis. Validation of the assay by 105 clinical DNA samples yields 100% concordance rate with the DNA sequencing results.

Determination of the GSTM1 gene deletion frequency in Parkinson's disease by allele specific PCR

1996 ◽  
Vol 2 (3) ◽  
pp. 151-154 ◽  
Author(s):  
Maudy C.M.J. Stroombergen ◽  
Rosemary H. Waring ◽  
Philip Bennett ◽  
Adrian C. Williams
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Gene Deletion ◽  
Gstm1 Gene ◽  
Specific Pcr ◽  
Allele Specific ◽  
Allele Specific Pcr ◽  
Deletion Frequency
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