Influence of IL10 (G1082A) and TNFα (G308A) Polymorphisms on the Survival of Pediatric Patients with ALL

Interleukin 10 (IL10) is a pleiotropic cytokine that stimulates various hematopoietic cells. The tumor necrosis factor alpha (TNFα) is a cytokine that may influence the transcriptional activity induced by glucocorticoids. This study examined the impact of TNFα (G308A) and IL10 (G1082A) polymorphisms at promoter regions in relation to the overall survival of 105 children (0≤18 years) with acute lymphoblastic leukemia (ALL) for a period of 126 months, treated according to the protocol GBTLI99. The G1082A and G308A polymorphisms were identified by allele-specific PCR and PCR-RFLP, respectively. Patients with IL10AA genotype had a higher death ratio (44%, P=0.0089). Patients with both IL10AA and TNFAA genotypes showed the worst survival when compared with the IL10GG and TNFGA genotypes (P=0.0043). The results of this study revealed a lower survival among patients with IL10AA genotype and the concomitant occurrence of IL10AA and TNFAA genotypes.

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

Thrombosis and Haemostasis ◽

10.1055/s-0038-1650362 ◽

1996 ◽

Vol 75 (05) ◽

pp. 757-759 ◽

Cited By ~ 11

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.

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Comparison of PCR-RFLP with Allele-Specific PCR in Genetic Testing for Spinal Muscular Atrophy

Genetic Testing ◽

10.1089/109065703322783626 ◽

2003 ◽

Vol 7 (4) ◽

pp. 277-281 ◽

Cited By ~ 10

Author(s):

Ruliang Xu ◽

Shuji Ogino ◽

Va Lip ◽

Hong Fang ◽

Bai-Lin Wu

Keyword(s):

Genetic Testing ◽

Spinal Muscular Atrophy ◽

Muscular Atrophy ◽

Specific Pcr ◽

Pcr Rflp ◽

Allele Specific ◽

Allele Specific Pcr

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A Cross-Sectional Study for Evaluation of KRAS and BRAF Mutations by Reverse Dot Blot, PCR-RFLP, and Allele-Specific PCR Methods Among Patients with Colorectal Cancer

Avicenna Journal of Medical Biotechnology ◽

10.18502/ajmb.v13i4.7203 ◽

2021 ◽

Author(s):

Fatemeh Sheikhsofla ◽

Behzad Poopak ◽

Sajjad Firuzyar ◽

Fatemeh Roudbari ◽

Mojtaba Ghadiany

Keyword(s):

Colorectal Cancer ◽

Gene Mutations ◽

Dot Blot ◽

Braf Mutations ◽

Kras Gene ◽

Specific Pcr ◽

Pcr Rflp ◽

Allele Specific ◽

Allele Specific Pcr ◽

Reverse Dot Blot

Background: KRAS and BRAF genes are the biomarkers in Colorectal Cancer (CRC) which play prognostic and predictive roles in CRC treatment. Nowadays, the selection of rapid and available methods for studying KRAS and BRAF mutations in anti-EGFR therapy of patients suffering from CRC plays a significant role. In this study, the mutations of these two oncogenes were evaluated by different methods. Methods: This study was performed on 50 Formalin-Fixed Paraffin-Embedded (FFPE) tissue blocks of patients diagnosed with colorectal cancer. After DNA extraction, KRAS and BRAF gene mutations were evaluated using reverse dot blot, and results were compared with PCR-RFLP and allele-specific PCR for KRAS and BRAF mutations, respectively. Results: KRAS gene mutations were detected in 42% of patients, of which 30% were in codon 12 region, and 12% in codon 13. The most frequent mutations of KRAS were related to G12D and 10% of patients had BRAF mutated genes. The type of KRAS gene mutations could be evaluated by reverse dot blot method. In general, the results of PCR-RFLP and allele-specific PCR were similar to the findings by reverse dot blot method. Conclusion: These findings suggest that PCR-RFLP and allele-specific PCR methods are suitable for screening the presence of the mutations in KRAS and BRAF oncogenes. In fact, another method with more sensitivity is needed for a more accurate assessment to determine the type of mutations. Due to higher speed of detection, reduced Turnaround Time (TAT), and possible role of some KRAS point mutations in overall survival, reverse dot blot analysis seems to be an optimal method.

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Multiplex allele-specific PCR combined with PCR-RFLP analysis for rapid detection of gyrA gene fluoroquinolone resistance mutations in Mycobacterium tuberculosis

Journal of Microbiological Methods ◽

10.1016/j.mimet.2011.10.015 ◽

2012 ◽

Vol 88 (1) ◽

pp. 175-178 ◽

Cited By ~ 4

Author(s):

Li-li Zhao ◽

Qiang Xia ◽

Nan Lin ◽

Zhi-guang Liu ◽

Xiu-qin Zhao ◽

...

Keyword(s):

Mycobacterium Tuberculosis ◽

Rapid Detection ◽

Rflp Analysis ◽

Fluoroquinolone Resistance ◽

Resistance Mutations ◽

Gyra Gene ◽

Specific Pcr ◽

Pcr Rflp ◽

Allele Specific ◽

Allele Specific Pcr

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ANALYSIS OF GENES IL-1Β (C511T), IL-2 (T330G), IL-13 (C1111T) POLYMORPHISM ASSOCIATION WITH THE DEVELOPMENT OF STOMACH DISEASES

Health and Ecology Issues ◽

10.51523/2708-6011.2015-12-3-22 ◽

2015 ◽

pp. 97-102

Author(s):

A. V. Voropayeva ◽

O. V. Karpenko ◽

E. V. Bredikhina ◽

T. P. Krivun ◽

O. V. Osipkina ◽

...

Keyword(s):

Gene Polymorphism ◽

Specific Pcr ◽

Cancer Of The Stomach ◽

Genetic Components ◽

Stomach Diseases ◽

Pcr Rflp ◽

The Status ◽

Allele Specific ◽

H Pylori ◽

Allele Specific Pcr

Objective: to study the role of IL-1β (C511T), IL-2 (T330G), IL-13 (C1111T) gene polymorphism in the development of stomach diseases in Belarusian population. Material and methods. The study included 194 patients diagnosed with «chronic gastritis» and 68 patients diagnosedwith «cancer of the stomach». To determine polymorphisms of IL-2 (T330G), IL-13 (C-1111T) and IL-1β (C511T) genes, we used the method of allele-specific PCR (AS-PCR) and PCR detection of the length of restriction fragments (PCR-RFLP). Results . By the loci of IL-2 (T330G), IL-13 (C1111T), IL-1b (S511T) we revealed the correlation with oncopathology depending on the status of infection by various strains of H. pylori. Conclusion . The use of the revealed association of cytokine gene polymorphism with the development of the diseases makes it possible to select genetic components that determine the sensitivityof the population to the development of stomach diseases depending on H. pylori infection in Belarusian population.

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Influence of Methylenetetrahydrofolate Reductase C677T, A1298C, and G80A Polymorphisms on the Survival of Pediatric Patients with Acute Lymphoblastic Leukemia

Leukemia Research and Treatment ◽

10.1155/2012/292043 ◽

2012 ◽

Vol 2012 ◽

pp. 1-6 ◽

Cited By ~ 3

Author(s):

Dayse Maria Vasconcelos de Deus ◽

Elker Lene Santos de Lima ◽

Rafaela Maria Seabra Silva ◽

Edinalva Pereira Leite ◽

Maria Tereza Cartaxo Muniz

Keyword(s):

Overall Survival ◽

Acute Lymphoblastic Leukemia ◽

Pediatric Patients ◽

Methylenetetrahydrofolate Reductase ◽

Lymphoblastic Leukemia ◽

Chemotherapeutic Agents ◽

Specific Pcr ◽

Pcr Rflp ◽

Chemotherapy Protocol ◽

Allele Specific

The influence of genic polymorphisms involved in metabolism of chemotherapeutic agents as the methotrexate (MTX) has been studied mainly in acute lymphoblastic leukemia (ALL) of childhood. Advances in treatment may be attributed to identification of prognostic factors added to chemotherapy protocol. The aim of this study was to analyze the association of the C677T, A1298C, and G80A polymorphisms on MTHFR gene and on the overall survival of pediatric patients (n=126) with lymphoblastic leukemia treated with MTX according to the Brazilian protocol in 187 months. The C677T and G80A polymorphisms were genotyped by PCR-RFLP and A1298C polymorphism by allele-specific PCR. We observed that ALL patients presented rate (dead/alive) of 0.36 for the 677CC genotype, corresponding also to lower overall survival (P=0.0013); on the other hand, the 677TT genotype showed a better survival (98%). Thus, we believe that patients with 80AA genotype presented a small reduction in MTX plasma level, suggesting that ALL children, carrying the 80AA genotype, showed a high toxicity to MTX (P<0.0001).

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MUPrimer : a tool for finding allele specific PCR-primers for homologous gene sequences

10.32469/10355/6660 ◽

2009 ◽

Author(s):

M. Mursaleen Ahmad

Keyword(s):

Pcr Primers ◽

Homologous Gene ◽

Gene Sequences ◽

Specific Pcr ◽

Allele Specific ◽

Allele Specific Pcr

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Development of genic KASP SNP markers from RNA-Seq data for map-based cloning and marker-assisted selection in maize

BMC Plant Biology ◽

10.1186/s12870-021-02932-8 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Zhengjie Chen ◽

Dengguo Tang ◽

Jixing Ni ◽

Peng Li ◽

Le Wang ◽

...

Keyword(s):

Marker Assisted Selection ◽

Inbred Lines ◽

Average Density ◽

Snp Markers ◽

Data Sets ◽

Rna Seq ◽

Specific Pcr ◽

Maize Inbred Lines ◽

Allele Specific ◽

Allele Specific Pcr

Abstract Background Maize is one of the most important field crops in the world. Most of the key agronomic traits, including yield traits and plant architecture traits, are quantitative. Fine mapping of genes/ quantitative trait loci (QTL) influencing a key trait is essential for marker-assisted selection (MAS) in maize breeding. However, the SNP markers with high density and high polymorphism are lacking, especially kompetitive allele specific PCR (KASP) SNP markers that can be used for automatic genotyping. To date, a large volume of sequencing data has been produced by the next generation sequencing technology, which provides a good pool of SNP loci for development of SNP markers. In this study, we carried out a multi-step screening method to identify kompetitive allele specific PCR (KASP) SNP markers based on the RNA-Seq data sets of 368 maize inbred lines. Results A total of 2,948,985 SNPs were identified in the high-throughput RNA-Seq data sets with the average density of 1.4 SNP/kb. Of these, 71,311 KASP SNP markers (the average density of 34 KASP SNP/Mb) were developed based on the strict criteria: unique genomic region, bi-allelic, polymorphism information content (PIC) value ≥0.4, and conserved primer sequences, and were mapped on 16,161 genes. These 16,161 genes were annotated to 52 gene ontology (GO) terms, including most of primary and secondary metabolic pathways. Subsequently, the 50 KASP SNP markers with the PIC values ranging from 0.14 to 0.5 in 368 RNA-Seq data sets and with polymorphism between the maize inbred lines 1212 and B73 in in silico analysis were selected to experimentally validate the accuracy and polymorphism of SNPs, resulted in 46 SNPs (92.00%) showed polymorphism between the maize inbred lines 1212 and B73. Moreover, these 46 polymorphic SNPs were utilized to genotype the other 20 maize inbred lines, with all 46 SNPs showing polymorphism in the 20 maize inbred lines, and the PIC value of each SNP was 0.11 to 0.50 with an average of 0.35. The results suggested that the KASP SNP markers developed in this study were accurate and polymorphic. Conclusions These high-density polymorphic KASP SNP markers will be a valuable resource for map-based cloning of QTL/genes and marker-assisted selection in maize. Furthermore, the method used to develop SNP markers in maize can also be applied in other species.

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Two User-Friendly Molecular Markers Developed for the Identification of Hybrid Lethality Genes in Brassica oleracea

Agronomy ◽

10.3390/agronomy11050982 ◽

2021 ◽

Vol 11 (5) ◽

pp. 982

Author(s):

Zhiliang Xiao ◽

Congcong Kong ◽

Fengqing Han ◽

Limei Yang ◽

Mu Zhuang ◽

...

Keyword(s):

Molecular Markers ◽

Brassica Oleracea ◽

Rapid Identification ◽

Inbred Lines ◽

Hybrid Lethality ◽

Specific Pcr ◽

Allele Specific ◽

User Friendly ◽

Allele Specific Pcr ◽

Kasp Marker

Cabbage (Brassica oleracea) is an important vegetable crop that is cultivated worldwide. Previously, we reported the identification of two dominant complementary hybrid lethality (HL) genes in cabbage that could result in the death of hybrids. To avoid such losses in the breeding process, we attempted to develop molecular markers to identify HL lines. Among 54 previous mapping markers closely linked to BoHL1 or BoHL2, only six markers for BoHL2 were available in eight cabbage lines (two BoHL1 lines; three BoHL2 lines; three lines without BoHL); however, they were neither universal nor user-friendly in more inbred lines. To develop more accurate markers, these cabbage lines were resequenced at an ~20× depth to obtain more nucleotide variations in the mapping regions. Then, an InDel in BoHL1 and a single-nucleotide polymorphism (SNP) in BoHL2 were identified, and the corresponding InDel marker MBoHL1 and the competitive allele-specific PCR (KASP) marker KBoHL2 were developed and showed 100% accuracy in eight inbred lines. Moreover, we identified 138 cabbage lines using the two markers, among which one inbred line carried BoHL1 and 11 inbred lines carried BoHL2. All of the lethal line genotypes obtained with the two markers matched the phenotype. Two markers were highly reliable for the rapid identification of HL genes in cabbage.

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