Genome-wide polymerase chain reaction primer design

2000 ◽  
Author(s):  
Hai-Hui Huang ◽  
G. E. Hedrick ◽  
Robert Burnap ◽  
Haobo Liu
Keyword(s):  
Polymerase Chain Reaction ◽  
Primer Design ◽  
Polymerase Chain Reaction Primer ◽  
Chain Reaction ◽  
Genome Wide ◽  
Polymerase Chain

scholarly journals Polymerase chain reaction primer sets for the detection of genetically diverse human sapoviruses

2020 ◽  
Vol 165 (10) ◽  
pp. 2335-2340
Author(s):  
Tomoichiro Oka ◽  
Seiji P. Yamamoto ◽  
Nobuhiro Iritani ◽  
Shigenori Sato ◽  
Chika Tatsumi ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Polymerase Chain Reaction Primer ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Primer Sets

scholarly journals Differential genome-wide array–based methylation profiles in prognostic subsets of chronic lymphocytic leukemia

Blood ◽  
2010 ◽  
Vol 115 (2) ◽  
pp. 296-305 ◽  
Author(s):  
Meena Kanduri ◽  
Nicola Cahill ◽  
Hanna Göransson ◽  
Camilla Enström ◽  
Fergus Ryan ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Chronic Lymphocytic Leukemia ◽  
Tumor Suppressor ◽  
Tumor Suppressor Genes ◽  
Lymphocytic Leukemia ◽  
Chain Reaction ◽  
Global Methylation ◽  
Suppressor Genes ◽  
Genome Wide ◽  
Polymerase Chain

Abstract Global hypomethylation and regional hypermethylation are well-known epigenetic features of cancer; however, in chronic lymphocytic leukemia (CLL), studies on genome-wide epigenetic modifications are limited. Here, we analyzed the global methylation profiles in CLL, by applying high-resolution methylation microarrays (27 578 CpG sites) to 23 CLL samples, belonging to the immunoglobulin heavy-chain variable (IGHV) mutated (favorable) and IGHV unmutated/IGHV3-21 (poor-prognostic) subsets. Overall, results demonstrated significant differences in methylation patterns between these subgroups. Specifically, in IGHV unmutated CLL, we identified methylation of 7 known or candidate tumor suppressor genes (eg, VHL, ABI3, and IGSF4) as well as 8 unmethylated genes involved in cell proliferation and tumor progression (eg, ADORA3 and PRF1 enhancing the nuclear factor-κB and mitogen-activated protein kinase pathways, respectively). In contrast, these latter genes were silenced by methylation in IGHV mutated patients. The array data were validated for selected genes using methylation-specific polymerase chain reaction, quantitative reverse transcriptase–polymerase chain reaction, and bisulfite sequencing. Finally, the significance of DNA methylation in regulating gene promoters was shown by reinducing 4 methylated tumor suppressor genes (eg, VHL and ABI3) in IGHV unmutated samples using the methyl-inhibitor 5-aza-2′-deoxycytidine. Taken together, our data for the first time reveal differences in global methylation profiles between prognostic subsets of CLL, which may unfold epigenetic silencing mechanisms involved in CLL pathogenesis.

scholarly journals RANCANGAN PRIMER SPESIFIK GEN MACROPHAGE MANNOSE RECEPTOR (MMR) UNTUK POLYMERASE CHAIN REACTION (PCR) DAN SEKUENSING DEOXYRIBO NUCLEIC ACID (DNA)

2018 ◽  
Vol 22 (2) ◽  
pp. 158
Author(s):  
Yani Triyani ◽  
Nurizzatun Nafsi ◽  
Lelly Yuniarti ◽  
Nanan Sekarwana ◽  
Endang Sutedja ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Sequencing ◽  
Mannose Receptor ◽  
Primer Design ◽  
Sequencing Analysis ◽  
Nucleotide Polymorphisms ◽  
Chain Reaction ◽  
Specific Pcr ◽  
Polymerase Chain ◽  
Dna Sequencing Analysis

The order (sequencing) determinationof DeoxyribonucleicAcid (DNA) bases is the gene’s most basic information, using the methodof Polymerase Chain Reaction (PCR) as its stage. A key factor of successful detection by PCR is specific PCR primer design choice. Thedetection of diversity of Mycobacterium Mannose Receptor (MMR) gene, responsible for recognizing mannosylated antigen structureof Mycobacterium tuberculosis (M.tb) by DNA sequencing of exon 7 chromosome 10p12, related to susceptiblity for PulmonaryTuberculosis(TB), was first performed in China in 2012. The purpose of this study was to find specific primerfromboth design originatedfrom the research in China/primer I and my own design/primer IIby using Primer3 software. This study was based on 10 healthy subjectsand was a preliminary study of a research titled. The Relationship of Single Nucleotide Polymorphisms (SNPs) of Macrophage MannoseReceptor Gene to Pulmonary Tuberculosis Cases. The examination materials consist of 3 mL of EDTA blood and DNA extraction from itsbuffy coat. The resulting DNA was processed by PCR to amplify MMR gene with primer I and II. The primer I successfully amplified DNAfragments up to 780bp while primer II only 329 bp. The MMR gene DNA sequencing analysis was performed on the amplification resultof both kinds primers by using DNA Baser and Ensembl−BLAST software. The results were different, DNA sequencing result by using theprimer I was found in several chromosomes and also in several loci. Whereas, by using the primer II, it was only found in chromosome10 and in the same locus. Based on this study, it can be concluded that the specific primer design is one of the most important factorsin the success of DNA sequencing.

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