Oligonucleotides used as template calibrators for general application in quantitative polymerase chain reaction
ABSTRACT The optimizing and controlling for polymerase chain reactions (PCRs) requires standard target sequences to measure reaction specificity and to obtain accurate gene quantification. However, defined target sequences are often not readily available. This situation is particularly evident in the study of rare splice variant transcripts. For gains in efficiency and reaction speed, a small size of PCR amplicon typifies real-time PCR formats, including hydrolysis probes. This study demonstrates the use of oligonucleotides resembling one strand of complete amplicon sequences used in real-time PCR to provide sustainable and precise amounts of the target sequence without the necessity of enlisting nucleic acid cloning procedures. The application of template oligonucleotides is modeled using all of the splice variant forms of human vascular endothelial growth factor.
- SourceAvailable from: Stuart D Carter
[Show abstract] [Hide abstract]
- "Primers were synthesised by MWG Biotech and probes were synthesised by Roche Diagnostics using locked nucleic acid analogues with a 5 0 end reporter dye fluorescein (FAM, 6-carboxy fluorescein) and a 3 0 end dark quencher dye. Template oligonucleotides (Mohammadi and Day, 2004) for the amplicon generated by each assay were synthesised by Eurogentec. Two reference (housekeeping) genes (MRPS7 and HIRIP5) were previously identified from micro-array data and confirmed as having stable expression in normal and OA bone and cartilage using a statistical algorithm (Vandesompele et al., 2002). "
ABSTRACT: The relationship between radiographic measures of severity of osteoarthritis (OA) and changes in gene expression in joints are not well characterised. In this study, the expression of 11 candidate genes was characterised by quantitative reverse transcriptase polymerase chain reaction in normal and OA cartilage and bone from the elbows of dogs with fragmented coronoid disease. The levels of expression of type I collagen alpha2 chain (COL1A2), type III collagen alpha1 chain (COL3A1), lumican (LUM), matrix metalloproteinase-2 (MMP2), -9 (MMP9) and -13 (MMP13) genes were increased and the expression of tissue inhibitor of metalloproteinase-2 (TIMP2) and cathepsin D (CTSD) genes were decreased in OA cartilage relative to normal cartilage. All differences correlated with radiographic measures of severity of OA. Levels of expression of COL1A2, MMP2, MMP9, MMP13 and TIMP1 were increased, whereas expression of TIMP2 was decreased in OA bone relative to normal bone. Cartilage gene expression may be correlated with the radiographic severity of OA.The Veterinary Journal 11/2007; 179(2):211-8. DOI:10.1016/j.tvjl.2007.08.027 · 1.76 Impact Factor
[Show abstract] [Hide abstract]
- "Real-time RT-qPCR data was then analysed by using LightCycler® 480 Basic Software (Roche Diagnostics; Lewes, UK). Standard curves were generated for each reference gene by employing cDNA or template oligonucleotides , the parameters of which are listed in Table 1. All samples were checked for absence of genomic DNA contamination using a canine genome specific RT-qPCR assay, previously described . "
ABSTRACT: Real-time reverse transcriptase quantitative polymerase chain reaction (real-time RT-qPCR) is the most accurate measure of gene expression in biological systems. The comparison of different samples requires the transformation of data through a process called normalisation. Reference or housekeeping genes are candidate genes which are selected on the basis of constitutive expression across samples, and allow the quantification of changes in gene expression. At present, no reference gene has been identified for any organism which is universally optimal for use across different tissue types or disease situations. We used microarray data to identify new reference genes generated from total RNA isolated from normal and osteoarthritic canine articular tissues (bone, ligament, cartilage, synovium and fat). RT-qPCR assays were designed and applied to each different articular tissue. Reference gene expression stability and ranking was compared using three different mathematical algorithms. Twelve new potential reference genes were identified from microarray data. One gene (mitochondrial ribosomal protein S7 [MRPS7]) was stably expressed in all five of the articular tissues evaluated. One gene HIRA interacting protein 5 isoform 2 [HIRP5]) was stably expressed in four of the tissues evaluated. A commonly used reference gene glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was not stably expressed in any of the tissues evaluated. Most consistent agreement between rank ordering of reference genes was observed between Bestkeeper(c) and geNorm, although each method tended to agree on the identity of the most stably expressed genes and the least stably expressed genes for each tissue. New reference genes identified using microarray data normalised in a conventional manner were more stable than those identified by microarray data normalised by using a real-time RT-qPCR methodology. Microarray data normalised by a conventional manner can be filtered using a simple stepwise procedure to identify new reference genes, some of which will demonstrate good measures of stability. Mitochondrial ribosomal protein S7 is a new reference gene worthy of investigation in other canine tissues and diseases. Different methods of reference gene stability assessment will generally agree on the most and least stably expressed genes, when co-regulation is not present.BMC Molecular Biology 02/2007; 8(1):62. DOI:10.1186/1471-2199-8-62 · 2.19 Impact Factor
- [Show abstract] [Hide abstract]
ABSTRACT: Canine atopic dermatitis (cAD) is a common and severe pruritic, inflammatory skin disease that can be considered a naturally-occurring, spontaneous model of human Atopic Dermatitis (hAD). The genetics of cAD are poorly understood and therefore the aim of this project was to investigate the genetic factors involved in the pathogenesis of cAD and to identify specific gene associations with cAD within and between dog breeds. It was hoped that this study would further strengthen the evidence that dogs are a suitable model hAD. Using dogs as a model to study the genetic basis of AD is advantageous because dog breeds form genetically isolated populations exhibiting strong linkage disequilibrium (LD). In contrast to humans where LD across the genome is weak (10-100 kb), domestic dog breeds have strong LD which extends over long distances (0.8 -5 Mb). This is highly advantageous in genetic studies because fewer genetic markers and smaller sample sizes are needed to find disease associations in dogs. To study the genetic basis of cAD a dual approach of candidate gene association study and genome wide association study (GWAS) was used. This gave not only a novel unbiased approach but also used information from previous studies on which gene selection was based. Therefore increasing the likelihood that the causative genes involved in cAD pathogenesis could be identified. This thesis demonstrated altered mRNA expression in 54 genes out of 22,000 transcripts by mRNA microarray in cAD. Further to this qPCR was used to confirm the microarray results and quantify gene expression in potential cAD candidate genes. This approach identified 11 genes with altered expression in cAD. The qPCR results were further correlated 2 with the clinical outcomes: Canine Atopic Dermatitis and Severity Index (CADESI-03) and number of responses on intra-dermal allergen tests. Eleven novel SNPs and 1 novel microsatellite were identified by transgenomic WAVE analysis. The microsatellite was further typed in 659 dogs and but no association with cAD was found. A GWAS with 22,362 SNPs was performed. The significant results were validated by Sequenom along with the SNPs from the candidate gene study (literature selected genes) in 659 dogs across 8 breeds. In total, 232 SNPs across 54 genes and 41 intergenic regions were genotyped on Sequenom. From this 45 putative associations were found in various breeds. A large number of these associations had relevant functions to AD and/or previous association with hAD.