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Journal ArticleDOI

Classification of PCR-SSCP bands in T2DM by probabilistic neural network: a reliable tool

01 Jun 2015-International Journal of Bioinformatics Research and Applications (Inderscience Publishers (IEL))-Vol. 11, Iss: 4, pp 308-314
TL;DR: This study proves to be very reliable and gives accurate and fast detection for mutation analysis in diabetes and could be extended for analysis in other human diseases.
Abstract: A Probabilistic Neural Network PNN is a statistical algorithm and consists of a grouping of multi-class data. The conventional method of detection of DNA mutations by the human eye may not detect the minute variations in PCR-SSCP bands, which may lead to false positive or false negative results. The detection by photographic images may contain a blare noise caused during the time of photography; therefore, image processing techniques were used to reduce image noise. PCR-SSCP gels of T2DM patients n = 100 and controls n = 100 were initially photographed with equal ratio of pixels and later subjected to a two-stage analysis: feature extraction and PNN. The evaluation of the results was done by quality training and the accuracy was up to 95%, and the human eye analysis showed 80% mutation detection rate. This study proves to be very reliable and gives accurate and fast detection for mutation analysis in diabetes. This method could be extended for analysis in other human diseases.
References
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Journal ArticleDOI
TL;DR: The mobility shift analysis of single-stranded DNAs on neutral polyacrylamide gel electrophoresis to detect DNA polymorphisms was developed and SSCPs were found to be allelic variants of true Mendelian traits, and therefore they should be useful genetic markers.
Abstract: We developed mobility shift analysis of single-stranded DNAs on neutral polyacrylamide gel electrophoresis to detect DNA polymorphisms. This method follows digestion of genomic DNA with restriction endonucleases, denaturation in alkaline solution, and electrophoresis on a neutral polyacrylamide gel. After transfer to a nylon membrane, the mobility shift due to a nucleotide substitution of a single-stranded DNA fragment could be detected by hybridization with a nick-translated DNA fragment or more clearly with RNA copies synthesized on each strand of the DNA fragment as probes. As the mobility shift caused by nucleotide substitutions might be due to a conformational change of single-stranded DNAs, we designate the features of single-stranded DNAs as single-strand conformation polymorphisms (SSCPs). Like restriction fragment length polymorphisms (RFLPs), SSCPs were found to be allelic variants of true Mendelian traits, and therefore they should be useful genetic markers. Moreover, SSCP analysis has the advantage over RFLP analysis that it can detect DNA polymorphisms and point mutations at a variety of positions in DNA fragments. Since DNA polymorphisms have been estimated to occur every few hundred nucleotides in the human genome, SSCPs may provide many genetic markers.

3,887 citations

Journal ArticleDOI
TL;DR: Athrosclerosis and cardiomyopathy in type 2 diabetes are caused in part by pathway-selective insulin resistance, which increases mitochondrial ROS production from free fatty acids and by inactivation of antiatherosclerosis enzymes by ROS.
Abstract: Oxidative stress plays a pivotal role in the development of diabetes complications, both microvascular and cardiovascular. The metabolic abnormalities of diabetes cause mitochondrial superoxide overproduction in endothelial cells of both large and small vessels, as well as in the myocardium. This increased superoxide production causes the activation of 5 major pathways involved in the pathogenesis of complications: polyol pathway flux, increased formation of AGEs (advanced glycation end products), increased expression of the receptor for AGEs and its activating ligands, activation of protein kinase C isoforms, and overactivity of the hexosamine pathway. It also directly inactivates 2 critical antiatherosclerotic enzymes, endothelial nitric oxide synthase and prostacyclin synthase. Through these pathways, increased intracellular reactive oxygen species (ROS) cause defective angiogenesis in response to ischemia, activate a number of proinflammatory pathways, and cause long-lasting epigenetic changes that drive persistent expression of proinflammatory genes after glycemia is normalized ("hyperglycemic memory"). Atherosclerosis and cardiomyopathy in type 2 diabetes are caused in part by pathway-selective insulin resistance, which increases mitochondrial ROS production from free fatty acids and by inactivation of antiatherosclerosis enzymes by ROS. Overexpression of superoxide dismutase in transgenic diabetic mice prevents diabetic retinopathy, nephropathy, and cardiomyopathy. The aim of this review is to highlight advances in understanding the role of metabolite-generated ROS in the development of diabetic complications.

3,822 citations

Journal ArticleDOI
TL;DR: A probabilistic neural network that can compute nonlinear decision boundaries which approach the Bayes optimal is formed, and a fourlayer neural network of the type proposed can map any input pattern to any number of classifications.

3,772 citations


"Classification of PCR-SSCP bands in..." refers methods in this paper

  • ...PNN was first developed by Donald Specht in 1990, derived from Bayes decision network (Specht, 1990)....

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Journal ArticleDOI
TL;DR: The relative paucity of mutations found in this study suggests that more LCA-associated genes remain to be discovered, and molecular diagnosis may be of benefit to patients affected with LCA.
Abstract: Objective To assess the frequency of mutations in the CRX , GUCY2D , and RPE65 genes in patients with Leber congenital amaurosis (LCA). Patients One hundred seventy-six probands with a clinical diagnosis of LCA were from 9 countries, with the largest subgroup being 39 probands from India. Methods Samples were screened with single-strand conformation polymorphism analysis followed by DNA sequencing of 3 genes ( CRX , GUCY2D , and RPE65 ) known to be associated with LCA. Results Of the 176 probands, 28 (15.9%) harbored possible disease-causing mutations. The relative contribution of each gene to the total number of mutations was as follows: CRX , 2.8%; GUCY2D , 6.3%; and RPE65 , 6.8%. No patients who harbored mutations in these genes had associated systemic abnormalities. Molecular diagnosis allowed definitive genetic counseling in a family affected with Best disease and LCA. Conclusions Molecular diagnosis may be of benefit to patients affected with LCA. The relative paucity of mutations found in this study suggests that more LCA-associated genes remain to be discovered. Clinical Relevance Molecular diagnosis can confirm and clarify the diagnosis of LCA. As genotype data accumulate, clinical phenotypes associated with specific mutations will be established. This will facilitate the counseling of patients on their visual prognosis and the likelihood of associated systemic anomalies.

161 citations


"Classification of PCR-SSCP bands in..." refers methods in this paper

  • ...1 Methods DNA extractions were done by a modified method of Lotery et al. (2000). Primers were designed by Primer 3 online software and PCR amplification was performed in Eppendorf Mastercycler Gradient machine....

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Journal ArticleDOI
TL;DR: The results suggest a large impact of passage through the digestive tract of L. terrestris on bacterial community structure and demonstrate the usefulness of the image analysis procedure for the determination of cell sizes and biovolumes and thus biomass of specific bacterial populations in different terrestrial habitats.

101 citations