Single Nucleotide Polymorphisms

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Single Nucleotide Polymorphisms

Author : Pui-Yan Kwok
ISBN : 9781592593279
Genre : Science
File Size : 75.11 MB
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A comprehensive collection of readily reproducible techniques for the difficult process of single nucleotide polymorphisms (SNP) discovery and genotyping. These cutting-edge protocols for mutation/SNP detection utilize denaturing high-performance liquid chromatography (dHPLC), single-strand conformation polymorphism (SSCP), conformation-sensitive gel electrophoresis (CSGE), chemical cleavage, and direct sequencing. Equally powerful and up-to-date methods are given for genotyping SNPs, including molecular beacons, the Taqman assay, single-base extension approaches, pyrosequencing, ligation, the Invader assay, and primer extension with mass spectrometry detection.
Category: Science

Single Nucleotide Polymorphism Snp Discriminations By Nanopore Sensing

Author : Ruicheng Shi
ISBN : OCLC:1099536944
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Single Nucleotide Polymorphisms (SNPs) are a common type of nucleotide alterations across the genome. A rapid but accurate detection of individual or SNP panels can lead to the right and in-time treatments which possibly save lives. In one of our studies, nanopore is introduced to rapidly detect BRAF 1799 T?A mutation (V600E), with the help of an Ap-dA cross-link right at the mutation site. These sequence-specific crosslinks are formed upon strong covalent interactions between probe based abasic sites (Ap) and target based deoxy-adenosine (dA) residues. Duplexes stabilized by the crosslink complexes create indefinite blocking signatures when captured in the nanopore, creating a high contrast compared to the "spike-like" translocations events produced by the un-crosslinked and wildtype duplexes. Those consistent blocking events couldn't be resolved unless an inverted voltage is applied. In a 1:1 BRAF mutant-wildtype mixture, the nanopore can successfully discriminate between the two sequences in a quantitative manner. In summary, nanopore paired with sequence-specific crosslink can detect a specific type of SNP with a high contrast manner. In another study, nanopore sensing is modified to be capable of detections with multiple SNPs in a single detection mix. To achieve this, an RNA homopolymer barcode is integrated into the probe sequence so nanopore can read out a distinctive level signature when the target-probe duplex is de-hybridizing through the pore. Since different RNA homopolymers (e.g. Poly rA and Poly rC) can generate signature levels distinctive from each other and other DNA sequences, they can be applied to generate characteristic patterns that simultaneously highlight multiple SNPs in the mixture. In this study, we assigned two different RNA barcodes (Poly rA and Poly rC) to label KRAS G12D and Tp53 R172H SNPs (both T?A mutations) in the solution. During nanopore readout, the KRAS G12D containing duplex generates a "downward" step pattern but Tp53 R172H always has an "upward" step pattern, the high contrast between those two patterns makes recognition easy enough with naked eyes, and further statistical analysis is unnecessary. Theoretically, at least four different barcodes can be implemented at the same time, furthermore, the length of the barcode can also affect the barcode pattern. Thus, in theory, a panel of more than 10 SNPs can be identified simultaneously.
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Single Nucleotide Polymorphisms Of The Sirtuin 1 Sirt1 Gene Are Associated With Age Related Macular Degeneration In Chinese Han Individuals

Author :
ISBN : OCLC:1051796630
Genre :
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Abstract : Abstract: To investigate whether 3 variants in sirtuin 1 (SIRT1) gene contributed differently in patients with age-related macular degeneration (AMD) in a Chinese Han population. We conducted a case–control study in a group of Chinese patients with AMD (n = 253) and contrasted the results against a control group (n = 292). Three single nucleotide polymorphisms (SNPs) of SIRT1 gene including rs12778366, rs3740051, and rs4746720 were genotyped using improved multiplex ligase detection reaction. The association between targeted SNPs and AMD was then analyzed by codominant, dominant, recessive, and allelic models. The genotyping data of rs12778366, rs3740051, and rs4746720 revealed significant deviations from Hardy–Weinberg equilibrium tests in the AMD group but not in the control group. We detected significantly differences of rs12778366 allele distribution between 2 groups in recessive and codominant model ( P
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Single Nucleotide Polymorphisms

Author : Anton A. Komar
ISBN : 1617796794
Genre : Medical
File Size : 90.82 MB
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In recent years, single nucleotide polymorphisms have received increased and special attention in a rapidly developing field of personalized medicine and drug treatment. Comprising more than eighty percent of all known polymorphisms, single nucleotide polymorphisms (SNPs) are primarily responsible for phenotypic differences between individuals, and have been suggested to affect the development of diseases in humans and the response to drug treatment and environmental stress. In Single Nucleotide Polymorphisms: Methods and Protocols, Second Edition, expert researchers explore the latest advances in this area, highlighting the substantial progress that has been made in SNP genotyping, examining recent developments in high-throughput genotyping approaches, and exploring our new understanding of the impact of SNPs on gene function. Chapters address the impact of SNPs on phenotype, examine SNP databases, look at methods that have been applied for SNP bioinformatics discovery and analysis, and discuss advanced experimental approaches used for SNP detection. Composed in the highly successful Methods in Molecular BiologyTM series format, each chapter contains a brief introduction, step-by-step methods, a list of necessary materials, and a Notes section which shares tips on troubleshooting and avoiding known pitfalls. Current and innovative, Single Nucleotide Polymorphisms: Methods and Protocols, Second Edition is an essential guidebook for individual researchers as well as institutions and companies working in the field.
Category: Medical

Single Nucleotide Polymorphisms Related To Cystic Fibrosis In Chronic Rhinositus A Pilot Study

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ISBN : OCLC:1028145858
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Abstract : Background: The clinical association between cystic fibrosis (CF) and chronic rhinosinusitis (CRS) is well known. Studies have identified several non‐CF transmembrane conductance regulator single nucleotide polymorphisms (SNPs) associated with disease severity in CF patients. We hypothesized that prevalence of these SNPs would be different between CRS patients and age/gender‐matched non‐CRS controls. Methods: This is a targeted SNP study of 1231 CRS patients identified through a large university hospital database who were compared with 8796 age‐ and gender‐matched controls without a history of rhinitis, sinusitis, allergies, or asthma. Prevalence of 5 relevant SNPs was compared between groups, with p
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Single Nucleotide Polymorphisms Of Tight Junction Component Claudin 5 And Leukoaraiosis

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ISBN : OCLC:1163819611
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Background: The bloodu2013brain barrier disruption plays a major role in the development of leukoaraiosis (LA). Claudins are the integral component of tight junction (TJ). Previous study showed that clauidn-3 and claudin-5 play a significant role in TJ formation and integrity of the BBB. The aim of this study was to evaluate whether genetic variations in claudin-5 gene are associated with the development of LA. Methods: LA has to be diagnosed based on Fazekas Scale and grouped into two classes: periventricular white matter (PVWM) and deep white matter (DWM) . A total of 183 LA-PVWM and 156 LA-DWM cases were enrolled from the individuals who underwent brain magnetic resonance imaging with obtainable vascular risk factors. Genotyping of claudin-5 single nucleotide polymorphisms (rs1548359, rs10314 and rs739371) was performed by real-time polymerase chain reaction with LightCycler 2.0. Results: The genotypic frequency of claudin-5 and combination effects of 3 SNPs showed no significant different between controls and both type of LA. However, to simplify synergistic allele combinations, the individuals carrying haplotypes C-G-C (rs1548359/rs10314/rs739371) increased development of LA-DWM by 1.44 times of control. Conclusions: This study provides weak evidence of genetic polymorphisms of claudin-5 associated with susceptibility of LA.
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Identification Of Single Nucleotide Polymorphisms In Inflammatory Bowel Disease Patients On Azathioprine Therapy

Author : Lyla Adam
ISBN : OCLC:1163877269
Genre :
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Azathioprine, an immunosuppressant used for many years in the medical sector to maintain long term disease remission in inflammatory bowel disease has a side effect profile that has raised many concerns over the years with numerous studies into the risk, cause and prevention of these adverse events. It is estimated that 18 in every 100 000 South Africans suffer from Crohn's disease, while 5 in every 100 000 suffer from ulcerative colitis. Of these inflammatory bowel disease patients at least 20% will suffer from leukopenia and eventually bone marrow suppression. Much of the side effect profile of Azathioprine can be linked to a single nucleotide polymorphism in the thiopurine methyltransferase gene which ensures the breakdown and efficacy of Azathioprine. The thiopurine methyltransferase single nucleotide polymorphism profiles of various American, Asian and European populations have been studied, but little literature is available for the South African population. The aim of this study was to determine if it is essential to include "early warning" single nucleotide polymorphism testing in South African health care before treatment with Azathioprine is initiated. This was performed by evaluating 40 patients suffering from inflammatory bowel disease who met the inclusion/ exclusion criteria and who were on continuous Azathioprine therapy. The prevalence of *3A, *3B or *3C thiopurine methyltransferase gene SNP's were determined to assess the efficacy of Azathioprine in reducing therapeutic markers and to compare the frequency of SNP's within the Azathioprine dosing groups. This study showed an increase in the allelic frequency of thiopurine methyltransferase *3B and a statistically significant presence (p
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Genetic Single Nucleotide Polymorphisms Gsnps In The Dna Repair Genes And Hepatocellular Carcinoma Related To Aflatoxin B1 Among Guangxiese Population

Author : Xue-Ming Wu
ISBN : OCLC:1154169213
Genre : Medicine
File Size : 33.69 MB
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Aflatoxin B1 (AFB1) is an important environmental carcinogen for the development of hepatocellular carcinoma (HCC). HCC is a complex disease likely resulting from genetic single nucleotide polymorphisms (GSNPs) of multiple interacting genes and gene-environment interactions. Recent efforts have been made to analyze the associations between risk of this malignancy and GSNPs in genes involved in the repair of DNA damage induced by AFB1. Here, we reviewed the results of published case-control studies that have examined the effects of common alleles of all susceptible DNA repair genes, including XRCC1, XRCC3, XRCC4, XRCC7, XPC, and XPD, on risk of AFB1-related HCC among Guangxi population. Statistically significant differences in genotype frequencies found in case-control comparisons were rs25487, rs80309960, rs861539, rs7003908, rs28383151, rs3734091, rs13181, and rs2228001 polymorphism. The overall effects of these GNSPs were moderate in terms of relative risk, with ORs ranging from 2 to 10. Furthermore, some evidence of the interaction of GSNPs in DNA repair genes and AFB1 exposure modulate risk of this cancer was also found, although the results require confirmation with larger sample size studies.
Category: Medicine

05 A Genotyping Array Of 3 400 Single Nucleotide Polymorphisms Snps Advances The Genetic Analysis Of The Iconic Tree Araucaria Angustifolia Showing That The Natural Populations Are More Differentiated Than Previously Reported

Author : Ananda Virginia Aguiar
ISBN : OCLC:1163814629
Genre :
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We have developed a genotyping u201cchipu201d for the iconic and endangered Araucaria angustifolia tree containing 3,400 SNPs, discovered from RNAseq and RAD-sequencing data. Of these, 1,643 were polymorphic in a sample of 192 individuals from a provenance/progeny collection involving 15 populations from Brazil (SP, MG, PR and SC). These same 192 individuals were genotyped with 30 microsatellites (SSR). Analysis of the population genetic structure with SSR and SNPs revealed substantial differences in the magnitude of population differentiation: Fst was 0.13 with SSR and 0.28 with an equivalent number of SNPs. This pattern was maintained with different estimators (Gst, Gu2019st, Dst) or Rst for microsatellites. Using all 1,643 SNPs covering the entire spectrum of allelic frequencies Fst was slightly higher (0.31). These results corroborate the recognized fact that the multiallelism of SSR restricts the maximum Fst value even in the absence of gene flow, and allele homoplasy tends to overestimate gene flow and homogeneity among populations resulting in largely underestimated population differentiation. Conversely, although bi-allelic and less informative individually, SNPs have a considerably lower mutation rate and a negligible mutation reversal rate, providing robust, accurate, genome-wide estimates of genetic differentiation. These results raise important questions about the validity of the low levels of genetic differentiation between natural populations typically reported for Araucaria based on microsatellites. An underestimated Fst has critical repercussions on inferences of genetic structure and gene flow and, more importantly, on strategic decisions about the conservation of natural populations and enrichment of germplasm banks of this ecologically keystone tree.
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In Vitro Functional Analysis Of Novel Single Nucleotide Polymorphisms In Oatp1b1 And Potential Clinical Relevance

Author : Zhiyuan Peter Yin
ISBN : OCLC:1069688809
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Statin-induced myopathy is a common adverse reaction of statin therapy. Patients with elevated plasma concentration of statins are thought to be at greater risk for myopathy. Statins are transported from the blood to hepatocytes via organic anion transporting polypeptide 1B1 (OATP1B1). Although single nucleotide polymorphisms (SNPs) in OATP1B1 have been associated with increased statin concentrations, we hypothesize that there may be other SNPs in OATP1B1 that can also contribute to reduced transport activity and increased plasma statin concentrations. OATP1B1 cDNA packaged in pEF6/V5-His TOPO was used as template, and 6 SNPs -- c.298G>A, c.419C>T, c.463C>A (*4), c.1007C>G, c.1463G>C (*9), and c.1738C>T -- were introduced separately and expressed in adenovirus. 3 SNPs abolished transport activity, 1 SNP decreased transport, 1 increased transport, and 1 did not affect transport activity. Our data support the hypothesis that there are additional loss of function SNPs in OATP1B1.
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A Study Of Single Nucleotide Polymorphisms Of Grin2b In Schizophrenia From Chinese Han Population

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ISBN : OCLC:1052047623
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Highlights: GRIN2B rs890 demonstrated significant difference between cases and controls. Results adjusted by confounding factors as age and sex remain positive. Rs890 and rs1806191 may form a haplotype and associated with schizophrenia. The GRIN2B might be associated with schizophrenia in Chinese Han population. Abstract: Schizophrenia is a severe and complex mental disorder with high heritability. There is evidence that mutations in the gene of Nmethyl-d -aspartate-type glutamate receptors (NMDAR) are associated with schizophrenia. GRIN2B encodes a subunit of NMDARs, and has been identified as a candidate gene for many psychiatric disorders, especially schizophrenia. In this study, we investigated whether single nucleotide polymorphisms (SNPs) in GRIN2B were associated with schizophrenia. Four SNPs (rs890, rs1806191, rs219872, rs172677) were genotyped in 752 schizophrenic patients and 846 healthy controls of the Chinese Han population. Our results indicate differences in allele and genotype frequencies of rs890 between case and control. These results were assessed by adapting different genetic models (codominant, dominant, recessive, overdominant, log-additive models). After controlling for confounding factors including sex and age, rs890 remained associated with schizophrenia. In addition, rs890 and rs1806191 were found to form a haplotype associated with schizophrenia. In summary, our results indicate that the GRIN2B SNP rs890 might be associated with schizophrenia in the Chinese Han population.
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