SNP and Mutation Analysis

Wang, Lu; Luhm, Robert A.; Lei, Ming

doi:10.1007/978-0-387-39978-2_11

Cited by 36 publications

(19 citation statements)

References 34 publications

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“…Added to that, pyrosequencing is simpler to implement and requires significantly less DNA than Sanger sequencing (Hastings, 2004). It also offers higher specificity and sensitivity in analysis of genomic DNA (Wang et al, 2007), much higher throughput, and lower cost than Sanger sequencing (Weber et al, 2007). Additional advantages include flexibility, high accuracy, and ability to automate sample preparation (Novais and Thorstenson, 2011).…”

Section: Discussionmentioning

confidence: 99%

Evaluation of pyrosequencing for large-scale identificationof plant species (grasses as a model)

Haider¹

2015

Turk J Agric For

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Grasses (Poaceae) are among the most important and widely cultivated plants. Identification of grass species using morphological characters is a difficult task for nonspecialists, and it is not always an accurate method. DNA-based molecular markers have been widely used as an alternative towards more accurate identification of plant species. The molecular method that can be effective for large-scale identification of grass species, however, must satisfy requirements for specific amplification of DNA and reveal enough variability to distinguish species. The goal of this study was to evaluate the ability of pyrosequencing to detect SNP polymorphisms for an optimal discrimination of grass species. PCR amplifications and the sequencing of 19 fragments of chloroplast genes were performed using a pooled DNA template of 32 British native grass species to be identified and chloroplast DNA-specific universal primers. Based on amplicon size and sequence variance, the 6 most variable loci (psbE&F, rbcL.1, ndhF.1, ndhF.2, ndhF.3, and clpP&rps12) were selected to be targeted for pyrosequencing of the species analyzed. The pyrosequenced regions contained sufficient polymorphisms to allow the complete diagnosis of all species analyzed, except for Elymus caninus and Elytrigia repens, which had identical sequences unique from the remaining species. When targeted loci were pyrosequenced in representative species of the 2 economically important grass genera Festuca L. (8 species) and Poa L. (11 species), all species in each genus could be separated. Should the SNP markers developed here proved to be species-specific, they can provide a valuable tool for reliable diagnosis of grasses and applications (e.g., forensic botany) moving forward.

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Section: Discussionmentioning

confidence: 99%

Evaluation of pyrosequencing for large-scale identificationof plant species (grasses as a model)

Haider¹

2015

Turk J Agric For

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“…Traditional approaches to identify and quantify genomic expression include mRNA microarrays [19], expressed sequence tags (EST) [20], serial analysis of gene expression (SAGE) [21], subtractive cloning for differential display (DD) [22] on mRNA, two-dimensional gel electrophoresis [23], mass spectrometry [24], protein microarray based antibody-binding for protein [25], single nucleotide polymorphism (SNP) microarray [26], and DNA-seq (whole genomics sequence and whole exome sequence) [27] for DNA. These traditional methods have been extensively utilized in the analysis of clinical specimens.…”

Section: Discussionmentioning

confidence: 99%

Feasibility of Whole RNA Sequencing from Single-Cell mRNA Amplification

Zheng

et al. 2013

Genetics Research International

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Single-cell sampling with RNA-seq analysis plays an important role in reference laboratory; cytogenomic diagnosis for specimens on glass-slides or rare cells in circulating blood for tumor and genetic diseases; measurement of sensitivity and specificity in tumor-tissue genomic analysis with mixed-cells; mechanism analysis of differentiation and proliferation of cancer stem cell for academic purpose. Our single- cell RNA-seq technique shows that fragments were 250–450 bp after fragmentation, amplification, and adapter addition. There were 11.6 million reads mapped in raw sequencing reads (19.6 million). The numbers of mapped genes, mapped transcripts, and mapped exons were 31,332, 41,210, and 85,786, respectively. All QC results demonstrated that RNA-seq techniques could be used for single-cell genomic performance. Analysis of the mapped genes showed that the number of genes mapped by RNA-seq (6767 genes) was much higher than that of differential display (288 libraries) among similar specimens which we have developed and published. The single-cell RNA-seq can detect gene splicing using different subtype TGF-beta analysis. The results from using Q-rtPCR tests demonstrated that sensitivity is 76% and specificity is 55% from single-cell RNA-seq technique with some gene expression missing (2/8 genes). However, it will be feasible to use RNA-seq techniques to contribute to genomic medicine at single-cell level.

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“…Several studies highlight the advantage of microarray technology in pathogen detection and biodefense (for review see [13,32]), molecular diagnostics [15], single nucleotide polymorphisms (SNP) and mutation analysis [33], and cancer [34], among many others. Several of these studies point to the need of robust microarray technologies for POCD.…”

Section: Discussionmentioning

confidence: 99%

A Platform for Combined DNA and Protein Microarrays Based on Total Internal Reflection Fluorescence

Asanov¹,

Zepeda

Vaca

2012

Sensors

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We have developed a novel microarray technology based on total internal reflection fluorescence (TIRF) in combination with DNA and protein bioassays immobilized at the TIRF surface. Unlike conventional microarrays that exhibit reduced signal-to-background ratio, require several stages of incubation, rinsing and stringency control, and measure only end-point results, our TIRF microarray technology provides several orders of magnitude better signal-to-background ratio, performs analysis rapidly in one step, and measures the entire course of association and dissociation kinetics between target DNA and protein molecules and the bioassays. In many practical cases detection of only DNA or protein markers alone does not provide the necessary accuracy for diagnosing a disease or detecting a pathogen. Here we describe TIRF microarrays that detect DNA and protein markers simultaneously, which reduces the probabilities of false responses. Supersensitive and multiplexed TIRF DNA and protein microarray technology may provide a platform for accurate diagnosis or enhanced research studies. Our TIRF microarray system can be mounted on upright or inverted microscopes or interfaced directly with CCD cameras equipped with a single objective, facilitating the development of portable devices. As proof-of-concept we applied TIRF microarrays for detecting molecular markers from Bacillus anthracis, the pathogen responsible for anthrax.

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SNP and Mutation Analysis

Cited by 36 publications

References 34 publications

Evaluation of pyrosequencing for large-scale identificationof plant species (grasses as a model)

Evaluation of pyrosequencing for large-scale identificationof plant species (grasses as a model)

Feasibility of Whole RNA Sequencing from Single-Cell mRNA Amplification

A Platform for Combined DNA and Protein Microarrays Based on Total Internal Reflection Fluorescence

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