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Next Generation Sequencing

Filed under Bioinformatics, Core facilities by on September 20, 2010 at 9:43 am no comments
Image of a DNA chain which shows the double he...
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The impact of DNA sequencing has touched most research laboratories across the world, either as part of historical landmarks such as the human genome project or simply through the use of what have become routine sequence analysis procedures. As a consequence, many successful efforts have been put in place to both improve the quality and decrease the cost of traditional DNA sequencing. Recently, some radically different approaches have been developed and introduced to the market
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Application of High-Resolution Melting to Large-Scale, High-Throughput SNP Genotyping: A Comparison with the TaqMan(R) Method

Filed under Bioinformatics, Core facilities by on July 15, 2010 at 7:57 pm no comments
(1) In intact probes, reporter fluorescence is...
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Because of the wide use of single-nucleotide polymorphisms (SNPs) as markers of genetic variation, several high-throughput genotyping methods have been developed and applied during the past decades. High-resolution melting (HRM) is a very attractive, advanced, fast, and cost-effective SNP genotyping technology based on the analysis of the melting profile of PCR products, using intercalating fluorescent dyes to monitor the transition from unmelted to melted DNA. The authors used HRM for genotyping 215 human DNA samples for SNPs in the ABCB1, NQO1, and SLC19A1 genes and 96 samples for SNPs in the IL1A and IL12B genes with the aim of assessing HRM sensitivity and accuracy in comparisons with the TaqMan® assay in view of large-scale, high-throughput SNP-typing applications.
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Protocol: a simple gel-free method for SNP genotyping using allele-specific primers in rice and other plant species

Filed under Bioinformatics, Cancer by on April 20, 2010 at 7:00 pm no comments
The original MRC Laboratory of Molecular Biolo...
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Conclusion: Our ASP methodology allows characterization of SNPs genotypes without electrophoresis, expensive probes or specialized equipment, and is highly versatile due to the flexibility in the design of primers. The method could be established easily in any molecular biology laboratory, and is applicable to diverse organisms. (Source: Plant Methods)
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SNP-RFLPing 2: an updated and integrated PCR-RFLP tool for SNP genotyping

Filed under Bioinformatics, Core facilities by on April 7, 2010 at 7:00 pm no comments
RFLP variation by VNTR loss.
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Conclusions: The user interfaces for functional SNP analyses have been substantially improved and integrated. SNP-RFLPing 2 offers a new and user-friendly interface for RFLP genotyping that can be used in association studies and is freely available at http://bio.kuas.edu.tw/snp-rflping2. (Source: BMC Bioinformatics - Latest articles)
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