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SNP-RFLPing 2: an updated and integrated PCR-RFLP tool for SNP genotyping.

Filed under Core facilities, Diagnostics by on October 2, 2010 at 11:03 pm no comments
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SNP-RFLPing 2: an updated and integrated PCR-RFLP tool for SNP genotyping. BACKGROUND: PCR-restriction fragment length polymorphism (RFLP) assay is a cost-effective method for SNP genotyping and mutation detection, but the manual mining for restriction enzyme sites is challenging and cumbersome. Three years after we constructed SNP-RFLPing, a freely accessible database and analysis tool for restriction enzyme mining of SNPs, significant improvements over the 2006 version have been made and incorporated into the latest version, SNP-RFLPing 2. RESULTS: The primary aim of SNP-RFLPing 2 is to provide comprehensive PCR-RFLP information with multiple functionality about SNPs, such as SNP retrieval to multiple species, different polymorphism types (bi-allelic, tri-allelic, tetra-allelic or indels), gene-centric searching, HapMap tagSNPs, gene ontology-based searching, miRNAs, and SNP500Cancer. The RFLP restriction enzymes and the corresponding PCR primers for the natural and mutagenic types of each SNP are simultaneously analyzed. All the RFLP restriction enzyme prices are also provided to aid selection. Furthermore, the previously encountered updating problems for most SNP related databases are resolved by an on-line retrieval system. 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. PMID: 20377871 [PubMed - in process]
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Biofortuna to Use TriLink’s CleanAmp dNTPs in PCR Kits

Filed under Industry news by on September 15, 2010 at 10:36 am no comments

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – TriLink Biotechnologies today announced a licensing agreement for use of its CleanAmpl dNTPs with Biofortuna’s freeze dried in vitro diagnostic PCR kits.

Terms of the deal were not disclosed.

In a statement, TriLink said that Biofortuna is developing unique HLA diagnostic kits that will address the transplantation, blood grouping, disease identification, and pharmacogenetic markets. The first product line will target the sequence-specific primer transplantation market.

Based in the UK, Biofortuna is an HLA molecular diagnostics firm.

The CleanAmp technology offers a “unique approach” to Hot Start activation in PCR by chemically modifying the essential DNA polymerase substrate, the dNTPs, Natasha Paul, TriLink scientific investigator, said in a statement. She added that CleanAmp dNTP can be used with different DNA polymerases and assay formats.

Biofortuna said that by using CleanAmp dNTPs as an alternative to standard dNTPs, it was able to improve the specificity of its genotyping assays. Mike Bunce, CEO of Biofortuna, added that the CleanAmp technology “allows us to create accurate, reproducible, and simple diagnostic kits, that greatly improve the quality of clinical testing and patient care.”

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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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Temperature Switch PCR (TSP): Robust assay design for reliable amplification and genotyping of SNPs

Filed under Diagnostics, Genotyping by on December 2, 2009 at 8:00 pm no comments
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Conclusion: Theoretically, TSP can be directly incorporated into the design of assays for most current single-marker SNP genotyping methods. TSP provides several technological advances for single-marker SNP genotyping including simplified assay design and development, increased assay specificity and genotyping accuracy, and opportunities for assay automation. By reducing the requirement for operator expertise, TSP provides opportunities to deploy a wider range of single-marker SNP genotyping methods in the laboratory. TSP has broad applications and can be deployed in any animal and plant species. (Source: BMC Genomics - Latest articles)
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