![]() ![]() The assay was able to detect down to 88 copies/mL of HIV-1 in plasma with 95% efficiency or the equivalent of a single infected cell. Semi-nested PCR increased detection sensitivity even further. Unlike a lead competing laboratory-developed assay, all major HIV-1 subtypes, and a wide range of recombinants from a 127-member diversity panel were detected and accurately quantified in spiked plasmas. A step-up amplification approach to allow binding of primers across polymorphic regions showed improved sensitivity compared to universal cycling. Real-time RT-qPCR and qPCR were performed on plasma viral RNA and cellular lysates. Inosine and mixed nucleotide bases were included at polymorphic sites. TaqMan qPCR primers and probes were designed against the NCBI/LANL HIV-1 compendium database by analyzing sequences used in assays for sensitive cross-clade detection of HIV-1 as reported in the literature and elucidating regions of improved cross-subtype specificity. Primer efficiency is enhanced by automatically avoiding template secondary structures.An LTR-based quantitative PCR (qPCR) assay was modified and optimized for the quantification of total HIV-1 nucleic acids in plasma and PBMC. The oligos designed can be BLAST searched, to verify their specificity. Highly specific oligos are designed by avoiding regions of significant homology found by automatically interpreting BLAST search results. ![]() ![]() For a partial set of pre-designed or published set of primers, AlleleID® can design compatible primers and probes for the rest of sequences for species or taxa specific assays.ĪlleleID® employs a sophisticated algorithm to assure assay success. For taxa or cross species assays, this feature is especially useful when the group or taxa is highly dissimilar. "Minimal Set", one of the most innovative features in AlleleID®, helps design the fewest number of primers and probes that uniquely identify each of the desired species/strain/taxa from the mix, lowering assay costs. This powerful functionality can also be used for detection, identification, quantification of contaminants. For cross species assays, AlleleID® identifies conserved regions of related organisms that can be used with samples from any of the organisms. The assays are designed to detect only the strain or species of interest from the mix. To design species identification assays, AlleleID® aligns sequences using ClustalW and analyzes conserved and species specific regions to design molecular probes for microarrays and TaqMan®/molecular beacon real time PCR assays. We are proud to have organizations such as FDA, CDC, and USDA as our customers." "We are pleased with how well AlleleID® has been received by researcher all over the world. "AlleleID® can be effectively used in developing assays for biodefense, environmental monitoring, prevention/control of infectious diseases, development of surveillance tests and biodiversity studies." says Kay Brown, V.P. In addition to designing single template and multiplex experiments version 4 includes support for designing species identification and taxa discrimation assays for popular real time PCR chemistries such as SYBR® Green, TaqMan® and TaqMan® MGB (Minor Groove Binding). Junction probes span exon-exon boundaries while intra-exon probes lie entirely within a single exon, making AlleleID® an effective tool in designing experiments to test novel splice forms. To detect the alternative splicing events, AlleleID® designs two types of probes called junction probes and intra-exon probes. AlleleID® now includes support for designing probes for splice variant arrays. Palo Alto, California-September 25, 2006, PREMIER Biosoft International today announced the world wide release of version 4 of AlleleID®, the only tool available for designing diagnostic assays for both real time PCR and microarrays. The new version includes support for designing splice variant microarrays to detect gene splicing and alternative splicing events. The only tool that helps design microarrays and real time PCR diagnostic assays for pathogen detection or bacterial identification. Home > Company > News > AlleleID® 4 Release News PREMIER Biosoft International today announced the world wide release of version 4 of AlleleID® ![]()
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