Mike here.
We got a great question submitted at www.thermofisher.com/ask so I asked Gina, in Technical Support here at Thermo Fisher Scientific to help us out with an answer.
“Some of your pre-designed Taqman gene expression assays offer species specific options. e.g. human specific with no cross-reactivity with mouse. Could you explain why some Taqman gene expression assay probes are made to span exon boundaries and yet it will detects genomic DNA?”
Our TaqMan Gene Expression Assays are designed to detect within the target species, but for some assays, there may be sequence homology such that the assay will also detect in other species. To check for this, you can use the Transgeneic Cross Reactivity Check Filter on the website. Here’s an example using NFKBIA:
There are 4 human assays to this target. If this assay was going to be used in a transgenic mouse, we would check the box for mouse (Mus musculus). Any assays that would cross react with mouse NFKBIA will be removed. Only assays that will not detect in mouse will remain.
After checking the box for mouse, we find that there are no assays left. So none of the current predesigned assays would be appropriate for use in a transgenic mouse experiment, since they will cross react to some extent.
So is there any way to get an assay that will detect human NFKBIA, but not cross react with mouse? Yes there is. The answer is to use our Custom Assay Design Tool.
In the design preferences, simply select the species that you do not want to be detected by the assay. The new assay that is created will now include this criteria in the design process.
Hope this helps! – Gina
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Who did the development of all these “Assay on Demand” technology in 1999 TaqMan ? Chris Heid and Andy Blidy let’s talk
polymerase chain reaction/ribonucleic acid
Introduction
Blood provides physicians and scientists with a relatively
safe and easily obtained source of human tissue to investigate cellular functions and the circulating level of important
proteins and other molecules in health and disease. A
characteristic set of cellular and molecular changes can be
studied in blood, providing an indication of the extent and
severity of physiological compromise (Dhabhar & McEwen,
2001). In recent studies of medical and health interventions, including exercise (Berk et al., 1990) and the eustress
of humor associated mirthful laughter, (Berk et al., 1989,
2001) various patterns of changes in circulating stress
mediators, inflammatory mediators, cytokines, and cellular
immune functions were documented from peripheral blood
samples. We now are actively engaged in identifying
characteristic messenger RNA (mRNA) expression in
specific circulating leukocytes and levels of plasma proteins
that accompany specific disease states. A widely used and
increasingly important technique to examine patient
responsiveness to pharmacological and medical interventions, is to measure gene expression of circulating leukocytes in whole blood. Gene expression assays also may be
used to evaluate disease progression or to provide diagnostic
assessments (Suchy et al., 2000; Eriksson et al., 2001;
Kreuzer et al., 2001; Schneider et al., 2001; Van Trappen
et al., 2001). Purification processes for total RNA from
blood, or more selectively for mRNA, may vary from
laboratory to laboratory. Storage times and temperatures
often vary significantly because of differences in collection,
transport, and processing of human whole blood. Accurate
Accepted for publication 12 June 2002
Correspondence: Michael A. Tanner, Applied Biosystems Mail Stop
407, 850 Lincoln Centre Drive, Foster City, CA 94404, USA. Tel:
+1 650 638 6838, Fax: +1 650 638 6838,
E-mail: tannerma@ appliedbiosystems.com
Clin. Lab. Haem.
2
Chris Heid did all the marketing for PDARS , Assay on Demand and Assays by design for mRNA TaqMan for 7700 system…..I lead a team to develop these product line ……the rest is history……
In early Tanner , Blidy paper is CD152 gene expression along with the immune profile of blood at the time ……fast forward and you will recognize CTLA-4 (CD152) was first assay as PDAR that Jim Allison won a Nobel Prize for in 2018 of immunotherapy
Applied Biosystems, Foster City, Ca. 1997 to 2003
Sr. Scientist Development SDS Real Time PCR: Technical Managed two major company mRNA projects Assay on Demand and Assay by Design. This included business and manufacturing infrastructure from the start of the project to launch. Project Lead for Gene Expression and Single Nucleotide Polymorphism (SNP) for Assay on Demand (AoD)and Assay by Design (ABD) product lines for TaqMan PCR from Human Genome. Order entry to Service: Sequence detection systems validation and verification of assays and systems. Developed and wrote QC Specifications, Manufacture Specifications, Bill of Materials, Standard Operating Procedure in a development/ manufacturing environment. Developed process and perform technology transfer and product launch for FDA and IVD approved products. Write documentation for performance vs. design test . Test systems instruments reagents and software. Managed formulating, packaging, distribution and QC of the PDAR, AoD and ABD product line in manufacturing environment.
• Development of 26,000 new gene expression for human assays products and greater than 150,000 SNP assay reagents that support 5700, 7700,7000,7300, 7500 and 7900 Sequence Detection Systems. Generates $100s mm revenue per year, with high customer satisfaction.
• Team leader on and developed 96 micro card and 384 Micro card mini arrays systems for use on the 7900. Assisted on problem solving for the thermal cycler blocks for the 7900 for microcard, Nano technology. Developed test method for dynamic range with artificial templates for Micro arrays. Use of automation process robots such as Hydra 96 well fluid plate delivery, Used Packard and Coulter Fx for 96, 384 and 1536 well plate delivery. Launched first 384 micro card that generates $10s mm revenue per year, with high customer satisfaction.
• mRNA Pre-developed TaqMan Assay Reagents gene expression (PDAR) over 600 assays in human, mouse and rat release products. Runs on instruments that support 5700, 7700,7000, and 7900 Sequence Detection Systems. Generates $10s mm revenue per year, with high customer. satisfaction. Developed test method TFG-beta assays standard for 7000 instrument
• Mechanical trouble shooting for 7200 plate reader, including an install kit.
• Research and developed mRNA purification and gene expression, SNP in human whole blood and tissues. Developed nine P450 SNP assays in 1999, first SNP on the market.
• Worked on several R&D Intellectual Property project with Invention Disclosures leading to patents.
Ask immunologic questions give molecular answers
Applied Biosystems, Foster City, Ca. 1997 to 2003
Sr. Scientist Development SDS Real Time PCR: Technical Managed two major mRNA company projects Assay on Demand and Assay by Design. This included business and manufacturing infrastructure from the start of the project to launch. Project Lead for Gene Expression and Single Nucleotide Polymorphism (SNP) for Assay on Demand (AoD)and Assay by Design (ABD) product lines for Taqman PCR from Human Genome. Order entry to Service: Sequence detection systems validation and verification of assays and systems. Developed and wrote QC Specifications, Manufacture Specifications, Bill of Materials, Standard Operating Procedure in a development/ manufacturing environment. Developed process and perform technology transfer and product launch for FDA and IVD approved products. Write documentation for performance vs. design test . Test systems instruments reagents and software. Managed formulating, packaging, distribution and QC of the PDAR, AoD and ABD product line in manufacturing environment.
• Development of 26,000 new gene expression for human assays products and greater than 150,000 SNP assay reagents that support 5700, 7700,7000,7300, 7500 and 7900 Sequence Detection Systems. Generates $10s mm revenue per year, with high customer satisfaction.
• Team leader on and developed 96 micro card and 384 Micro card mini arrays systems for use on the 7900. Assisted on problem solving for the thermal cycler blocks for the 7900 for microcard, Nano technology. Developed test method for dynamic range with artificial templates for Micro arrays. Use of automation process robots such as Hydra 96 well fluid plate delivery, Used Packard and Coulter Fx for 96, 384 and 1536 well plate delivery. Launched first 384 micro card that generates $100s mm revenue per year, with high customer satisfaction.
• Pre-developed TaqMan Assay Reagents gene expression (PDAR) over 600 assays in human, mouse and rat release products. Runs on instruments that support 5700, 7700,7000, and 7900 Sequence Detection Systems. Generates $100s mm revenue per year, with high customer. satisfaction. Developed test method TFG-beta assays standard for 7000 instrument
• Mechanical trouble shooting for 7200 plate reader, including an install kit.
• Research and developed mRNA purification and gene expression, SNP in human whole blood and tissues. Developed nine P450 SNP assays in 1999, first SNP on the market.
• Worked on several R&D Intellectual Property project with Invention Disclosures leading to patents.
Ask immunologic questions give molecular answers