Our Frequently Asked Questions
Our Frequently Asked Questions
Our Frequently Asked Questions
What is the Aptamarker platform?
The Aptamarker platform is a top-down approach to next-generation high- plex proteomics. We convert protein abundance information to DNA abundance in a manner analogous to what Olink and SomaLogic have developed, but with several improvements based on the following innovations:
- FRELEX binding assays: We use an antisense immobilized on resin to act as a competitor for aptamer binding rather than to the target. This enables the detection of aptamer binding to proteins without a need to immobilize them, thus retaining capacity for detecting protein complexes and folding patterns.
- Neomer library: We have reinvented aptamer development by reducing the number of random nucleotides while increasing the structural diversity of the library. We currently apply a library of the same 16.8 million aptamers (Aptamarkers) to each sample.
- The Aptamarker concept: To discover non-canonical biomarkers we focus on discovering Aptamarkers that bind to such targets without a need to know the identity of the target. We then have the capacity to identify the target once we have determined it is of diagnostic value.
How is this different from other biomarker discovery technologies?
Other biomarker discovery technologies are bottom-up approaches. Both companies have expended tremendous effort identifying probes (antibodies or aptamers) that bind to the canonical form of specific proteins, one protein at a time. Our approach is more powerful and simpler because we apply a library of 16.8 million Aptamarkers to every sample. These Aptamarkers bind to both canonical proteins and non-canonical forms of these proteins including post-translational modifications, cleavage events, folding, and complexes. Pathophysiologies often arise from non-canonical forms of proteins (proteins breaking bad…). Our platform has the capacity to identify these directly.
Why this is different from other omics approaches?
Traditional proteomics is based on direct measurement of the proteins. By translating protein information into DNA information, it is possible to employ the power of next generation sequencing and qPCR analysis for rapid and simple quantification. Transcriptomics is closer to our platform than traditional proteomics, but transcriptomics is limited to information at the RNA level. This does not include important variables such as translation rates and protein half-life.
Is it possible to commercialize Aptamarkers?
Yes, unlike other platforms we are prepared to release sequences to collaborators in projects for direct commercial development of diagnostic test kits.
How do you translate the platform to a commercial diagnostic kit?
In the Aptamarker process we validate information gained from next generation sequencing through qPCR analysis. Thus, qPCR applications are implicit in the discovery of the Aptamarkers. It is a simple matter to translate this to a commercially feasible, regulatory approved diagnostic application.
Is this a high throughput?
The technology can be readily developed for high throughput liquid handling. Our process does not require specialized equipment, all that is needed is the capacity to spin samples and Aptamarkers down, and PCR amplify the supernatant to prepare for NGS analysis.
What volume of sample do you need for a discovery assay?
We routinely use 10 to 15 uL of plasma per sample.
Do you know what the Aptamarkers bind to?
Currently we have not characterized our libraries in terms of what they bind to, but we are initiating projects that will change this. We intend to have the binding patterns of thousands of proteins completed by the end of 2024.
What do you mean by agnostic discovery?
The basis of an Aptamarker experiment is the application of the Aptamarker library to samples that differ phenotypically (a contrast). We do not need to have any pre-conceived hypothesis as to why the samples might differ on a molecular level, we let the Aptamarker data inform us.
Does this platform use animals ?
At no point in this process are animals involved, unless the samples under study are derived from them. Aptamarkers are chemically synthesized.
What is the Aptamarker platform?
The Aptamarker platform is a top-down approach to next-generation high- plex proteomics. We convert protein abundance information to DNA abundance in a manner analogous to what Olink and SomaLogic have developed, but with several improvements based on the following innovations:
- FRELEX binding assays: We use an antisense immobilized on resin to act as a competitor for aptamer binding rather than to the target. This enables the detection of aptamer binding to proteins without a need to immobilize them, thus retaining capacity for detecting protein complexes and folding patterns.
- Neomer library: We have reinvented aptamer development by reducing the number of random nucleotides while increasing the structural diversity of the library. We currently apply a library of the same 16.8 million aptamers (Aptamarkers) to each sample.
- The Aptamarker concept: To discover non-canonical biomarkers we focus on discovering Aptamarkers that bind to such targets without a need to know the identity of the target. We then have the capacity to identify the target once we have determined it is of diagnostic value.
How is this different from other biomarker discovery technologies?
Other biomarker discovery technologies are bottom-up approaches. Both companies have expended tremendous effort identifying probes (antibodies or aptamers) that bind to the canonical form of specific proteins, one protein at a time. Our approach is more powerful and simpler because we apply a library of 16.8 million Aptamarkers to every sample. These Aptamarkers bind to both canonical proteins and non-canonical forms of these proteins including post-translational modifications, cleavage events, folding, and complexes. Pathophysiologies often arise from non-canonical forms of proteins (proteins breaking bad…). Our platform has the capacity to identify these directly.
Why this is different from other omics approaches?
Traditional proteomics is based on direct measurement of the proteins. By translating protein information into DNA information, it is possible to employ the power of next generation sequencing and qPCR analysis for rapid and simple quantification. Transcriptomics is closer to our platform than traditional proteomics, but transcriptomics is limited to information at the RNA level. This does not include important variables such as translation rates and protein half-life.
Is it possible to commercialize Aptamarkers?
Yes, unlike other platforms we are prepared to release sequences to collaborators in projects for direct commercial development of diagnostic test kits.
How do you translate the platform to a commercial diagnostic kit?
In the Aptamarker process we validate information gained from next generation sequencing through qPCR analysis. Thus, qPCR applications are implicit in the discovery of the Aptamarkers. It is a simple matter to translate this to a commercially feasible, regulatory approved diagnostic application.
Is this a high throughput?
The technology can be readily developed for high throughput liquid handling. Our process does not require specialized equipment, all that is needed is the capacity to spin samples and Aptamarkers down, and PCR amplify the supernatant to prepare for NGS analysis.
What volume of sample do you need for a discovery assay?
We routinely use 10 to 15 uL of plasma per sample.
Do you know what the Aptamarkers bind to?
Currently we have not characterized our libraries in terms of what they bind to, but we are initiating projects that will change this. We intend to have the binding patterns of thousands of proteins completed by the end of 2024.
What do you mean by agnostic discovery?
The basis of an Aptamarker experiment is the application of the Aptamarker library to samples that differ phenotypically (a contrast). We do not need to have any pre-conceived hypothesis as to why the samples might differ on a molecular level, we let the Aptamarker data inform us.
Does this platform use animals ?
At no point in this process are animals involved, unless the samples under study are derived from them. Aptamarkers are chemically synthesized.
What is the Aptamarker platform?
The Aptamarker platform is a top-down approach to next-generation high- plex proteomics. We convert protein abundance information to DNA abundance in a manner analogous to what Olink and SomaLogic have developed, but with several improvements based on the following innovations:
- FRELEX binding assays: We use an antisense immobilized on resin to act as a competitor for aptamer binding rather than to the target. This enables the detection of aptamer binding to proteins without a need to immobilize them, thus retaining capacity for detecting protein complexes and folding patterns.
- Neomer library: We have reinvented aptamer development by reducing the number of random nucleotides while increasing the structural diversity of the library. We currently apply a library of the same 16.8 million aptamers (Aptamarkers) to each sample.
- The Aptamarker concept: To discover non-canonical biomarkers we focus on discovering Aptamarkers that bind to such targets without a need to know the identity of the target. We then have the capacity to identify the target once we have determined it is of diagnostic value.
How is this different from other biomarker discovery technologies?
Other biomarker discovery technologies are bottom-up approaches. Both companies have expended tremendous effort identifying probes (antibodies or aptamers) that bind to the canonical form of specific proteins, one protein at a time. Our approach is more powerful and simpler because we apply a library of 16.8 million Aptamarkers to every sample. These Aptamarkers bind to both canonical proteins and non-canonical forms of these proteins including post-translational modifications, cleavage events, folding, and complexes. Pathophysiologies often arise from non-canonical forms of proteins (proteins breaking bad…). Our platform has the capacity to identify these directly.
Why this is different from other omics approaches?
Traditional proteomics is based on direct measurement of the proteins. By translating protein information into DNA information, it is possible to employ the power of next generation sequencing and qPCR analysis for rapid and simple quantification. Transcriptomics is closer to our platform than traditional proteomics, but transcriptomics is limited to information at the RNA level. This does not include important variables such as translation rates and protein half-life.
Is it possible to commercialize Aptamarkers?
Yes, unlike other platforms we are prepared to release sequences to collaborators in projects for direct commercial development of diagnostic test kits.
How do you translate the platform to a commercial diagnostic kit?
In the Aptamarker process we validate information gained from next generation sequencing through qPCR analysis. Thus, qPCR applications are implicit in the discovery of the Aptamarkers. It is a simple matter to translate this to a commercially feasible, regulatory approved diagnostic application.
Is this a high throughput?
The technology can be readily developed for high throughput liquid handling. Our process does not require specialized equipment, all that is needed is the capacity to spin samples and Aptamarkers down, and PCR amplify the supernatant to prepare for NGS analysis.
What volume of sample do you need for a discovery assay?
We routinely use 10 to 15 uL of plasma per sample.
Do you know what the Aptamarkers bind to?
Currently we have not characterized our libraries in terms of what they bind to, but we are initiating projects that will change this. We intend to have the binding patterns of thousands of proteins completed by the end of 2024.
What do you mean by agnostic discovery?
The basis of an Aptamarker experiment is the application of the Aptamarker library to samples that differ phenotypically (a contrast). We do not need to have any pre-conceived hypothesis as to why the samples might differ on a molecular level, we let the Aptamarker data inform us.
Does this platform use animals ?
At no point in this process are animals involved, unless the samples under study are derived from them. Aptamarkers are chemically synthesized.