The Aptamarker Platform
The Aptamarker Platform applies the same 268 million aptamer sequences to a wide range of samples, including biological fluids, cells, and tissue sections on slides. This unified approach enables researchers to identify variations in protein abundance across different phenotypes with a single Next-Generation Sequencing (NGS) analysis that captures all aptamer-target complexes.
Moreover, the Aptamarker Platform matches—and often exceeds—the capabilities of other next-generation proteomics technologies. Its depth allows multiple Aptamarkers to bind to the same protein, making direct epitope mapping possible. As a result, researchers can characterize epitopes and go beyond canonical reference proteins to analyze the actual protein forms found in vivo during disease states. This includes detecting complexes, isoforms, cleavage events, post-translational modifications, and conformational foldings.
Currently, we are developing a comprehensive knowledge base to identify all proteins in the human proteome. This goal will be achievable using a single Aptamarker library and one NGS analysis per sample.
The Technology
Aptamers are single stranded oligonucleotides that mimic antibodies in their ability to bind to target molecules. Up until now, aptamer selection has been based on SELEX, a method that implicitly requires the use of different sequences for each selection and requires immobilization of the target in order to facilitate separation of bound and unbound sequences. We have made the following proprietary innovations to enable the Aptamarker approach.
FRELEX Selection
The FRELEX selection allows the partitioning of bound Aptamers from unbound ones. This enables selection of Aptamarkers without the need to immobilize the target.
Protein information is a sample (abundance and characteristics) translates to DNA barcoding.
NEOMER Library
We have designed a novel NEOMER library where the random sequences are interspersed with fixed sequences.
The library becomes reproducible where the same 268M probes are applied to each sample.
Structure Analysis
We have predicted the structures of all 268M sequences.
Differences in the frequencies of structures equates to differences in protein abundance in any sample.
Omics Integration
Discrete networks of related structures are defined. Each network represents a different epitope on the target protein.
Differences in protein abundance can be characterized with volcano plots, Cytoscape relationships and integration with other omics platforms.
Validation of the Aptamarker Platform
With financial support from the Alzheimer’s Drug Discovery Foundation (ADDF) and access to samples from the AIBL cohort, we conducted a validation study of the Aptamarker Platform for predicting brain amyloid deposition in individuals who were either cognitively normal or exhibited mild cognitive impairment. To build the predictive model, we applied machine learning to the Aptamarker structure frequencies within a well-defined training set of samples. In addition, we integrated relevant clinical variables to enhance model performance. As a result, the most effective model from this training phase included eight distinct Aptamarkers and one clinical factor, age.
When tested on an independent sample set, this model achieved a predictive accuracy of 82%. Following this success, we extended the validation by conducting a blind trial in Portugal at the Centro Hospitalar de Entre Douro e Vouga (CHEDV), with financial support from Roche Diagnostics. In this subsequent trial, the gold standard for comparison shifted from PET scans to cerebrospinal fluid biomarkers. Nevertheless, the Aptamarker Platform still demonstrated strong performance, maintaining an overall accuracy of 75%.
Commercial Application: qPCR Test
Results from the Aptamarker library can be translated to simple qPCR assays based on single or pools of subsets of Aptamarkers through the use of the same FRELEX platform.
Get Commercial Access
NeoVentures Biotechnology Europe provides partners with commercial access of Aptamarkers for their targets for diagnostic applications.