![]() An aptamer-based detection system for aflatoxin is currently marketed as AflaSense. OTA-Sense aptamer-based technology to detect ochratoxin, a mycotoxin and potential carcinogen in agricultural products, has been developed by Neoventures Biotechnology Inc. Several commercial aptamer diagnostic platforms have entered the market in recent years 7. ![]() Several aptamer candidates are currently being tested in clinical trials to treat age-related macular degeneration 4, Duchenne muscular dystrophy 5, chronic lymphocytic leukaemia 6 and other illnesses 7.Īptamer-based diagnostic assays have a great potential to become point-of-care diagnostics: they are affordable, sensitive, specific, user-friendly, robust and can be performed outside a laboratory or hospital. Most aptamers are developed for therapeutic or diagnostic purposes 2, 3. The feasibility of our approach is demonstrated by performing aptamer selection against a clear cell renal cell carcinoma (ccRCC) RCC-MF cell line using the RC-124 cell line from healthy kidney tissue for negative selection.Īptamers are short (20–100 nt) oligonucleotides that, contrary to most other functional nucleic acids, bind specific molecular targets due to their folded three-dimensional (3D) structures 1. We propose a fast and practical high-throughput aptamer identification method to be used with the cell-SELEX technique to increase the aptamer selection rate against live cells. Here, we present a differential binding cell-SELEX (systematic evolution of ligands by exponential enrichment) workflow that adapts the FASTAptamer toolbox and bioinformatics tool edgeR, which are primarily used for functional genomics, to achieve more informative metrics about the selection process. This approach does not take full advantage of HTS because the enrichment of sequences during selection can be due to inefficient negative selection when using live cells. HTS data in aptamer research are primarily used to compare sequence enrichment between subsequent selection cycles. Despite the availability and advantages of HTS compared to Sanger sequencing, there are only 50 aptamer HTS sequencing samples available on public databases. High-throughput sequencing (HTS) has revolutionized aptamer research by increasing the number of reads from a few (using Sanger sequencing) to millions (using an HTS approach). Aptamers have in recent years emerged as a viable alternative to antibodies.
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