title: Large scale analysis of the mutational landscape in HT-SELEX improves aptamer discovery.
abstract: High-Throughput (HT) SELEX combines SELEX (Systematic Evolution of Ligands by EXponential Enrichment), a method for aptamer discovery, with massively parallel sequencing technologies. This emerging technology provides data for a global analysis of the selection process and for simultaneous discovery of a large number of candidates but currently lacks dedicated computational approaches for their analysis. To close this gap, we developed novel in-silico methods to analyze HT-SELEX data and utilized them to study the emergence of polymerase errors during HT-SELEX. Rather than considering these errors as a nuisance, we demonstrated their utility for guiding aptamer discovery. Our approach builds on two main advancements in aptamer analysis: AptaMut-a novel technique allowing for the identification of polymerase errors conferring an improved binding affinity relative to the 'parent' sequence and AptaCluster-an aptamer clustering algorithm which is to our best knowledge, the only currently available tool capable of efficiently clustering entire aptamer pools. We applied these methods to an HT-SELEX experiment developing aptamers against Interleukin 10 receptor alpha chain (IL-10RA) and experimentally confirmed our predictions thus validating our computational methods.
authors: National Center of Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA.
authors: Jan
authors: J
authors: Hoinka
authors: Department of Microbiology & Immunology, University of Miami Miller School of Medicine, Miami, FL 33101, USA.
authors: Alexey
authors: A
authors: Berezhnoy
authors: National Center of Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA.
authors: Phuong
authors: P
authors: Dao
authors: Laboratory of Hemostasis, Division of Hematology, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA.
authors: Zuben E
authors: ZE
authors: Sauna
authors: Department of Microbiology & Immunology, University of Miami Miller School of Medicine, Miami, FL 33101, USA.
authors: Eli
authors: E
authors: Gilboa
authors: National Center of Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA przytyck@ncbi.nlm.nih.gov.
authors: Teresa M
authors: TM
authors: Przytycka
mesh_terms: D000465:Algorithms; D052157:Aptamers, Nucleotide / Q000378:metabolism; D003198:Computer Simulation; D059014:High-Throughput Nucleotide Sequencing; D053709:Interleukin-10 Receptor alpha Subunit / Q000378:metabolism; D015233:Models, Statistical; D016296:Mutagenesis; D009154:Mutation; D052156:SELEX Aptamer Technique / Q000379:methods*; D012984:Software
chemical_list: D052157:Aptamers, Nucleotide; D053709:Interleukin-10 Receptor alpha Subunit