Credentials of Corresponding Author
M2 - Stritch School of Medicine (Loyola University Chicago)
Name of Faculty Advisor
Dr. Gwendolyn Stovall
Problem
Aptamers are short, single-stranded nucleotide sequences that can bind to a given target molecule with high specificity, allowing for a robust range of industrial, diagnostic, clinical, and therapeutic applications. Aptamers have been the subject of more than 144,000 papers to date. However, there has been a growing concern that discrepancies in the reporting of aptamer research limit the reliability of these reagents for research and other applications.
Purpose
These observations noting inconsistencies in the use of our RNA anti-lysozyme aptamer served as an impetus for our systematic review of the reporting of aptamer sequences in the literature. Our purpose was to determine the depth and breadth of aptamer sequence infidelity throughout the literature.
Search strategy
The ten most cited aptamers were examined using a standardized methodology in order to categorize the extent to which the sequences themselves and altered sequences were adequately described in the literature. Our review of 780 aptamer publications spanned decades, multiple journals, and research groups, and revealed that 41% of the papers reported unexplained sequence alterations. We identified ten common categories of sequence alterations including deletions, substitutions, additions, among others.
Results of literature search
Our detailed examination of literature citing the RNA anti-lysozyme aptamer revealed that 93% of the 61 publications reviewed reported unexplained altered sequences with 96% of those using DNA variants. We expanded our search to analyze each of the ten most cited aptamers, where we discovered that 41% of the 780 aptamer publications we reviewed reported unexplained sequence alterations.
Synthesis of evidence
Our literature search bolsters the argument that the field of aptamer research is experiencing considerable inconsistencies in aptamer sequence reporting. Further, these widespread inconsistencies warrant the application of collaborative, evidence-based aptamer publication guidelines to improve reproducibility and consistency within the literature.
Implications for practice
Overall our findings can be used as a starting point for building better practices in author submissions and publication standards, the rigor, and reproducibility of aptamer research.
Evidence of In Silico Unexplained Aptamer Sequence Alterations Demands Collaborative Evidence-Based Aptamer Publication Guidelines