New Guidelines for Accurate Spike-In Normalization in DNA-Protein Interaction Studies

New criteria developed by researchers at the University of California San Diego may greatly enhance the accuracy of results obtained by scientists when assessing the interactions between proteins and DNA. Comprehending these interplays is imperative for understanding human biology in its entirety, and it can also facilitate the creation of novel therapies for an extensive array of ailments, including numerous malignancies.

Spike-in normalization is a popular molecular biology approach that helps guarantee precise and dependable results. Spike-in normalization lets researchers adjust for differences between many samples being compared to one another by introducing a known quantity of chromatin (DNA and the accompanying proteins) to a sample before it is examined.

When comparing two circumstances, such as the effects of a medicine (treated vs. untreated) or a mutation or deletion in a critical gene (normal vs. mutant), spike-in normalization is especially helpful.

By looking through publicly available datasets that use spike-in normalization, the researchers identified common scenarios where spike-in normalization is easily misused and where incorporating additional quality control measures and other “guardrails” into the technique could improve results or prevent misinterpretation.

Through a reanalysis of this data and further research, the team was able to formulate a set of nine essential guidelines for researchers utilizing spike-in normalization, which might significantly improve the precision of their findings. These precautions include following uniform quality control procedures, adhering to computational analysis best practices, and cross-checking the outcomes using alternative analysis methods.

Many studies utilize spike-in normalization, and our results call the biological conclusions drawn from this approach into question. Our recommendations can help account for some of the pitfalls of spike-in normalization so we can still reap the benefits of this valuable technique.”

Alon Goren, Ph.D., Study Senior Author, University of California San Diego

The study was published in the journal Nature Biotechnology.