Researchers at University of California San Diego have published latest guidelines that would help scientists significantly improve their results when quantifying the interactions between DNA and proteins. Understanding these interactions is critical to our understanding of human biology basically, and can even help scientists develop latest treatments for a big selection of diseases, including many cancers.
The researchers focused on spike-in normalization, a widely-used molecular biology technique that helps ensure accurate and reliable results. Spike-in normalization involves adding a known quantity of chromatin (DNA and the associated proteins) to a sample before it’s studied, which helps researchers account for variations between multiple samples being in comparison with each other. Spike-in normalization is especially useful for comparing two conditions — equivalent to to guage the impact of a drug (comparing treated vs untreated) or a mutation or a deletion in a key gene (comparing normal vs mutant).
By exploring publicly-available datasets that utilize spike-in normalization, the researchers were capable of discover common scenarios where spike-in normalization is well misused and during which constructing in additional quality control measures and other “guardrails” into the technique could improve results or avoid misinterpretation. By reanalyzing these data and conducting additional experiments of their very own, the team was capable of develop a listing of nine key recommendations for researchers using spike-in normalization that would greatly increase the accuracy of their results. These measures include ensuring consistent quality control steps are taken, following best practices for computational evaluation, and validating the outcomes with other evaluation techniques.
“Many studies utilize spike-in normalization, and our results call the biological conclusions drawn from this approach into query,” said senior writer Alon Goren, Ph.D. “Our recommendations may help account for a few of the pitfalls of spike-in normalization so we are able to still reap the advantages of this useful technique.”
The study published on September 13, 2024 in Nature Biotechnology and was conducted by Lauren Patel and Yuwei Cao at UC San Diego and Eric Mendenhall, Ph.D. at HudsonAlpha Institute for Biotechnology. The study was co-led by Alon Goren, Ph.D., and Christopher Benner, Ph.D., each associate professors within the Department of Medicine at UC San Diego School of Medicine.
