UC San Diego Researchers Continue to Make Strides in Research Reproducibility

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Anita Bandrowski of the Neuroscience Information Framework is seen here participating in a group discussion about the 3D Virtual Cell project. Bandrowski and her colleagues have developed systems and standards to help researchers select and document biological reagents such as antibodies to better ensure that research can be replicated.

A University of California San Diego-led effort to improve biomedical research reproducibility continues to gain traction, with experts at the recent Global Biological Standards Institute (GBSI) workshop agreeing to adopt a scoring system based in part on the UC San Diego researchers’ recommendations. The system will help researchers choose reliable antibodies for their experiments and better ensure that research can be replicated.

Antibodies are large proteins that are akin to police search dogs – they bind to specific biomolecules, helping researchers track and identify those molecules. But when researchers are not specific about the types of antibodies they use in research methodologies, reagents used in subsequent studies can detect the wrong target and lead to false findings, wasted resources and scientific controversy. A scoring system would provide a way to validate an antibody’s performance for different kinds of experiments (since not all experiments use antibodies in the same way) and improve researchers’ confidence that a particular antibody will work as expected.

Suggestions for how to develop such a scoring system were published by UC San Diego neuroscientist Anita Bandrowski and her colleagues prior to the GBSI workshop in the journal Nature Methods. The GBSI organizers aim to spend the next six months drawing on these suggestions for each of the major kinds of experiments that rely on antibodies.

The agreement comes on the heels of announcements by Cell Press and Thermo Fisher Scientific that they will also adopt new labeling and identification standards promoted by Bandrowski and her colleagues at the Center for Research in the Biological Science (CRBS), which is based at the UC San Diego Qualcomm Institute. Cell Press announced in August that it has redesigned the methodology section in its leading biomedical journal, Cell, to include Structured, Transparent, Accessible Reporting (STAR) Methods. The STAR Methods are designed to label biological reagents (such as specific cell lines, antibodies, chemical agents or types of mice) in a way that makes scientific information flow easier for the author to describe and easier for the reader to replicate. The new methods are designed to align with new reporting guidelines from the National Institutes for Health’s Rigor and Reproducibility Initiative, as well as recommended guidelines from the Resource Identification Initiative, which Bandrowski oversees.

Dorota Skowronska-Krawczyk, an associate project science with the UC San Diego School of Medicine, was one of the first researchers to have a paper published in Cell during the pilot phase of the STAR roll-out.

“These new standards reflect the general need – especially in the Health Sciences – for reproducible data and transparency of the process,” she said. “New standards imposed by publishers are very important, as they may -- and should-- become just the ‘standard’ procedure in data recording and publishing. I think that the new way of sharing important information about research, once adapted by scientists will not only help to optimally use the limited resources but also will become one of the pillars of faster progress.”

Thermo Fisher Scientific – a San Diego-based multinational biotech company – has also announced it will adopt newly proposed methods (originally proposed by Bandrowski and colleagues in Nature Methods for specifying the antibodies it uses in research.

“Labeling and identification standards of research materials promotes transparency and reproducibility of important scientific research,” said Matt Baker, Director of R&D and Business Development, RUO Antibodies at Thermo Fisher Scientific.  “We believe the goal of Research Identification Initiative is one very important part of what the International Working Group on Antibody Validation is striving to accomplish – standardized guidelines for antibody specificity, functionality and reproducibility.”