Collaborating to bring journal clubs to PubMed Commons: A librarian’s perspective

Journal clubs can be a great tool in graduate and medical education. They provide opportunities for students to practice important skills: literature searching, critical reading, scholarly debate, and in some cases, even writing. But are there ways to enrich the journal club experience? How can journal clubs become contributors to broader discourse? These questions intersect with traditional and evolving roles of librarians in higher education. Julie Hartwell shares how a collaboration with faculty on PubMed Commons got started and its initial impact.

Before joining the Miller Nichols Library at the University of Missouri-Kansas City, Hartwell was in the A.R. Dykes Library at the University of Kansas Medical Center. When the PubMed Commons Journal Clubs pilot launched, Hartwell and her library colleagues were enthusiastic about bringing local journal club discussions to PubMed. So she talked to the School of Nursing faculty about PubMed Commons Journal Clubs. Clinical Assistant Professor Chito Belchez shared her excitement about the idea.

Complementary missions

Evidence-based practice research is a core element of the Baccalaureate of Science in Nursing (BSN) program at the University of Kansas. Belchez was leading a course called “Nursing in an Evolving Healthcare System.” For this and related courses, the journal club format offers flexibility to cover current developments in nursing practice. It also helps students develop the skills needed for critical literature review.

Univ of Kansas Nursing-img

“They have to go through PubMed. They have to go through CINAHL [Cumulative Index to Nursing and Allied Health]. They have to go through all those databases to find an article outside their required readings to review,” Hartwell describes. Students do their individual work outside class. In class, groups read and review the paper they’ve selected. Next, reviews go into Blackboard, an online learning management system (LMS). “They’ve been posting to discussion boards – creating a new thread, posting a review, and commenting on each others’ work.”

“Librarians have been trying to bring in this [Association of College and Research Libraries (ACRL)] standard of ‘Scholarship as Conversation,’” Hartwell shares. The ACRL framework recognizes that research is not a one-and-done event. It casts scholarly discourse as an ongoing process, taking place in many venues.  It suggests that, although systems may favor experts’ voices, “novice learners” can contribute in meaningful ways.

But there are barriers to dissemination, even with online systems. Hartwell notes, “It’s not brick and mortar so much as the walls of an LMS. You have all these great ideas… but they’re hiding in the LMS where only your classmates can see them.” It’s one reason she was excited about the prospect of PubMed Commons Journal Clubs. It was a chance to expand the journal club’s reach and to promote the principles of Scholarship as Conversation.

Building on frameworks

The University of Kansas School of Nursing Journal Club joined PubMed Commons in March 2015. As of June 2017, they’ve posted 23 comments.

Not every review written for the course makes it into PubMed Commons. “The students are given a rubric that’s based kind of on the PRISMA [reporting] guidelines – what do you need to do to review an article,” Hartwell explains. Although it was already in use, faculty began to think more about the rubric. They wanted to have clear guidelines for deciding which comments would appear in PubMed.


Hartwell talks about the journal club at the 2015 Annual Meeting of the Medical Library Association

Along the way, Hartwell assisted with structure and support. She facilitated the PubMed Commons joining process. She was also able to get an inside look at what was being taught. “I was able to work with instructors on that rubric to make sure they were using the right terminology and providing students with the right resources,” she notes. She was also able to see how students search for and select articles.

The addition of PubMed Commons posts seems to have provided a new incentive for students. They started following the rubric more closely. Faculty saw search strategies and writing improve. Hartwell comments, “The faculty will tell you that it’s created a healthy kind of competition. ‘We’ve got to do a really good review to get in PubMed.’” (You can read their comments here. They have a strong interest in nursing leadership and shared governance. They’ve also covered publications about workplace environment, quality improvement measures, and the impact of transnational migration on nursing workforces.)

There are some unique advantages to librarians teaming up with journal club instructors. Hartwell shares, “What I found interesting was to… see what articles they’re reviewing and how faculty communicate library resources to their students.” Collaborations like this give librarians the chance to see what’s being put into practice. And that means they can point faculty and students to up-to-date or alternate resources and provide tips for using databases like PubMed.

PubMed Commons also affords an opportunity to archive discussions and present them to a broader audience. “Without PubMed Commons, these good reviews and challenging questions would be lost in LMS. No one would ever see them again,” Hartwell says. “Share. Don’t leave these awesome enriching discussions hidden or, for face-to-face journal clubs, just lost. Preserve them.”


Want to share and preserve your journal club’s reviews on PubMed Commons? Learn more here.

Critiquing systematic review search strategies on PubMed

More than 1.1 million publications were indexed in PubMed in 2016, bringing the total number of PubMed records to more than 27 million. It’s no wonder that systematic reviews have become popular (currently there are more than 40,000 systematic reviews in PubMed Health alone). Systematic reviews and related methods aim to pull together all relevant studies on a defined topic and synthesize the evidence to evaluate what’s known. The approach has been used to inform clinical research and practice for decades, and its use is spreading.

As with any research, systematic reviews are only as good as their methods. A critical method here is literature searching. Some librarians and information specialists have taken to PubMed Commons to tackle issues surrounding the quality and efficacy of search strategies and their reporting. They also hope to raise awareness of librarians’ expertise in this area. We interviewed 5 librarians to learn more about their perspectives and how they’re using PubMed Commons.


Designing and reporting for reproducibility

Melissa Rethlefsen2

Melissa Rethlefsen

Melissa Rethlefsen is deputy director of the Eccles Health Sciences Library at University of Utah and section director of the Systematic Review Core, which is integrated with the Center for Clinical and Translational Science. She has been investigating the quality of reported systematic review search strategies. She and colleagues at Mayo Clinic found that systematic reviews that included librarians as co-authors were more likely to meet standards such as those recommended by the Institute of Medicine. “It really does benefit you to have an information specialist or librarian on your team,” Rethlefsen says.

“Just like any other type of research, your method should be described clearly enough that it can be reproduced. We see so many systematic reviews that are published without this really critical information, and then it’s really hard to assess their quality,” Rethlefsen notes.

A number of journals have endorsed the use of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Michelle Fiander, a systematic review librarian at the University of Utah, says, “PRISMA tells you what to say, what to report, the types of information that should be there. But they don’t tell you how.”

Mary Klem, a research and instruction librarian in the Health Sciences Library System at the University of Pittsburgh, has noticed the disconnect between statements concerning PRISMA and actual implementation. “In the article I commented on, the authors’ primary rationale for completing their review was that a prior review on the topic had not used a systematic or well-defined search strategy,” she shares. “I thought it was awesome that someone had critiqued a review like that! So I was disappointed to see that the documentation and searches in this new improved review weren’t thorough or comprehensive, and felt like I needed to note that.”


Putting expertise forward

Some librarians have used PubMed Commons because it’s visible, it’s fast, and they see potential for the impact to extend beyond a single publication.


Donna Berryman

“In a practical sense, using PubMed Commons seemed to be a better choice than writing a letter to the editor because of its immediacy and visibility,” Donna Berryman, the director of the Miner Libraries in the Institute for Innovative Education at the University of Rochester Medical Center, says. “Many, many people will find the article I commented on by doing a search in PubMed. If they look at the record for the article, my comment will be there. I’m not sure how many people would even look at a letter to the editor. In addition, there’s always a chance the letter won’t get published, and, if it does, there’s generally a long gap between when an article appears in a journal and when the letter to the editor might appear. All of those things argue against visibility. So, PubMed Commons gives my words visibility and immediacy.”

Wichor Bramer also favors the transparency and timeliness of PubMed Commons. He is a biomedical information specialist at Erasmus University Medical Center in the Netherlands, where he’s also currently working on his PhD on search methodologies for systematic reviews. He shares, “My last comment was on the details of a search strategy. Julie Glanville, who’s a famous searcher for reviews, responded to that, so you can communicate publicly with the authors.” Author responses can create a “vivid discussion that’s available for anyone to see.”


Michelle Fiander

Bramer is also finding value as an author himself. He notes that he’s used comments on his first article comparing PubMed and Google Scholar to change the way he did some things for his second article. “The comments that we get help me create better articles in the future.”

For Fiander, PubMed Commons offers an opportunity to “get my voice out there and point out things. Maybe it will end up stirring some better standards among journal editors. If you have a paper and you’re indexed in there, you can comment. It’s easier than writing a letter to the editor. I think the freedom of it is good.”


Commenting with care

But freedom doesn’t mean off the cuff for these commenters. “I tend to read my comment, be careful that I’m being accurate, that I’m not overstating or saying something that’s inaccurate,” Fiander notes.

Berryman has commented once but suspects she will comment again. “PubMed Commons strikes me as a place to have reasoned, deliberate comments. It’s not like commenting on Facebook or Twitter. So, one thing I always think about is whether I can write my comment in a way that is constructive and will add to the body of knowledge – and that takes both thought and time.”

I see it as post-publication peer review,” Bramer says. “I first create it. I don’t post it immediately. I put it away for maybe a day and look at it the next day and see different things, see if I can improve some things.”

Rethlefsen understands that commenting on PubMed, especially the first time, isn’t necessarily easy. “It’s not really a space where librarians had actively engaged before. Irreproducible search strategies were always a thing that librarians talked to each other about.” But she had concerns about what looked like, on the face of it, an excellent search strategy that she couldn’t reproduce. So she decided to go to PubMed Commons. “I worked on it, I deleted it, I re-wrote it, and I deleted it. And finally I pushed the publish button. It was intimidating because I’d never done it before. But once I got the reaction that I did [from colleagues and the librarian community], it became really clear to me that this was a more important space than I’d thought before.”


Joining in

Feeling inspired? If you have a publication indexed in PubMed, then you’re eligible to join PubMed Commons and start commenting! Learn more about getting started with PubMed Commons.

PubMed Commons stats through March 31, 2017. Members: 10962 joined, 1637 commented. Comments: 6372 comments posted to 5078 publications.

Authors alerting readers via PubMed Commons

Journals can issue correction and errata notices to notify readers of errors and, as necessary, revise text and data in publications. Yet these processes can take time. Authors sometimes encounter obstacles to publishing corrections. Some authors use PubMed Commons to alert readers to issues or to refine language and interpretations. Correcting the record via journal notices is important, and it’s great to see authors add speed and transparency with post-publication updates.

corr2Earlier this year, Garret Stuber commented on a publication on hormonal control in social reward. In the days after it appeared in press, some errors came to his attention, which he was working to address through a formal correction notice. Stuber told Retraction Watch that, in the meantime, he commented “in an effort for immediate notice and transparency to what occurred.”

Sometimes an error may significantly change the results of a study. Stefan Hofmann commented on a meta-analysis he co-authored, examining the effects of oxytocin on an array of psychiatric symptoms. However, readers raised some points, prompting another look at the data. Errors were made in specifying the direction of outcomes investigated. Hofmann reported the re-calculated effect sizes and indicated that the article is being retracted.

Here are some more authors setting this great example:

Journal corrections revise the version of record for a publication, and PubMed Commons does not replace that. But it does offer another way for authors to provide clarifications, point to interim and published corrections, and alert readers to errors quickly. And it’s good to see authors taking advantage of PubMed Commons to pass that information along to the community.

PubMed comments & their continuing conversations

bubbles_3aWe have many options for communication. We can choose platforms that fit our style, approach, and time constraints. From pop culture to current events, information and opinions are shared and discussed across multiple channels. And scientific publications are no exception.

PubMed Commons was established to enable commenting in PubMed, the largest biomedical literature database. In the past year, commenters posted to more than 1,400 publications. Of those publications, 80% have a single comment today, and 12% have comments from multiple members. The conversation carries forward in other venues.

Sometimes comments pull in discussion from other locations or spark exchanges elsewhere.Here are a few examples where social media prompted PubMed Commons posts or continued the commentary on publications.

Debating disease association

On June 3, 2016, Daniel MacArthur took to Twitter to express his skepticism of a report describing an association between a gene mutation and familial multiple sclerosis published in the journal Neuron. His critique stirred a bit of interest. A few days later, he posted a comment, co-written with Eric Minikel, to PubMed Commons. MacArthur and Minikel highlighted, “Enrichment in cases over controls is one important criterion for establishing pathogenicity of sequence variants.” The comment prompted more discussion on Twitter.

Over the following days, author Carles Vilariño-Güell responded, and MacArthur and Minikel replied. Shortly Chris Cotsapas posted a comment on behalf of the International Multiple Sclerosis Genetics Consortium. His comment summarized an attempt to validate the findings, linking to results posted in a bioRχiv preprint. With Simon Heath, Daniel Weeks noted further concerns in an August comment on the journal’s website, which he linked from PubMed Commons.

As the critiques unfolded, some readers commented on blog posts highlighting the results, (such as here and here) to point to the comments on PubMed. In September, STAT published a story reviewing the concerns that had been raised on PubMed Commons and elsewhere. In October, Neuron published letters from the International Multiple Sclerosis Genetics Consortium and Minikel and MacArthur, as well as a response from the authors. In an accompanying editorial note, the editors remark that the peer-reviewed letters offer “an important complement to other forms of commentary” including social media, PubMed Commons, and the journal’s online comments section.

Comments also sparked discussion of topics beyond the specific gene variant in question.

Self-correcting statements

In July 2016, a publication co-authored by Thomas Nichols reported on an artifact that might give rise to high false-positive rates in functional magnetic resonance imaging (fMRI) analyses. Across blogs and professional publications, there was consideration of what the findings meant for neuroscience research. But some in the community thought results were being too broadly extrapolated to all fMRI studies, not just the specific issues examined.

As the publication was discussed online, the authors recognized that some wording was being interpreted in ways they had not anticipated. So they asked to publish an erratum. That was initially rejected by the journal, since there was no change to the results or conclusions. Nichols published the note on his blog. Following an exchange on Twitter, he subsequently posted a comment on PubMed Commons to make a more circumspect significance statement.

At least one blogger updated a post to reflect the authors’ statement.

Although the journal ultimately published a correction a month later, PubMed Commons enabled authors to rapidly communicate a reframed interpretation of their work.

Replicating and reviewing search strategies

Comments can initiate discussion of specific results and interpretations. But they can also serve as a jumping off point to evaluate approaches and highlight practices.

Literature search strategies lie at the core of systematic reviews and meta-analyses. Melissa Rethlefsen posted a comment describing an attempt to replicate the search strategy reported in a meta-analysis. She noted key missing information such as date ranges. She concluded: “This study highlights the need for more accurate and comprehensive reporting needed for search strategies in systematic reviews and other literature search-based research syntheses, and the need for better peer review of search strategies by information specialists/medical librarians.”

One library used this example to encourage the use of structured reporting guidelines for systematic reviews and meta-analyses.

Another library used the comment to illustrate the importance of reviewing search strategies. And medical librarians and researchers chimed in on Twitter.

Extending the reach of scientific discourse

As you browse the web, you might just run across a mention of a comment on PubMed. Blog authors and readers might mention comments, as they have about a genetic variant associated with body mass index , ‘bad luck’ and cancer, or the occurrence of amphetamines in water systems. They might even appear in the references list, such as a roundup of publications on cancer risk or a look at psychological debriefing after traumatic events. Perhaps the most talked-about comments were those from Jennifer Doudna and Emmanuelle Charpentier on a perspective of the history of CRISPR. The comments were shared and discussed on social media. They were also mentioned in several blog posts and articles, including ones from news outlets such as the Washington Post.

PubMed Commons offers a key place to quickly anchor critical points for future readers to see­­—in one of biomedical science’s most heavily used resources. On a typical day in 2016, 1.6 million users ran 2.5 million web searches on PubMed and viewed more 8 million records.

Through October 31, 2016, PubMed Commons had 10,632 members. They’ve posted 5,739 comments to 4,595 publications. Want to join in? Check out our Get Started page for more information!

The PubMed Commons Team

Signposts from research to resources

Woman working at computerFrom repositories to blogs, the web has expanded means to share information and resources widely. Access to data and code enables other researchers to check published analyses and undertake new ones. Having another way to look at results can help people connect with them and deepen understanding. PubMed Commons members are tying these pieces back to publications by adding external links to PubMed records.

Tagging inputs 

High-throughput assays generate heaps of data, which can require custom software tools to process and analyze. Some authors are annotating current locations and updates for data and code via PubMed Commons.

Proteomics studies approach a wide range of questions about proteins and pathways, often with mass spectrometry data at the core. Author David Simpson provides the identifier and URL to access the dataset for a recent publication. Attila Csordas has also connected several proteomics articles to deposited data.

Patrick Schloss and colleagues published an approach for characterizing microbiomes using a particular high-throughput sequencing platform. He links to “a fully executable version” of his paper. The repository includes the R code, as well as raw and processed data, so that users can reproduce results in the publication.

With the end of Google Code on the horizon, researchers are moving projects to new locations. Pedro Mendes has migrated code for a tool used in modeling of biochemical networks to GitHub. He’s added a comment to point to the code’s new home.

Sometimes authors will update code and append new options. Ross Lazarus summarizes features added to a toolkit for high-throughput biology workflow software. He also includes a link to the new version.

Adding dimensions

Three-dimensional structures of biological molecules can offer useful insight into how proteins function. But as figures in papers, structures can fall flat. Some are using PubMed Commons to restore depth.

Michael Cianfrocco and colleagues solved the structure of a transcription factor complex bound to DNA. He provides a link to FigShare where users can download files for a visualization program. They can then dive into the structure and even create their own figures.

Sandra Porter links to a blog post, where she writes, “One of the most amazing things, to me at least, is how spider silk changes from a liquid form, inside the spider, to a solid, strong material that we see in their webs and other constructions.” She shows readers how to use their tablets to explore the structure and properties of a protein in spider silk that permit this change.

Mary Mangan offers a resource for a literal hands-on approach. She used data from an X-ray crystal structure to create a 3D-printable model of γ-hemolysin, a pore forming protein from Staphylococcus aureus. She points readers to the model on the NIH 3D Print Exchange.

Have something you want to add to a publication? Any author of a PubMed-indexed publication is eligible to join PubMed Commons. Learn how! And check out more examples of how PubMed Commons is being put to use.

The PubMed Commons Team

Refining & revising research on the public record

179024690The life of a research project often doesn’t end when a publication appears in a journal. Experiments continue. Errors are found. Supporting or refuting data is published. Alternative explanations emerge… So PubMed Commons members are posting updated and complementary information to keep work current.

Honing interpretations

Consider, for example, Daniel Haft’s reflection on his publication from 2009. He identified some peptides in two Bacillus strains that he referred to as putative “bacteriocins”. The term describes bacterial peptides that are toxic to related strains. Use of the term was “overconfident”, he notes, “…given the lack of evidence then that these heterocycle-containing natural products were toxins rather than, say, peptide pheromones.” But now results from another group suggest he was on the right track after all.

Andrew Sharp’s group studies how genome structure relates to human disease including X-chromosome inactivation. He considers how a new publication describing DNA methylation in development might be relevant to their own work.

Meta-analysis can show patterns and discrepancies between results from different studies. The data can be calculated in different ways. Valeria Fadda provides alternative data visualizations by posting forest plots for risk differences from published meta-analyses.

Dopamine is a central player in addiction in rodents. Many factors, including where it acts, influence the effects of this neurotransmitter. Roy Wise notes how his group’s work supports recent findings on the consequences of location and what this might mean for the field.

“The mechanisms for establishing, maintaining, and reinstatement of cocaine self-administration have been studied extensively, but have not yet led to a proven medication for cocaine addiction,” Wise remarks. “Perhaps it is time to turn attention to the endogenous mechanisms for what appears to be a state of drug satiety.”

Amending prior work

Some authors highlight work that might strengthen or refine interpretations. Others note how new or existing data might change conclusions.

With co-author Raphael Silberzahn, Eric Uhlmann documents their new work on names and career outcomes. They had previously reported, “Germans with noble-sounding surnames, such as Kaiser (“emperor”), König (“king”), and Fürst (“prince”), more frequently hold managerial positions…” Their new analysis seems to overturn their previous conclusions.

Like many researchers trying to identify new antitumor agents, Miguel Lopez-Lazaro and his colleagues began by testing compounds in a cancer cell line. Since publishing their work, they followed up in other cell lines. Now he considers whether these in vitro effects will really translate to therapeutic potential.

Teasing apart the functions of specific proteins in cells or animals can get complicated. Using inhibitors or genetic manipulation doesn’t always provide a clear picture.

For example, Jens Staal explored the interplay of the protease MALT1 and the deubiquitnase CYLD in immune cells. After further experiments, he updates his interpretation.

Meanwhile, Jim Woodgett notes that care should be taken with assigning specific functions to a single protein isoform. He highlights the trouble with glycogen synthase kinase-3 inhibitors. After a few comments on the subject, he remarks, “…no small molecule inhibitors are isoform selective – I am a scratched record.”

Bridging published updates

When substantive errors are found, updates are not always clearly connected to original publications. PubMed Commons gives authors a chance to link pieces together in PubMed.

Sometimes errors are reported in follow-up studies. Consider a mutation in an HIV protein that was correlated with survival. Stuart Ray notes that a subsequent report of an alignment error invalidates the findings.

Other times, flaws in methods or results lead to correction or retraction of a report.

Randy Blakely finds that a paper about the human dopamine transporter continues to be improperly cited, despite a correction to the results. He says, “I am hoping the PubMed Commons forum will provide a suitable opportunity to redirect readers attention to the, as yet, unknown properties of the E602G mutation…”

Ivan Oransky uses PubMed Commons to annotate recent retractions. He includes links with more about the history of the publication and why it was withdrawn. For instance, here he points to where co-blogger Adam Marcus notes, “Failure to cite leads to ignoble end for xenon paper, and a correction.”

If you’re an author of a PubMed-indexed publication and ready to get involved, check out this page to learn how you can get started.

The PubMed Commons Team


Spotlight on… Amanda Capes-Davis, setting the cell line record straight

450755747You think you’ve found what you need – a cell model for a specific type of cancer you’re studying. But the label on those cells may have you fooled. In labs around the world, many cell lines are mistaken for characters they are not. Dr. Amanda Capes-Davis has seen it happen, time and again. She received her medical training and PhD in cancer genetics from the University of Sydney. After six years as a research officer at the Children’s Medical Research Institute (CMRI), she helped establish CellBank Australia, a non-profit cell line repository. Now working as a cell culture consultant and chair of the International Cell Line Authentication Committee (ICLAC), Capes-Davis is on a mission to bring the long-standing problem of cell line misidentification to light – and she’s using PubMed Commons as a tool in this fight.

Mistaken identities

Cell culture is a part of everyday life for many life science and biomedical researchers. To address biological questions, scientists often work with populations of cells grown in incubators. Typically, cells isolated from a human or other animal will only survive and multiply for a few days or weeks, even under optimal conditions. “Immortalized cell lines,” on the other hand, can be grown in flasks or dishes for months, even years. Often these lines are derived from cancers that allow cells to bypass checkpoints that would normally stop them from dividing.

The advent of immortalized cell culture 60 years ago opened doors for new studies, but there are also persistent problems. Many cell lines bear mistaken identities. So far, ICLAC has identified 472 cross-contaminated or misidentified cell lines, based on 89 publications. The cell type or tissue origin of cells grown is sometimes mislabeled at the outset. Other times, a cell line cross-contaminates another, overtaking the original line. “Perhaps 10-15% of all cell lines are cross-contaminated,” Capes-Davis reports.

HeLa cells exemplify the potential and the pitfalls of cell culture. Henrietta Lacks was a woman who unknowingly pushed biomedical science forward. While she was under treatment for aggressive cervical cancer, a sample of her tumor was taken. Shortly before her death in 1951, those cells were used to establish the first reported immortalized human cell line. Within a few years, the cells were widely used, including in development of the polio vaccine. However, HeLa cells grow so robustly that, if a few cells mistakenly get mixed in with another cell type, HeLa can quickly overtake the others. In their survey of the literature, ICLAC has noticed an abundance of HeLa contamination. Capes-Davis notes, “There are 135 different cell line contaminants, but HeLa is by far the commonest. We list 113 misidentified cell lines where HeLa is the contaminant.”

HeLa cross-contamination of cell lines was first reported in 1967. Yet many new publications continue to misidentify cross-contaminated cell lines. “It’s very understandable, I think, for a scientist,” Capes-Davis says. “You’re doing research in that field. You’re seeing everyone else using this cell line. You think this must be appropriate because all of your colleagues use it.” Reports of cross-contamination disappear under the mountain of other publications using the cell line. In doing as they were trained – building on work published by others – many scientists are actually perpetuating errors. Capes-Davis notes, “They say, research is meant to be self-correcting, but with these cell lines, that doesn’t appear to be the case.”

It’s impossible to fully assess the impact that cell line contamination has had – and continues to have – on research and development. “You only really get hints here or there,” Capes-Davis says. “I first learned about cell line contamination as a PhD student… The lab I was working in started to require testing as I was writing up my PhD.  That was quite a stressful experience for me – my PhD was entirely cell culture-based, and it was frightening to think that all my hard work might be wasted if those cell lines were contaminated.” In some cases, experimental results from misidentified cell lines supported patenting and testing of compounds in people. “These days, I think, with the level of regulation that comes in, problems with cross-contaminated cell lines will be picked up before an agent is trialed, but you have to wonder about the waste of time and waste of money required to get to that point.Amanda Capes-Davis

For Capes-Davis, though, solving cell line misidentification is about more than scientists’ time and research funding. “I am also a medical doctor and would go in to operating theatres to collect tissue samples from individuals who consented to their tissue being used in research.  Many cell lines represent a legacy from donors who have died as a result of that disease.  To me, testing of cell lines is part of our responsibility to the donor, and makes sure that we put the donor’s gift to the best use we can in finding future treatments.”

Correcting the record and the future course

In 2009, Capes-Davis joined two initiatives to address cell line misidentification. The American Type Culture Collection (ATCC) Standards Development Organization established a workgroup (ASN-0002) to develop standards for human cell line authentication. Capes-Davis recalls, “Some members wanted to have an ongoing group on cross-contamination.” During this time, she also collaborated with Ian Freshney to develop a database of cross-contaminated cell lines. “We could really see the value of having involvement of a larger group of people, the advantages of people being able to contribute data or having additional expert opinions on whether a cell line was cross-contaminated, whether or not it’s possible to find authentic stocks.” In 2012, she and other scientists  with a shared interest in the problem of cell line misidentification founded ICLAC.

“I think publicity and awareness is always a challenge. It’s always a bit of a surprise to people, even people who’ve been in the field a number of years,” Capes-Davis notes. “A lot of what we’re involved with is making people aware of the need for quality, even when they’re doing preclinical research. It’s not a series of steps that are going to be difficult to do, but it’s something that should be part of good lab practice. It’s part of good research.” ICLAC is also seeking to establish infrastructure for researchers, such as maintaining the database she and Freshney created, developing guidelines for best practices, and making resources available online.

Capes-Davis has taken to PubMed Commons to annotate publications that misreport identities of known cross-contaminated cell lines. “Ideally we want these things picked up as part of peer review, but it’s not as easy sometimes as you might think,” she notes. “Correcting the scientific record is a really important thing because even if you take the assumption that a signaling pathway isn’t going to be affected, that’s not necessarily going to be the case for another paper that cites that work. The assumption is that if you describe a cell line as oral carcinoma, that’s what it is. It might not matter for one person’s work, but it could well matter for the person who reads that paper.”

“I use PubMed pretty much everyday… it’s an area where a lot of people come to look at abstracts and hunt down papers,” Capes-Davis notes. “So [PubMed Commons] seemed like a great opportunity to raise awareness of our database… We’re hoping that if we do the best we can to bring all the known publications that relate to cross-contaminated cell lines into our database, that will be a useful resource for people. It’s not enough…but it’s certainly a step in the right direction.”

Learn more about PubMed Commons. If you’re an author in PubMed, join and make your own contribution to scientific discourse.