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High-Impact Journals, Large Vendors Contributing to Lack of Quality Control for qPCR Data Publication


By Ben Butkus

GÖTEBORG, Sweden – Quality control for publication of quantitative PCR data is still severely lacking – and, in the case of high-profile scientific journals such as Nature and Science, it is "absolutely appalling and scandalous" – according to Stephen Bustin, one of the scientists leading the drive to adopt a set of standards intended to guide high-quality and reproducible qPCR experiments within the field.

In addition, large companies in the PCR space, such as Life Technologies and Qiagen, are contributing to the problem by refusing to share PCR probe and primer sequences with their customers, said Bustin, who suggested that researchers should boycott these firms until they decided to reveal such information.

Bustin, a professor of molecular science at the Barts and the London School of Medicine and Dentistry at Queen Mary University of London and one of the earliest and most vociferous proponents of adopting qPCR data standards, made his remarks during TATAA Biocenter's Developments in Real-Time PCR conference, held here this week.

In a presentation on quality control for publication of qPCR data, Bustin outlined events over the last several years – including the debunking and retraction of several high-profile papers whose conclusions were based on misinterpreted qPCR data – that led to the development and publication in early 2009 of the minimum information for publication of quantitative real-time PCR experiments, or MIQE, guidelines, by himself and other leading qPCR researchers.

In a December interview with PCR Insider, Bustin said that the guidelines, which were intended to serve as a checklist for authors to ensure their qPCR-based experiments could be reproduced by others and for journal editors and reviewers to assess the quality and validity of submitted research, were "slowly filtering" through the PCR community (PCR Insider, 12/31/2009).

This week at the TATAA Biocenter meeting, however, Bustin said that the lack of interest from major journals such as Nature and Science has been discouraging.

During his talk, Bustin provided examples of papers published in both journals within the last six months that included no information on how the qPCR experiments were performed despite the technique being integral to the study's findings. Subsequent searches through referenced papers purportedly describing the methods also revealed little to no information.

In an interview with PCR Insider following his talk, Bustin said that both Science and Nature have essentially ignored requests from Bustin and others to discuss the adoption of MIQE guidelines to guide research submitted for publication. "It's rather a scandal, the data requirements for qPCR in high-impact-factor journals," he said. "You really can't judge a result if you don’t know how people went about doing it."

Bustin did cite the BMC series of journals for doing a reasonable job in requiring adherence to MIQE guidelines.

And although individual qPCR researchers seem to be starting to pick up the guidelines, an informal survey of attendees at the conference showed that only about half had ever heard of MIQE.

"The purpose of MIQE is to design qPCR experiments," Bustin said. "If you follow all the steps, the quality of the assay is going to be good. But, if you are using an assay designed 10 years ago, it would be cumbersome to go through all the guidelines. But then you probably shouldn't be using a 10-year-old assay."

Withholding Information

Another factor contributing to a lack of quality control for qPCR data is the fact that many researchers are using assays provided by large life science research tool vendors, but don’t know what primer and probe sequences are being used in the assays. Despite this, many researchers continue to use the assays, which often end up being irreproducible by them or others.

Though in December Bustin applauded Life Technologies' Applied Biosystems, among other companies, as having taken an interest in understanding and implementing MIQE, he said this week that both Life Tech and Qiagen "refuse" to provide sequences for primers and probes, even to customers that used assays and want to later return and find information on them.

Bustin did applaud Thermo Fisher for having made an effort to provide its customers with probe and primer sequences for its custom-designed Solaris qPCR assays; and said that a small UK-based company called Primer Design is doing the same.

Others at the TATAA conference expressed their dismay over non-disclosure policies at some of the larger companies.

David Schuster, director of research and development for qPCR shop Quanta Biosciences, cited a specific example involving Life Technologies where "I saw a specific assay in a paper, and went to look it up on the website. You should be able to click through and find it, but it's nowhere to be found," he said.

"It makes you suspicious that it was removed perhaps because it represented some sort of diagnostic biomarker," Schuster added.

Bustin's advice to scientists experiencing such issues with Life Technologies, Qiagen, or any other company that will not disclose assay information is to boycott their assays and "design your own experiments. This "would put some pressure on the big players" to change their disclosure policies, he added.