Genotyping mistake costs lab two papers and year of work

Researchers are retracting two papers about molecular signalling in plants — including one from the Proceedings of the National Academy of Sciences (PNAS) — after discovering some inadvertent genotyping errors. But that was only after they used the problematic plants for an entire year without realizing they’d made a mistake.

In a pair of refreshingly transparent and detailed notices, the authors explain that the transgenic plants used in the papers included genotyping errors, which invalidated their findings. According to the notices, first author Man-Ho Oh generated the problematic transgenic plants, while corresponding author Steven C. Huber, based at University of Illinois, Urbana-Champaign (UIUC), took responsibility for omitting some critical oversight.

Huber told us that there were only two papers that used the transgenic plants in question, so no other retractions will be forthcoming.

Here’s the notice in PNAS for “Autophosphorylation of Tyr-610 in the receptor kinase BAK1 plays a role in brassinosteroid signaling and basal defense gene expression:” 

The authors wish to note the following: “We wish to retract the information in this article pertaining to the phenotype of transgenic plants expressing BAK1 (Y610F)-Flag presented in Figs. 2 and 3 and Tables 1 and 2. After publication of this article, we became aware that the transgenic plants described in this manuscript were not correct because of inadvertent errors in genotyping of the plants, and thus the in planta results presented are not valid. However, the results identifying Tyr-610 as an autophosphorylation site (in vitro and in vivo) and all results obtained with recombinant proteins (presented in Figs. 1 and 4) are valid, and conclusions drawn from functional and interaction studies in vitro are correct. The responsibility for this experimental error rests with only two of the authors: the senior author (M.-H.O.), who was a Senior Research Scientist when these studies were conducted with extensive experience in molecular biology and whose primary responsibility was production of the transgenic plants. The other responsible individual is the corresponding author (S.C.H.), who failed to provide adequate oversight for the production of the transgenic plants; as a result, critical checks and balances were not in place. The other authors (X.W., Y.Z., and S.D.C.) are not responsible in any way for this regrettable situation.

The mistake had a major impact on the lab, which is trying to recover, the notice continues:

We are currently producing transgenic plants expressing BAK1 (Y610F)-Flag in the bak1 bak1 / bkk1 bkk1 double null background to redo these experiments and plan to publish the results in the near future. We deeply and sincerely regret any scientific misconceptions that have been caused by the above paper. Because we had no reason to question the transgenic plants at the time of publication, the corresponding author’s laboratory spent more than an additional year studying these plants before the error was discovered. We hope to spare others from doing the same. We apologize to the entire scientific community for the misinformation and any adverse consequences that may have resulted.”

The 2010 paper has been cited 79 times, according to Thomson Reuters Web of Science.

The other notice, in Frontiers in Plant Science, is equally forthcoming about what went wrong with “The Carboxy-terminus of BAK1 regulates kinase activity and is required for normal growth of Arabidopsis:”

The Journal and Authors retract the 4 February 2014 article cited above for the following reasons provided by the Authors:
“After publication of this article, we became aware that the transgenic plants described in this manuscript were not correct because of inadvertent errors in genotyping of the parent plants, and thus the results presented in Figures 4 and 6 are not valid. We realized from the immunoblot result presented in Figure 4B, that immunoprecipitated BAK1-ΔCT-Flag had the same apparent molecular weight as did BAK1-Flag, despite the fact that truncated protein should have been ~4-kDa smaller but that size difference was not apparent. We subsequently confirmed that the BAK1 construct used was not truncated but was full length. At the moment we cannot explain why the transgenic plants show reduced growth, but it is clear that it is not related to the BAK1 transgene. However, the results presented in Figures 1, 2, 3 and 5 with recombinant proteins in vitro are valid, and thus conclusions drawn from functional and interaction studies in vitro are correct. Regrettably, the relevance to the function of BAK1 in vivo remains uncertain and it is no longer clear whether the carboxy-terminus of BAK1 is “required for normal growth of Arabidopsis” as stated in the title. The responsibility for this experimental error rests with only two of the authors: the senior author (MHO) who was a Senior Research Scientist when these studies were conducted with extensive experience in molecular biology and whose primary responsibility was production of the transgenic plants. The other responsible individual was the corresponding author (SCH), who failed to provide adequate oversight to the production of the transgenic plants and as a result, critical checks and balances were not in place. The other authors (WX, SYK, XW and SDC) are not responsible in any way for this regrettable situation. We are pursuing follow-up experiments to correctly generate the BAK1-ΔCT-Flag transgenic plants in the bak1 bkk1 double null background that are required to test the functional role in vivo and hope to publish soon.

We sincerely regret any scientific misconceptions that have been caused by the above paper; the corresponding author’s laboratory wasted an additional year studying these plants before the error was discovered. We apologize to the entire scientific community for the misinformation and any adverse consequences that may have resulted.”

That 2014 paper has been cited eight times.

Huber told us more about the wasted effort due to the mistake:

A new postdoc in the lab (Sang Yeol Kim) spent a great deal of his time over the course of his first year in my lab analyzing gene expression in these transgenic plants (using microarrays and RNAseq) to try to understand the basis for the observed growth phenotypes.  We were hoping to develop this into a new grant proposal, which was not possible when the mistakes were realized.  But fortunately a graduate student was not involved, but the postdoc involved probably lost 6 months of effort.

He added:

This problem came out of left field for us (i.e., the potential problem wasn’t even on my radar screen), so we have indeed put in place some new lab rules to try to insure that this sort of thing does not happen in the future.

For instance, the lab is working to better preserve and archive data, and his revised rule book for lab work notes that researchers need to provide sequencing and genotyping for new transgenics in the paper, whether or not the data are included.

According to Huber, Man-Ho Oh is a faculty member at Chanung National University in Korea.

Kyle Galbraith, research integrity officer at UIUC, told us that these two retractions “are not due to any research misconduct allegations brought to me:”

As the Research Integrity Officer for the Urbana-Champaign campus, I have not received any complaints about the research presented in the two original publications. Based on the retraction notices, it looks like the researchers are trying to do the right thing by correcting the research record after finding an error in their published work.

We agree that the transparent nature of the retractions serve as an example of “doing the right thing;” Huber said he didn’t see an alternative:

…we felt that being totally transparent is the best way (only way) to move forward for all involved, including the co-authors and the greater scientific community.

Huber said he plans to resubmit the paper:

We hope to publish a ‘correction paper’ in the near future with properly prepared transgenic plants but the first step was to retract the original publication.

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