Retraction Watch

Tracking retractions as a window into the scientific process

Archive for the ‘genetics retractions’ Category

Misidentified genetic sequence causes retraction of pathogen paper one month after publication

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Genome Announcements

The author of an article mapping the genome of an infectious bacterium is pulling the paper because — well, it wasn’t the bacterium she thought it was.

Study author Celia Abolnik is retracting her paper in Genome Announcements because it didn’t actually map out the DNA of Mycoplasma meleagridis, a bacterium that typically infects turkeys but has recently been found in chickens.

The trouble was, the sequence for Mycoplasma meleagridis in the National Institute of Health’s DNA database, Genbank, was actually a different variety of bacteria — Mycoplasma gallinaceum, another scourge of poultry.

Here’s the notice for “Complete Genome Sequence of Mycoplasma meleagridis, a Possible Emerging Pathogen in Chickens:”

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Corrections (and one EoC) propagate for distinguished plant biologist, Olivier Voinnet

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Olivier Voinnet

Olivier Voinnet

There may be some deeply rooted issues in the work of high-profile plant biologist Olivier Voinnet, biology department research director at ETH in Zurich. Corrections have continued to pile up months after his work was hit with a barrage of criticism on PubPeer. We’ve tracked a total of seven corrections over the past five months (not including the April retraction of a 2004 paper in The Plant Cell). One of the corrected papers also received an Expression of Concern this week.

Collectively, the corrected papers have accumulated more than 1200 citations.

In January, Voinnet said he planned to correct multiple papers, after receiving “an anonymous email.”

One of the recent corrections we found is for a 2004 article in The Plant Journal, “An enhanced transient expression system in plants based on suppression of gene silencing by the p19 protein of tomato bushy stunt virus,” which details using proteins from a tomato virus to help alter gene expression. The study has been cited 862 times, according to Thomson Scientific’s Web of Knowledge. Here’s the correction notice, posted June 8:

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High-profile aging paper posts old erratum, requested by author more than one year prior

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GenomeBioGenome Biology has partially retracted a high-profile paper about an epigenetic biomarker of aging – a year and a half after the author alerted the journal to a software coding error that invalidated one of its findings.

The paper, “DNA methylation age of human tissues and cell types,” garnered some media coverage and forms the basis of its author Steve Horvath‘s work on measuring human aging. It has been cited 73 times, according to Thomson Scientific’s Web of Knowledge. The article is also recommended on the post-publication peer review site Faculty of 1000.

The lengthy, peer-reviewed erratum notice, written by Horvath, refers to several figures and files, as well as a conclusion:

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Written by Alla Katsnelson

June 15th, 2015 at 11:30 am

Nature retraction, resignation result after lung cancer cell lines “cannot be those specified”

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cover_natureUpon realizing they had experienced a case of mistaken cell-line identity, the authors of a 2014 Nature paper on lung cancer think “it prudent to retract pending more thorough investigation,” as they explain in a notice published Wednesday.

The problem seems to stem from more than just honest error, according to corresponding author Julian Downward, a scientist at the Francis Crick Institute in the UK.

In a 1,215 word statement, sent to us via the Director of Research Communications and Engagement at Cancer Research UK, which funds Downward’s research, Downward told us the backstory not presented in the journal’s retraction note:

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Cell Press investigating possible image manipulation in influential yeast genetics paper

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cellCell Press is looking into anonymous allegations that a pair of influential papers on gene activation in yeast may contain more than two dozen instances of image manipulation, according to a spokesperson for the journal.

The accusations first appeared in March on PubPeer, where they triggered a small avalanche of comments, including one asserting “unambiguous and repeated examples of data re-use.”

The concerns raised on PubPeer have even sparked an investigation by an institution in Spain, which found no evidence to support the allegations. But not everyone agrees with that verdict.

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NIH cancer paper retracted for faked data

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JCIFollowing an investigation into research misconduct, the Journal of Clinical Investigation has retracted a cancer genetics paper from a laboratory at the National Institutes of Health due to “data falsification and fabrication” of four figures and a table in the paper.

The paper, “FOXO3 programs tumor-associated DCs to become tolerogenic in human and murine prostate cancer,” describes an overexpressed gene in mouse prostate cancers that appears to suppress immune system cells.

The journal retracted the paper following an investigation into author Stephanie K. Watkins, then a postdoctoral fellow at the National Cancer Institute. According to a NIH press release released about the study in March 2011, the work “has led to the submission of a patent application by the NIH on behalf of Hurwitz and Watkins to target FOXO3 as a way to boost immune responses in cancer and to silence excessive immune responses in autoimmune diseases.” We found an NIH record of the patent application, but no record of an approved patent at the United States Patent and Trademark Office under either Hurwitz or Watkins’ names.

The paper has been cited 62 times, according to Thomson Scientific’s Web of Knowledge. Here’s the full notice: Read the rest of this entry »

Genetics journal isn’t down with O.P.D. – stealing other people’s data

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GMR logoGenetics and Molecular Research, an online-only journal, has retracted two articles about gastric cancer by a group of Iranian researchers who appear to have put their own names on other people’s data.

Both articles were published in 2014. One was titled “Absolute quantification of free tumor cells in the peripheral blood of gastric cancer patients;” the other, “ZNF797 plays an oncogenic role in gastric cancer.” The list of authors on the two papers isn’t identical, but both papers share a few in common, including the same two last authors: F. Ghasemvand and S. Heidari-Keshel.

It turns out, Saeed Heidari-keshel wasn’t down with other people’s data, and alerted the journal to the problem.

Here’s more from the retraction notice for the first article, which was found to be “substantially equal” to another paper: Read the rest of this entry »

New favorite plagiarism euphemism: “Inadvertently copied text”

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biodata miningPlagiarism earned genomics researchers an erratum, not a retraction, in BioMed Central journal BioData Mining.

We keep a list of best euphemisms for plagiarism, and this one is right up there.

Here’s the notice for “An iteration normalization and test method for differential expression analysis of RNA-seq data”: Read the rest of this entry »

Drug company lawyer letter results in “utterly tedious” retraction

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Image via Intropen

Image via Intropen

What’s in a name?

Well, if it’s the same name as a treatment with nearly $1 billion in sales per year in the U.S., a retraction.

A “mind numbingly boring one,” that is.

Here’s the Twin Research and Human Genetics notice for “EpiPen: An R Package to Investigate Two-Locus Epistatic Models”: Read the rest of this entry »

Authors retract PNAS brain genetics paper for statistical issues

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pnas 1113The authors of a paper on brain genetics published online in June in the Proceedings of the National Academy of Sciences (PNAS) are retracting it for “a potential confound relating to statistical inference.”

Here’s the notice for “Identification of gene ontologies linked to prefrontal–hippocampal functional coupling in the human brain:” Read the rest of this entry »