Friday, February 8, 2013

Originally posted on 3:

This is one of the original posts about the Anil Potti retractions which were taken down at due to a fraudulent DMCA violation notice. It will probably take up to 14 days before they will be again available. Therefore I am posting these in the meantime on my blog:


"A “retraction in part” for Anil Potti and colleagues, in Molecular Cancer Therapeutics

A partial retraction has joined the ten retractions and five corrections of Anil Potti’s papers, this one of a 2008 paper in Molecular Cancer Therapeutics. The move comes 14 months after theretraction of the Nature Medicine paper upon which much of the Molecular Cancer Therapeuticspaper was based.
Here’s the notice:
Retraction in Part: A Genomic Approach to Identify Molecular Pathways Associated with Chemotherapy Resistance
We wish to retract Table 1 and Supplemental Table 1 from our article entitled “A genomic approach to identify molecular pathways associated with chemotherapy resistance,” which was published in the October 2008 issue of Molecular Cancer Therapeutics (1).
Using previously published annotations for chemotherapy sensitivity in the NCI-60 series of cancer cell lines (2), we performed gene set enrichment analysis on predefined groups of sensitive and resistant NCI-60 cell lines for a range of chemotherapies to identify biological pathways associated with resistance. We purposefully used the annotations for sensitivity and resistance published in the Nature Medicine article and applied a complementary computational approach in order to glean biological insight from the differential gene expression. The article upon which our annotations were based has now been retracted (3). After re-examination, the annotations for the cell lines with respect to chemotherapy sensitivity were erroneous. Thus, our manuscript propagates this error and the results in Table 1 and Supplemental Table 1 from our manuscript are invalid.
The majority of the paper reports our work including in vitro sensitivity testing for 40 lung cancer cell lines, identification of pathways associated with resistance to tested agents, and functional validation of a lead candidate pathway in vitro. These data appear in the remaining Figures 1–7 and Table 2 of the paper and we remain confident in our analysis and findings.
The partial retraction, which appeared online on March 29, 2012, was first reported by DukeCheck. The paper has been cited 29 times, according to Thomson Scientific’s Web of Knowledge.
As we’ve noted:
Duke has said that about a third of Potti’s 40-some-odd papers would be retracted, and another third would have “a portion retracted with other components remaining intact.”
We’d seem to be a bit more than halfway through the roughly two dozen papers that will be retracted or corrected. We’ve been keeping a tally here.
As we’ve noted before, partial retractions are rare, and the Committee on Publication Ethics recommends against them:
Partial retractions are not helpful because they make it difficult for readers to determine the status of the article and which parts may be relied upon.
The partial retraction comes a week after the Institute of Medicine recommended stronger oversight of biomarkers, in areport responding to the Potti case.
Hat tip: Steven McKinney

Originally posted on 2:

This is one of the original posts about the Anil Potti retractions which were taken down at due to a fraudulent DMCA violation notice. It will probably take up to 14 days before they will be again available. Therefore I am posting these in the meantime on my blog:


"Lead author of major breast cancer study announced at ASCO co-authored two corrected papers with Anil Potti

One of the biggest stories so far out of the American Society of Clinical Oncology (ASCO) meeting that just ended in Chicago was that of T-DM1, which, according to Ivan’s Reuters colleagues, “extended the length of time breast cancer patients lived without their disease getting worse.” (The news was even the subject of an embargo break.)
The widely-hailed study of Roche’s drug was led by Duke’s Kimberly Blackwell, who toldThe New York Times:
“We’ve envisioned a world where cancer treatment would kill the cancer and not hurt the patient,” Dr. Kimberly L. Blackwell, a professor of medicine at the Duke Cancer Institute and the lead investigator in the trial, said in an interview. “And this drug does that.”
Blackwell, as Duke watchdog DukeCheck noted over the weekend, published two studies with Anil Potti, the now-former Duke oncologist who has retracted or corrected 17 papers after resigning in the midst of an investigation into his work. Those two studies — one in the Journal of Clinical Oncology, the other in PLoS Medicine — have not been retracted, but both have been the subject of significant corrections.
It didn’t look to us as though Potti was involved in the T-DM1 work, and Blackwell confirmed that was the case. She also confirmed that the now-corrected papers she co-authored with Potti are not related to the T-DM1 work.
We want to be clear: Despite the fact that work by Blackwell and Potti has been found to have flaws, that doesn’t mean everything Blackwell ever works on needs to be scrutinized more carefully, forever. But we think it’s relevant to note the association, and that she was the point person quoted in a press release saying very positive things about one of the now-corrected papers. A selection:
“The breast tumors that arose in younger women shared a common biology, and this discovery was truly remarkable,” Blackwell said. “The genes that regulate things like immune function, oxygen supply and mutations that we know are related to breast cancer, such as BRCA1, were preferentially expressed in the tumors taken from younger women, but when we compared younger women’s tumors to older women’s tumors, we found those same gene sets were not expressed in the ’older’ tumors.”
We also asked Blackwell if, given all of the issues with Potti’s work, whether oncology research at Duke, or Blackwell’s work in particular, was scrutinized more closely before being made public. She tells Retraction Watch:
Duke has learned a great deal from the issues raised by the Potti situation and we now have developed better research oversight that is benefitting Duke researchers and our peers.

Originally posted on 1:

This is one of the original posts about the Anil Potti retractions which were taken down at due to a fraudulent DMCA violation notice. It will probably take up to 14 days before they will be again available. Therefore I am posting these in the meantime on my blog:


"Another retraction for Anil Potti, with an inscrutable notice"

We’ve seen a lot of retraction notices for work by Anil Potti — 10, to be precise, along with 7 corrections and one partial retraction notice. As notices go, they tend to be pretty complete. So when we saw one in CHEST for this 2008 abstract, we were expecting something similar.
Instead, we were confused.
Here’s the notice:
We would like to withdraw our abstract “Upregulated Oncogenic Pathways in Patients Exposed to Tobacco Smoke May Provide a Novel Approach to Lung Cancer Chemoprevention,” which appeared in CHEST2 and was presented as a poster on October 29, 2008.
The results reported in this abstract and poster presentation were obtained using chemotherapeutic predictors developed in the Nature Medicine article, “Genomic Signatures to Guide the Use of Chemotherapeutics”1,that have since been shown to be inaccurate, and the article has been retracted.3The authors relied on the results reported by Potti1, and they were not aware of the errors subsequently reported. We apologize for any negative impact on scientific research or clinical care caused by the presentation of our abstract.
1. Potti A, Dressman HK, Bild A et al. Genomic signatures to guide the use of chemotherapeutics. [retracted in: Nat Med. 2011;17(1):135] Nat Med. 2006;12(11):1294-1300.
2. Redman RC, Acharya CR, Anguiano A et al. Upregulated oncogenic pathways in patients exposed to tobacco smoke may provide a novel approach to lung cancer chemoprevention [abstract]. Chest. 2008;134(4):158001S.
3. Potti A, Dressman HK, Bild A et al. Retraction: Genomic signatures to guide the use of chemotherapeutics.Nat Med. 2011;17(1):135.
This was the sentence we found difficult to interpret:
The authors relied on the results reported by Potti1, and they were not aware of the errors subsequently reported.
That’s because “The authors” include Potti, so “they” would seem to include him too. How exactly was he not aware of the errors subsequently reported?
We’ve asked one of the authors, and the journal’s editor, who actually signed the notice, since the journal doesn’t indicate that, and also asked what that sentence meant. We’ll update with anything we learn.
Potti is now working at a cancer center in North Dakota, the state where he completed some of his medical training. On September 8, neighboring Minnesota granted him a medical license, as DukeCheck reported. He had allowed his previous Minnesota license to expire in 2008.

Thursday, February 7, 2013 coverage of the Anil Potti case

In the last 48 hours or so the blog has been hit with a DMCA take down notice in regards to ten posts which covered the Anil Potti case (the now infamous Duke University oncologist who was found to have manipulated research findings, resulting in - among other things - the stop of three clinical trials and now pending civil law suits against the university brought up by patients and their families). More after the jump...

Friday, January 18, 2013

Growth of Human Genomic and Exonic DNA Sequences in NCBI's Short Read Archive since 2009

Figure presenting the growth of total number of bases sequenced from human genomic and exonic DNA submitted to the NCBI Short Read Archive since 2009. The plots are based on SRA Run Summary numbers retrieved through the NCBI E-Utilities interface, sorted by year.

Thursday, November 15, 2012

Fixing the proxy problem in Mendeley Developer preview 1.7 on Ubuntu 12.04 LTS

I am a big fan of Mendeley ( as a tool for storing and organizing my references. In particular the pretty robust extraction of bibliographic data from PDFs saves me a couple of steps in the workflow that I was used to when doing this with Endnote.
I recently received my new (proper) workstation and I have switched from running Ubuntu 10.04LTS in a virtual machine to using Ubuntu 12.04LTS as the main OS and rather running a virtual machine instance of Windows 7 for the few remaining pieces of software which need a Windows OS. Since switching over to Linux, I have not been able to use the Linux version of Mendeley, as it steadfastly refuses to connect to the internet via our work proxy server. While it is possible to configure the proxy settings under "Tools/Options/Connection" the connection test (which can be invoked by pressing Ctrl+Shift+D to bring up the debug console - "Test Internet Connection") reported that it wasn't able to provide proxy authentication. I tried several fixes as outlined in the Mendeley support forums (e.g. but none of them worked...

Eventually a combination of defining system wide proxy settings as described here:

and here some GNOME specific settings:

and setting the "Tools/Options/Connection" settings in Mendeley to

"No Proxy"

have fixed this problem.

Now Mendeley uses the system-wide proxy setting for connecting to the server and nicely syncs my library the way I was used to. Unfortunately I cannot tell which environment variable is relevant to Mendeley, but as I am using a number of applications which need internet access and everyone of them seems to read out different variables the best way seems to be to set all possible PROXY variables with the relevant connection information.

Thursday, October 25, 2012

Installing "mixOmics" under R-2.15.1 - fixing missing dependencies


The package "mixOmics" depends on a nunber of packages which render some of the 3D graphics output, among them "rgl" which in turn needs a OpenGL libraries/header files for successful compilation. These can be installed by issuing following command in a separate terminal window:
sudo apt-get install libglu1-mesa-dev libgl1-mesa-dev
 Once the system packages have been installed, issuing following command in your R session will install the "mixOmics" package: