Analysis of XMRV integration sites reveals contamination from cell lines (Silverman)

[Jemal]

I found this article on the other forum. I had to shorten the title a lot, I hope I didn't botch it up. Anyway, this study is from Silverman, one of the discoverers of XMRV.

Analysis of single nucleotide polymorphisms in XMRV patient-derived integration sites reveals contamination from cell lines acutely infected by XMRV

Alice Rusmevichientong1, Jaydip Das Gupta2, Petra S. Elias1, Robert H. Silverman2, and Samson A. Chow1,*
1 Department of Molecular and Medical Pharmacology, and UCLA AIDS Institute, UCLA School of Medicine, Los Angeles, California 90095
2 Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195

We analyzed xenotropic murine leukemia virus-related virus (XMRV) integration site sequences previously identified from human prostate tissues for single nucleotide polymorphisms (SNPs) to discriminate between patient and potential cell line sources of the proviruses. The SNPs of two integration sites were identical to those in cell lines but not the patients, whereas the data on the remaining 12 integration sites were inconclusive. Our results provide direct evidence for contamination during analysis of XMRV integration sites.

http://jvi.asm.org/cgi/content/abstract/JVI.05624-11v1

 

[eric_s]

Not a good way to start the day. But from the abstract they only seem to have conclusive data on 2 of the integration sites. And even if the entire discovery of human integration were to be due to contamination that would not necessarily mean XMRV is not for real.

I guess the BWG results will be what's most important, but even these don't have to be the last word. It will also be interesting to hear from Maureen Hanson. Also Dr. Bieger has made a new video in July, i don't know if it has been posted here already. It's in German anyway. There he says they have now analyzed over 100 cases and continue to find XMRV, but significantly less often than it was reported by the WPI or Lo. We will have to see, but no matter what the BWG results are, i will still want to hear from the Ruscettis, Lo, Alter, Bieger, IrsiCaixa, etc. I would want this to be answered thoroughly, no serious questions should be left open. I don't think we should move on before all the doubts are cleared.

 

[Bob]

Thank you Jemal.

I posted this on the blood working group thread, but it might be more appropriate here...


This study seems very familiar... Hadn't they already done this study, or something very familiar?
I seem to remember that they already knew that two of the integration sites were identical to those in the cell line.
Or is there a significant difference between the two papers? This one investigates SNPs, but I seem to remember the other one investigated the position of the integration sites.

I don't know the significance of the SNPs in this study, but after the previous similar paper was published, we had discussions where it was said that it is likely that some integration sites would be identical.

 

[Jemal]

Whoops! Like Bob I also posted this in a less appropriate thread. Sorry.

I think I started it by posting on that thread
It seemed relevant though.

 

[alex3619]

Hi, I think the Silverman paper was discussed some time ago, or at least aspects of it were. There is nothing new here. We already know that some contamination is likely to occur, the issue is how much and what is contamination and what isn't. The majority of the prostate cancer integration sites do not appear to be contamination - they still might be, but it is likely that a few contamination cases will complicate the results in any study, XMRV and related viruses appear to be everywhere. This is why controls are so critical in these studies, and so far contamination has been equal for controls and test subjects.

Since we might know the outcome of the BWG results in 5+ hours there is no point in speculating about this till later.

Bye
Alex

 

[Bob]

Hi, I think the Silverman paper was discussed some time ago, or at least aspects of it were. There is nothing new here. We already know that some contamination is likely to occur, the issue is how much and what is contamination and what isn't. The majority of the prostate cancer integration sites do not appear to be contamination - they still might be, but it is likely that a few contamination cases will complicate the results in any study, XMRV and related viruses appear to be everywhere. This is why controls are so critical in these studies, and so far contamination has been equal for controls and test subjects.

Since we might know the outcome of the BWG results in 5+ hours there is no point in speculating about this till later.

Bye
Alex

Good points Alex.

 

[currer]

On another forum they point out that MLVs often integrate into the same site. They have a preference for certain points on the genome, so this finding does not have to be a s significant as it is being made out to be.

Unfortunately, due to other factors in my life I am unable to give the time to following the research as closely as I would like nowadays, but this all looks like politics to me and Im not going along with it.
I believe in MLVs as a cause of disease.