Doctors Mc.Clure & Kaye respond to Annette Whittemore in "Expert-Reviews.com"

[Eric Johnson from I&I]

In a book I saw a bet drawn up by Hawking and his friend, over the existence of some debatable phenomenon in physics, "naked singularities":

"[...] The loser will reward the winner with clothing to cover the winner's nakedness. The clothing is to be embroidered with a suitable, truly concessionary message. [...]"

 

[Bob]

... But she can no longer be so naive and she is responsible for public comments she makes. It seems to me she has been plainly inaccurate in a number of public comments, the latest of which appears in this article, as picked up earlier in this thread by Bob:

I'm not sure about the accuracy of the following quote:

One technical difference stands out from these studies. PCR was employed to amplify XMRV sequences in all four studies. Only the study from the Whittemore Peterson Institute [1] was able to detect XMRV sequences following single-round PCR, indicating that copies of the XMRV genome were not in short supply. All the others found it necessary to employ a nested PCR, a modification of the standard reaction designed to enhance sensitivity and specificity.

Additionally McClure's article says (bolding mine):

The new connection of XMRV with CFS reported from the Whittemore Peterson Institute (NV, USA), was published in Science last year [1], and claimed that, of 101 CFS patients recruited to investigate the virus etiology of the disease, 68 (67%) were XMRV positive by single-round PCR amplification of the proviral DNA from peripheral blood mononuclear cells.

Compare the above to a direct quote from the WPI Science paper second para (bolding mine):

we isolated nucleic acids from PBMCs and assayed the samples for XMRV gag sequences by nested polymerase chain reaction (PCR) (5, 6). Of the 101 CFS samples analyzed, 68 (67%) contained XMRV gag sequence.

I understand nested PCR is double round PCR, not single round PCR.

I can't see how the McClure article can be interptreted as anything other than a misrepresentation of the facts in relation to the WPI study. Much of the criticism of the WPI in the article revolves around this PCR issue. I cannot fathom how McClure, with her intimate knowledge of WPI study, could have got this point wrong accidentally, unless there has been some 3rd party journalistic or editorial intervention here that has got things mixed up. Or maybe the other person wrote it. Not that that excuses anything.

If there is anyone here that understands how the above quotes can be reconciled then please enlighten us. Otherwise I think we should be writing to the journal asking for a public correction to be made and questioning how someone of McClure's knowledge and standing could be making such errors.

Megan, I've just noticed that it seems that your understanding about the nature of 'nested PCR' is actually confirmed, in your own post, by McClure herself:

I'm not sure about the accuracy of the following quote:

One technical difference stands out from these studies. PCR was employed to amplify XMRV sequences in all four studies. Only the study from the Whittemore Peterson Institute [1] was able to detect XMRV sequences following single-round PCR, indicating that copies of the XMRV genome were not in short supply. All the others found it necessary to employ a nested PCR, a modification of the standard reaction designed to enhance sensitivity and specificity.

On re-reading this quote carefully, McClure is clearly saying that 'nested PCR' is not 'single-round PCR'...
She seems to be saying, with apparent certainty, that the WPI used "single-round PCR" (not 'nested PCR'), whereas the other studies used the alternative method of "nested PCR" (not 'single-round PCR') which is "designed to enhance sensitivity and specificity".

This, as you say, is contradicted in the statement you included from the WPI:

we isolated nucleic acids from PBMCs and assayed the samples for XMRV gag sequences by nested polymerase chain reaction (PCR) (5, 6). Of the 101 CFS samples analyzed, 68 (67%) contained XMRV gag sequence.

McClure is clearly saying that the WPI study used 'single-round PCR', and not 'nested PCR', whereas the WPI are clearly saying the opposite. So I can't see how the McClure statement can possibly be correct when the WPI have so clearly stated that they used 'nested PCR'.

(This is obviously exactly what you were pointing out Megan... but I've only just worked it out for myself! Sorry if I'm being a bit slow to catch up here!)