HGRVs - Constructive general discussion - for exploring HGRV research

[Firestormm]

Oh right. Thanks.

Hey, Bob. I was saying on the 'Lipkin Thread' about that old post from Jenny Spotila which I think we discussed when it was originally posted.

The information might have now improved regarding his studies, I forget now without checking what it is we do know and what we don't to be honest (just that we don't really know a great deal!!) but I happened to watch again the link she included to that NIH State of Knowledge:

It was interesting to hear again Harvey Alter's thoughts on this Lipkin Study. I had forgotten how much faith he had placed in it (Jenny quotes him as also saying it to be 'definitive' for example) but I was more interested in what he had to say about how it was being put together.

There was also a comment from Coffin I think and it reiterated what I believe Miller had to say on that other thread, that PCR is required before NGS can be performed. To me this would seem logical I suppose i.e. you have to really know what you are looking for before looking for it and PCR identifies what to look for.

But this does seem to go against what I have been given to understand elsewhere. I get the impression that NGS is some sort of 'uber-scan' that can simply 'dig deep' and reveal 'anything' and 'everything'. Presumably though it has to be primed and I think from her links in the post above, one of the articles did indicate that Lipkin will be looking for already associated viruses in the CFI project.

Any thoughts? Thanks.

 

[Bob]

Oh right. Thanks.

Hey, Bob. I was saying on the 'Lipkin Thread' about that old post from Jenny Spotila which I think we discussed when it was originally posted.

The information might have now improved regarding his studies, I forget now without checking what it is we do know and what we don't to be honest (just that we don't really know a great deal!!) but I happened to watch again the link she included to that NIH State of Knowledge:

It was interesting to hear again Harvey Alter's thoughts on this Lipkin Study. I had forgotten how much faith he had placed in it (Jenny quotes him as also saying it to be 'definitive' for example) but I was more interested in what he had to say about how it was being put together.

There was also a comment from Coffin I think and it reiterated what I believe Miller had to say on that other thread, that PCR is required before NGS can be performed. To me this would seem logical I suppose i.e. you have to really know what you are looking for before looking for it and PCR identifies what to look for.

But this does seem to go against what I have been given to understand elsewhere. I get the impression that NGS is some sort of 'uber-scan' that can simply 'dig deep' and reveal 'anything' and 'everything'. Presumably though it has to be primed and I think from her links in the post above, one of the articles did indicate that Lipkin will be looking for already associated viruses in the CFI project.

Any thoughts? Thanks.

Hi Firestormm,

It's interesting isn't it.

I had the same understanding, as you, about how next generation sequencing (NGS) works.

Like you, I thought that NGS could be used for all pathogens, and that it replaced PCR, and that it wasn't necessary to use PCR and NGS as complimentary processes.
Maybe it depends on the funding and resources available.
I think NGS requires an enormous amount of DNA and data processing, and maybe narrowing down what's being hunted for might reduce those costs.
I'm quite sure that Lipkin has said in the past that NGS can find new viruses.

I can't remember exactly what Miller said about it.
But it ran counter to my understanding about NGS.

I understand that PCR is extremely sensitive, and that NGS might not be so sensitive.
But with enough resources, maybe NGS can be equally effective?
Also, NGS confirms exactly what sequences you have detected, whereas with PCR there is some uncertainty.

I don't yet understand Lipkin's methodology. I need to do some more reading.

And I haven't got around to reading the second blog that you linked to in your post on another thread.
So I'll read that and have a look at the video a bit later.

 

[Wally]

Hi Firestormm,

It's interesting isn't it.

I had the same understanding, as you, about how next generation sequencing (NGS) works.

Like you, I thought that NGS could be used for all pathogens, and that it replaced PCR, and that it wasn't necessary to use PCR and NGS as complimentary processes.
Maybe it depends on the funding and resources available.
I think NGS requires an enormous amount of DNA and data processing, and maybe narrowing down what's being hunted for might reduce those costs.
I'm quite sure that Lipkin has said in the past that NGS can find new viruses.

I can't remember exactly what Miller said about it.
But it ran counter to my understanding about NGS.

I understand that PCR is extremely sensitive, and that NGS might not be so sensitive.
But with enough resources, maybe NGS can be equally effective?
Also, NGS confirms exactly what sequences you have detected, whereas with PCR there is some uncertainty.

I don't yet understand Lipkin's methodology. I need to do some more reading.

And I haven't got around to reading the second blog that you linked to in your post on another thread.
So I'll read that and have a look at the video a bit later.

I believe Lipkin discussed NGS during his Lecture at the WPI in June of 2011. Here is the link.

http://imedia.unr.edu/unsom/whittemore_peterson_institute/dr_ian_lipkin.html

The slides from this lecture, which I felt were an important piece of the lecture, were not included when the video of the lecture was taped. I have not seen the slides released elsewhere for public review. I will try to go back through the lecture and see if I can find the places where he discusses NGS.

It was my understanding that NGS would allow him to find known and unknown pathogens. I think it is a very important follow-up question that could be asked of Dr. Lipkin as to which ME/CFS study that he is involved with will be using NGS to look for known and unknown pathogens in ME/CFS patients.

Here is some additional information that might be helpful in understanding the advancement in technology using techniques like NGS.

1) http://www.ted.com/speakers/joe_derisi.html

2) http://www.ted.com/talks/joe_derisi_hunts_the_next_killer_virus.html

3) http://www.dnatube.com/video/1523/Talks--Joe-DeRisi-Hunting-the-next-killer-virus

 

[Wally]

Bob,

Here is some additional information you may want to review about NGS.

http://icarusconsultants.com/page/4/

This link is to a Biotech blog, which includes in one of the blog posts, a videotaped interview with a doctor (Gordon Mills) from the M.D. Anderson Cancer Center. At around the 7:00 minute mark, he discusses how the advancements in research, using technology like NGS, can create a whole new set of issues when trying to interpret/use this information along side prior studies that have used less advanced technology to arrive at their conclusions.

Wally

 

[Bob]

Thanks very much for all of that, Wally. Much appreciated.

 

[Firestormm]

Perhaps we could have a thread: NGS Room 101 or something? I'd certainly like to better understand how this all works. Am a simple chap though so the less complex the explanation the better

 

[Wally]

Perhaps we could have a thread: NGS Room 101 or something? I'd certainly like to better understand how this all works. Am a simple chap though so the less complex the explanation the better

I like that idea as well. I never understood why there was not more discussion about this technology, since Dr. Lipkin said this is what he would use for his first choice to go hunting for pathogens in this illness.

I would like to know exactly how this kind of research is conducted, how much it would cost (based on his lecture at the WPI I assume a starting point would be $1 million). I don't believe Dr. Lipkin is the only person who could perform this research even thought he is obviously considered the top dog in how he hunts. Perhaps there are other researchers who also possess similar skills and I wonder if with the necessary funding they would also be interested in going hunting. It seems to me if more skilled researchers are in on the hunt it would assist in understanding how definitive a particular finding might be.

Not sure what the thread would be called to capture information from other posts and keep this type of discussion going. However it might be helpful if XMRV was not the main identifier in the title, so it would allow discussion to encompass a broader range of topics.

 

[Bob]

Wally, I think you should feel free to discuss any retroviral issues in the XMRV sub-forums, especially if they are related to XMRV research or ME in any way. We all look at these forums to learn more about the subject.

I noticed this posted on another forum:

New York Genome Center Purchases Four Ion Proton™ Sequencers for its new Innovation Center​

http://www.prnewswire.com/news-rele...-for-its-new-innovation-center-164480446.html​

The article says that the New York Genome Center has purchased new next generation sequencers that can sequence an entire human genome in a few hours for under $1000.

At the bottom of the page, it says that Columbia University (Lipkin's university) is a founding member of the New York Genome Center. So maybe Lipkin will have access to these next generation sequencers.

If either of you, Wally or Firestormm, want to start up a new thread about NGS, then maybe you could use this article as a starting point? And then post all of your recent links for info for anyone who wants to learn more? Just a thought.

I'm still catching up with a load of reading, so I've not yet read up any more about Lipkin's study or NGS.

 

[Firestormm]

Good idea. It seems I have rather a lot to read this morning (not that I am complaining). I want to have a read also of the NGS stuff out there before popping a thread together. Get some basic information kobbled together first. If Wally would like to begin though I can always catch up. This CFI NGS was always ambitious but I'm only now beginning to realise just how ambitious and how long it is likely to take