25 replies to this topic

[Mind]

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[Mind]

For Immortality Institute  Members:

Osiris Green is offering a 30% discount. You can find the discount code here: http://www.longecity...ember-discount/

 

 

Edited by caliban, 24 January 2017 - 02:13 AM.
name & pic

[neilcopes]

Hi, I’m Dr. Neil Copes, CEO of Osiris Green.  The service that we’re offering is a mail-in saliva testing service that can give an estimate of your chronological age based on observed epigenetic changes in your DNA.  I am very interested in the life extension community and I’m hoping that this service might be as a useful tool for people who want to monitor their age from an epigenetic standpoint.  The FAQ page on our website is a useful place to start if you’re interested.  Also, I recently gave an interview at FightAging.org that might provide some additional background on what we’re trying to do.

 

Feel free to ask me any questions, and I’ll replay as time permits.

[Tom Andre F. (ex shinobi)]

Hi,

 

can you please explain deeper this topic please ? for instance, whats the difference between DNA methylation and mtDNA methylation please though aging ?

 

Is it more reliable than the telomeres lenght test ? your opinion please

 

And status of γH2AX ? wich is used as very reliable to give DNA damage status

 

Is saliva reliable to know what state are generally our others cells ?

 

And finally is it possible to directly reverse this clock biomarker ?

 

thank you !

[neilcopes]

Hi.  Thank you for the questions, and I apologize for the EXTREMELY long delay in responding (a combination of being out of town, along with a wicked head cold).  

 

The main difference between DNA methylation and mtDNA methylation, as far as I’m aware, is that mtDNA methylation has been much less studied.  Likely due to its low levels and higher degree of variability, mtDNA methylation wasn’t fully confirmed by the scientific community until the early 2000s.  As far as age-related methylation is concerned, I know that several mtDNA methylation sites have shown a linear correlation to chronological age (Mawlood SK, et al. 2016), but the coefficient of correlation (the tightness of the scatter in the data) was reported as lower than in other methods.

 

As far as I’m aware, epigenetic methods of chronological age determination are more accurate than telomere length measurements.  Telomere length is affected by multiple factors, including oxidative stress.  (Global DNA methylation too is affected by a huge number of environmental factors, but multiple specific DNA regions seem to be more affected by chronological age than anything else.)  As for y-H2AX, as you stated it is a very reliable marker for double-strand breaks in DNA, and the level of y-H2AX expression has been shown to increase with age until around the age of 57, when it’s increase plateaus (Schurman SH, et al. 2012).  I have not seen y-H2AX levels used as a predictor of chronological age, although I suppose it potentially could be for individuals below 60 years old. 

 

The method I’m using relies on DNA isolated from buccal cells (epithelial cells of the cheek and gums).  From my personal experience, these are more than adequate for purposes of DNA methylation analysis for estimating chronological age.  I can’t state as to how these cells in general compare to other cell types within the body, but if I had to make an educated guess I would say that they are probably fairly similar in physiology and gene expression to other epithelial cells.

 

As to your last question: is it possible to reverse this clock biomarker?  I certainly hope so.  My assumption is that most age-related DNA methylation changes are the result of random epigenetic drift (hypermethylation) and inadequate recovery of epigenetic state after DNA repair (hypomethylation).  Some of these age-related epigenetic changes though likely reflect gene regulation that is part of the general developmental inertia that occurs past puberty (there’s an excellent book by Dr. Richard Walker that discusses this topic – he doesn’t get enough attention in my opinion) as well as cellular changes happening in response to body-wide factors such as senescent cell accumulation and immune system decline.  Likely, any effective antiaging therapy would at least slow those epigenetic changes, if not reverse them entirely.

[Tom Andre F. (ex shinobi)]

Hi,

 

thank you for your answer !

 

I retain this and would need more information about it please:

 

 

 

 

As far as I’m aware, epigenetic methods of chronological age determination are more accurate than telomere length measurements.  Telomere length is affected by multiple factors, including oxidative stress.  (Global DNA methylation too is affected by a huge number of environmental factors, but multiple specific DNA regions seem to be more affected by chronological age than anything else.) 

 

 

Basically you say DNA methylation a better biomarker because less influenced by external factors. However, please share more data or info about this exact sentence "multiple specific DNA regions seem to be more affected by chronological age than anything else"

 

is this though replication ? Mutation ? what protein can influence it ?

 

 

[neilcopes]

I suppose a more accurate way of saying it would be that for certain gene promoters the degree of methylation has an exceptionally high correlation with chronological age, and the strength of this correlation is generally greater than for other biomarkers, such as telomere length.  The best paper on this subject is really the original epigenetic clock paper by Steve Horvath.

Edited by neilcopes, 13 March 2017 - 01:11 PM.

[Mind]

I ordered my analysis today.

[neilcopes]

Wonderful.  Thank you for your support.

[Mind]

Got my results back.

 

Maybe my lifestyle, diet, and exercise are paying some dividends.

 

Chronological age=46

 

Biological age according to DNA methylation=36 (+/- 2.6 years)

 

Anyone else get results back yet?

[hav]

Found this informative article on Aging and DNA Methylation, Jung & Pfeifer (2015)

 

Howard

[Michael]

Neil, as far as I can see from the FAQ on your website and from the below interview with Reason at FightAging!, you are only running a couple of gene promoters, not the 353 CpG sites included in the Horvath "clock" or the 71 included 71 in that by Hannum and colleagues — correct? And you've only validated it against a small number of "friends and family members,"? And you've only looked at its correlation with chronological age — unlike the Horvath or Hannum epigenetic "clocks," you have no evidence that a discordance between age as estimated by your assay and chronological age predicts any hard outcomes such as risk of age-related disease or death in the future — again, unlike the Horvath or Hannum epigenetic "clocks.

 

Right?

 

[Reason]: How did you settle on the particular combination of genes you are testing?

[Neil:] I remembered a 2011 paper from Eric Vilain's lab linking chronological age with a fairly linear trend in methylation in the promoters of a small set of genes. We did a test run using just the TOM1L1 and NPTX2 promoters, which were among the top genes in the paper and fairly easy to work with from a technical standpoint. The initial results looked good so we developed the service from there.

 

[Reason]: You are forging ahead with your own implementation of part of the Horvath approach to epigenetic age; how are you validating it?

[Neil:] We're still a fairly small operation. So far validation has consisted of getting as much saliva as we could from friends and family members, and processing the samples. We then used CpG methylation and known chronological ages to calibrate our model. So far the linear model is estimating samples with an error of 7 years standard deviation from chronological age. The idea then is to continue performing estimates on paid samples and refining the model as necessary, even providing new estimates on older samples so that users can continue to get any refinements to their existing data as time goes on.

 

 

[neilcopes]

Yes, the method we are using is based on the three gene promoters with the tightest correlation to age, as outlined in the 2011 Bocklandt paper (link).  The decision to go with these three tightly-correlated gene promoters as opposed to the full 353 set, or any other set, was primarily a decision of cost.  Three genes can be examined individually with basic lab techniques.  Large sets would require a microarray approach, which would drive the price up dramatically.

 

The mathematical model that we’re using was originally based on a data set of as many friends and family members as we could get (as I said, we’re a small operation).  The data set has expanded since then.

 

As far as I’m aware, there have been no studies looking at a correlation between disease or mortality risk for these three gene promoters – unlike the Horvath or Hannum sets.  Nor are we in a position to make such an investigation ourselves.  We’re offering the service based just on what has been reported and what we have seen – as a measurement of a genetic parameter that corresponds with chronological age.

Edited by neilcopes, 23 June 2017 - 11:59 AM.

[neilcopes]

By the way, we had some longer-than-expected downtime this year due to a move to a new location, renovations, and a hurricane.  We are finally open and taking a small number of orders again.  The discount code for Longecity members still applies.

 

Best regards,

Neil Copes

 

[Turnbuckle]

 

By the way, we had some longer-than-expected downtime this year due to a move to a new location, renovations, and a hurricane.  We are finally open and taking a small number of orders again.  The discount code for Longecity members still applies.

 

Best regards,

Neil Copes

 

 

 

I sent in my sample 3 weeks ago and when I checked this morning, the site said, "New orders are temporarily suspended while we make the final preparations for rolling out the second version of our Osiris Green epigenetic analysis service. We apologize for any inconvenience."

 

So does that mean samples 3-weeks in the pipeline will also be delayed? And if so, by how much?

[neilcopes]

Hi,

 

I actually just sent out a few emails to customers about 15 minutes ago, so you'll probably receive an email from me about this.  We're suspending new orders until we introduce the new service and make the new version of the website live.  In the meantime, we are still processing current orders. 

 

The transition to our new laboratory method unintentionally slowed the analysis of a few orders by an additional one to two weeks.  We hate going past three weeks on sample processing though so I went ahead and initiated a full refund for delayed orders that are at or approaching the three week mark.  Sorry about that.  The delayed samples are currently undergoing DNA sequencing, so results should be posted in about one more week.

 

Best regards,

Neil Copes

[Turnbuckle]

We hate going past three weeks on sample processing ...

 

 

And yet that seems to be the normal situation, as I've submitted a second sample that is approaching a month. That aside, I wonder if this second sample will be comparable with the first given the different sources of cells. The first was saliva (version 2.0) and the second was a gum swab, at least according to the directions on the collection kit. I wonder about that as well, as it is inconsistent with the "cheek cell collection kit" mentioned in the FAQs.

[neilcopes]

Oh no, I am very sorry.  We’ve had two samples in the last several weeks that didn’t pass quality control in the DNA sequencing process and had to be sent back for additional sequencing.  One of those sample is on its third trip back to the sequencing facility as of yesterday morning, so that sample has to be yours.  We need to get better at making sure customers are updated on re-sequencing events, since each one slows the process down a bit.  I sincerely apologize, especially given that your previous sample was greatly delayed due to our lab turnaround.

 

Since your previous sample was version 2.0, the results should be very comparable.  The swab is designed to harvest a small amount of buccal cells (which are gum and cheek cells).  I just updated the FAQ to make the wording clearer on that point, so thank you for point that out.  These cells are always unnoticeably shedding inside the mouth, and are present at a surprisingly high concentration in saliva.  Rubbing a swab along the gums is enough to harvest quite a bit of them, which is what the directions on the collection kit instruct to do, but a sample taken from anywhere within the mouth would also be adequate.  When we first developed version 1.0 of this test, we initially had customers deposit saliva directly into a vial.  As long as DNA is recovered from a mouth-based sample, the process beyond that point is the same and comparable.

[Turnbuckle]

 

Oh no, I am very sorry.  We’ve had two samples in the last several weeks that didn’t pass quality control in the DNA sequencing process and had to be sent back for additional sequencing.  One of those sample is on its third trip back to the sequencing facility as of yesterday morning, so that sample has to be yours.  

 

 

Would having too big a change from a previous test cause it to fail quality control?

[neilcopes]

No, we just need a certain quality of data from DNA sequencing to properly analyze percent methylation and to estimate biological age.  There is a bit of unavoidable variation in the DNA sequencing process, which causes about 10 – 15% of samples to lack usable information.  We’ve tried to account for this in the way we manage samples, but we still get unlucky sometimes.  For instance, occasionally a sample doesn’t just fail once, but twice.

[Turnbuckle]

No, we just need a certain quality of data from DNA sequencing to properly analyze percent methylation and to estimate biological age.  There is a bit of unavoidable variation in the DNA sequencing process, which causes about 10 – 15% of samples to lack usable information.  We’ve tried to account for this in the way we manage samples, but we still get unlucky sometimes.  For instance, occasionally a sample doesn’t just fail once, but twice.

 

If this is truly my sample (ends with a 59) then I wouldn't be surprised if there was a strong bimodal element, due to endogenous stem cell treatments.

[neilcopes]

That is interesting!  The sample that has given us the most trouble does end in 59.  I always expect users on this site to be experimenting with life extension techniques, but the mention of endogenous stem cell treatments caught me off guard.  To be honest, I have NO IDEA what affect that will have on the results, but I am super curious.  We should have the results back from the latest re-sequencing by Friday, so hopefully I can have a definitive analysis for you by then.

[Turnbuckle]

We should have the results back from the latest re-sequencing by Friday, so hopefully I can have a definitive analysis for you by then.

 

 

Thanks. I got the results and posted them in the thread, Reversing the Clocks. One gene plunged in age while two others did not. I assume that if this is due to stem cells, that it is just happenstance that the de novo methylation pattern only included that one gene and not the others.

[neilcopes]

Good!  I was just logging in to tell you the results were ready, but you beat me to it.  : )

[Turnbuckle]

Good!  I was just logging in to tell you the results were ready, but you beat me to it.  : )

 

I'd like to get another follow-up, but I see you are presently closed to new orders. Do you have an estimated date for reopening?

[neilcopes]

I don’t want to give a specific date and then be wrong.  We’re still dealing with a backlog right now, which is why we went ahead and suspended ordering.  I’ll post an update here when I know we’re ready to open up new orders.