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#61 cariaso

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Posted 12 April 2009 - 04:11 AM

Its pretty useless to know your huntington trait status anyway

Not so. Surprising this comes from a sensist.. (hope youre not in charge of anything.. lol)

Identify the physiological consequence of the genetic aberration and correct it by whatever means possible.


whereas that might be good for me as it would give me a research direction, it isn't going to do much for your average Huntington's patient with medicine where it is right now.

In a few more years it will be very valuable.


http://www.pubmedcen...i?artid=2587014
A snp has been identified as linked to 50% of Huntington's cases, and seems to be useful for targetting a siRNA treatment. perhaps a few years = later this year.
http://www.scienceda...90409134754.htm

#62 m86

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Posted 12 April 2009 - 11:27 AM

Thanks for your effort on SNPedia.com and Promethease! I find both to be extremely useful.

For a number of alleles, Promethease says the results are "ambiguous". I gather these are when the common versions are A and T, for example, instead of A and G, so that the convention of which strand to report makes a difference. With 23andme.com, on the "raw data" view, one can click on the "+" sign and it will tell you whether their convention is positive or negative relative to the standard convention. Is there any chance that 23andme.com could provide in the downloaded information the resolution to the ambiguity? Or could Promethease connect to 23andme.com to query the convention on each gene? Maybe one could enter by hand on each SNPedia.com entry what the 23andme.com convention is for each SNP?

Thanks for the work! This is very interesting to me.


See
http://www.snpedia.c.../Ambiguous_flip

http://www.snpedia.c.../Rs1265181(G;G)
is currently the best example of the problem. I expected it would happen between Navigenics and 23andMe users, since those are based on two very different platforms (Affymetrix vs Illumina), but was quite surprised to see it happening between 23andMe and deCODEme since both are based on Illumina.

Is is important to me that SNPedia/Promethease remain able to work with all platforms, not just 23andMe. The most direct route to a solution is for 23andMe to write a + or - onto each line of their raw data file. With that change I could adapt Promethease in a matter of minutes to eliminate this problem for that platform. In time the other platforms would probably follow. Please consider telling 23andMe that this is an important feature for you.


hmm.. feel free to correct me if I'm off-base, but isn't the 23andme data (all of it) already formatted +ly?

# This data file generated by 23andMe at: Tue Nov 11 19:52:52 2008
#
# Below is a text version of your data. Fields are TAB-separated
# Each line corresponds to a single SNP. For each SNP, we provide its identifier
# (an rsid or an internal id), its location on the reference human genome, and the
# genotype call oriented with respect to the plus strand on the human reference
# sequence. We are using reference human assembly build 36. Note that it is possible
# that data downloaded at different times may be different due to ongoing improvements
# in our ability to call genotypes.
#
# More information on reference human assembly build 36:
# http://www.ncbi.nlm....i...06&build=36

Edited by m86, 12 April 2009 - 11:28 AM.


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#63 Brainbox

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Posted 13 April 2009 - 11:21 AM

As version 0.1.50+ there is the ability to pay $2 and speed things up. This works by downloading a single file cache containing a compressed version of much of the information in SNPedia. Since its a single request and compressed it runs faster, but as a side benefit there is no need to request the pages for your genotypes. This greatly improves your privacy, and leaves SNPedia with no way to know what genotypes you have. However since the cache is not yet perfectly up to date, nor fully comprehensive, during even paid Promethease runs most users will need to request a *few* genotypes directly from SNPedia, which leaks some information.Even for a perfect cache which doesn't need to read any pages, most users will eventually click through with their webbrowser to look at the full details of some of their genotypes. Again this leaks information into the server logs.

I did try the version that is currently available and it works. The first time it didn't, I suppose because I placed the files in an encrypted (TrueCrypt) folder. This is useless anyway, better to store it there afterwards and restart your computer. I must say that I like the comprehensive overview, especially if compared against the navigation prone 23andme user interface. And it has more information. On the flip-side, if you are concerned about security (wearing tin-foil hats or not), I'm sure this program currently does not offer the same level of security that is provided by 23andme and submitting some fake data would be a good thing to obfuscate ISP URL logs.

I did find some more minor health risks (about x3 factor) that can be compensated by applying healthy lifestyle. I also seem to have all the known SNP's variants that are correlated with high intelligence. I seem to be a major nerd. :)

Furthermore, in general, I think that risks > factor x10 should be taken seriously, below that it's just some form of indication that can be used to adapt lifestyle for compensation. Any more thoughts on this?

If you are fond of tinfoil toques Promethease may not yet be for you. ...

Hmmm, given the current culture and structure of society, you don't need to display that kind of behaviour while still being legitimately concerned about security. But I agree, talking to younger people about these issue's, I'm convinced that the current fear of exposing sensitive data will decline within one or two generations, provided that structure and operations of health risk management does change in equal pace.

Edited by Brainbox, 13 April 2009 - 11:24 AM.


#64 cariaso

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Posted 13 April 2009 - 11:54 AM

Thanks for your effort on SNPedia.com and Promethease! I find both to be extremely useful.

For a number of alleles, Promethease says the results are "ambiguous". I gather these are when the common versions are A and T, for example, instead of A and G, so that the convention of which strand to report makes a difference. With 23andme.com, on the "raw data" view, one can click on the "+" sign and it will tell you whether their convention is positive or negative relative to the standard convention. Is there any chance that 23andme.com could provide in the downloaded information the resolution to the ambiguity? Or could Promethease connect to 23andme.com to query the convention on each gene? Maybe one could enter by hand on each SNPedia.com entry what the 23andme.com convention is for each SNP?

Thanks for the work! This is very interesting to me.


See
http://www.snpedia.c.../Ambiguous_flip

http://www.snpedia.c.../Rs1265181(G;G)
is currently the best example of the problem. I expected it would happen between Navigenics and 23andMe users, since those are based on two very different platforms (Affymetrix vs Illumina), but was quite surprised to see it happening between 23andMe and deCODEme since both are based on Illumina.

Is is important to me that SNPedia/Promethease remain able to work with all platforms, not just 23andMe. The most direct route to a solution is for 23andMe to write a + or - onto each line of their raw data file. With that change I could adapt Promethease in a matter of minutes to eliminate this problem for that platform. In time the other platforms would probably follow. Please consider telling 23andMe that this is an important feature for you.


hmm.. feel free to correct me if I'm off-base, but isn't the 23andme data (all of it) already formatted +ly?

# This data file generated by 23andMe at: Tue Nov 11 19:52:52 2008
#
# Below is a text version of your data. Fields are TAB-separated
# Each line corresponds to a single SNP. For each SNP, we provide its identifier
# (an rsid or an internal id), its location on the reference human genome, and the
# genotype call oriented with respect to the plus strand on the human reference
# sequence. We are using reference human assembly build 36. Note that it is possible
# that data downloaded at different times may be different due to ongoing improvements
# in our ability to call genotypes.
#
# More information on reference human assembly build 36:
# http://www.ncbi.nlm....i...06&build=36


It is oriented to the human reference assembly, build 36. Unfortunately re-builds frequently occur (hence the 36), and that assembly is not the basis of the dbSNP orientations. Since dbSNP is who created the rs# we've decided to use that as the ultimate authority. As an example:

The very first snp in your 23andMe raw data is probably reported as
rs3094315 1 742429 AA
which has a corresponding dbSNP entry at
http://www.ncbi.nlm.....cgi?rs=3094315

while 23andMe calls it as A/G, you'll see that the dbSNP record calls it as a C/T snp.

I can't blame 23andMe, the notation introduced by dbSNP is is just not sufficiently unambigous.
Illumina has an unambigous, but painful solution
http://www.illumina....note27Jun06.pdf
while even the primary papers often mess this up
http://www.ncbi.nlm....1?dopt=Abstract

#65 cariaso

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Posted 13 April 2009 - 12:12 PM

I did try the version that is currently available and it works. The first time it didn't, I suppose because I placed the files in an encrypted (TrueCrypt) folder.

If you can reproduce the failure please tell me more about it.

This is useless anyway, better to store it there afterwards and restart your computer. I must say that I like the comprehensive overview, especially if compared against the navigation prone 23andme user interface. And it has more information. On the flip-side, if you are concerned about security (wearing tin-foil hats or not), I'm sure this program currently does not offer the same level of security that is provided by 23andme and submitting some fake data would be a good thing to obfuscate ISP URL logs.


23andMe needs strong security since they store your information, need to keep it linked to your name/email, and are in the business of making it accessible. That large central repository makes a very attractive target. Promethease has no need to store your information, and has no central target for hackers. SNPedia may eventually need to scrub its logs, but I think that is still a bit premature, relative to the value those logs provide me.


Furthermore, in general, I think that risks > factor x10 should be taken seriously, below that it's just some form of indication that can be used to adapt lifestyle for compensation. Any more thoughts on this?


Hard and fast rules are too simplistic. Firstly 10x is only a magic number because of how many fingers you have. A 20x risk factor may not matter if there is simply nothing that can be done, or if the effect isn't medical (ie 50x risk of freckles). 10x risk matters more for semi-common diseases, then for truely rare ones (your odds of disease X just went from 1 in 10 billion to 1 in 1 billion). What matters most is the ill defined concept of 'actionableness'. This is most relevant for medicines, since they influence future decisions, and this is why the box about medicines is above the box about medical conditions.

Hmmm, given the current culture and structure of society, you don't need to display that kind of behaviour while still being legitimately concerned about security. But I agree, talking to younger people about these issue's, I'm convinced that the current fear of exposing sensitive data will decline within one or two generations, provided that structure and operations of health risk management does change in equal pace.


I think of it as the facebook effect. David Brin has an excellent book on the topic The_Transparent_Society. However, Bruce Schneier has some excellent critisms of the work. I generally trust Schneier as one of the true authorities on all things security related, but we're all trying to read a crystal ball here.

#66 maestro949

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Posted 17 April 2009 - 09:07 PM

23andMe in the Economist. Dr. Church predicts that these services will eventually be Free in order to up-sell other services.

I found this strikingly odd:

But Novartis’s Dr Vasella still rejects the notion of personalised medicine, pointing out that it would be economic folly for firms to develop a special pill for every patient. He accepts that linking individual genetics with specific therapies is the big challenge for his industry today, but he is still looking for a suitable business model.


A special pill for every patient? This guy works for a drug company?!?

#67 Brainbox

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Posted 17 April 2009 - 09:54 PM

23andMe in the Economist. Dr. Church predicts that these services will eventually be Free in order to up-sell other services.

I found this strikingly odd:

But Novartis’s Dr Vasella still rejects the notion of personalised medicine, pointing out that it would be economic folly for firms to develop a special pill for every patient. He accepts that linking individual genetics with specific therapies is the big challenge for his industry today, but he is still looking for a suitable business model.


A special pill for every patient? This guy works for a drug company?!?

The real problem could be that if pills are prescribed more efficiently due to decreased trial-and-error, they're going to sell less pills. What is needed is a paradigm shift in economics that quality is the prime driver to generate returns, not quantity.

#68 cariaso

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Posted 18 April 2009 - 06:09 AM

Since I fumbled the last release I thought I'd try and do an actual beta and announce it here first.

http://www.snpedia.c...php/Promethease

now has links for 0.1.57. This version should work just like the old one, but has 2 important new features.

1. There is now a button in the upper left labeled 'Wizard'. Clicking on this will use a new experimental wizard workflow. Some people really hate wizards
http://msdn.microsof...31.aspx#wizards
but in this case I think it is a better approach. Opinions welcome.

2. If you use the wizard and pay the $2, there is the ability to generate a report which only shows articles which have changed since a specified date. This should help to draw attention to only things which have changed since your last run. Be warned that (as of April 18) the cache has not been updated since roughly April 1. Therefore the absolute newest changes won't show. This will be fixed on the server side shortly. This feature is of no use to first timers, but should be valuable for people who want to check their results on a recurring basis.

#69 eternaltraveler

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Posted 18 April 2009 - 09:43 PM

thanks for creating these tools cariaso.

If I may ask how did you end up stumbling on our forum and do you have any interest in the subject matter?

#70 cariaso

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Posted 19 April 2009 - 01:17 AM

thanks for creating these tools cariaso.

If I may ask how did you end up stumbling on our forum and do you have any interest in the subject matter?


I found you via inbound traffic from my server logs. A few years ago I attended a few of the foresight gatherings and became familiar with alcor, uploading, transhumanism, and topics which I consider related to this forum. I'm well aware of Aubrey de Grey and consider the Methuselah mouse project to be a valuable scientific goal. But I confess my own beliefs on this topic seem to align with Randal Munroe - http://xkcd.com/568/ . My hope is that despite being something of an outsider, there may be a valuable overlap in our respective goals. It is not my intention to crash a party where I am not invited.

#71 eternaltraveler

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Posted 19 April 2009 - 02:56 AM

It is not my intention to crash a party where I am not invited.


on the contrary, you are very much invited. I hope I didn't somehow imply otherwise? I was only curious when some of us started wondering how to use your tools and then suddenly you were here explaining and updating (which I appreciated).

I'm certainly not remotely sure we'll get it done in the next 80 years either. I happen to think it's a worthy goal to work in the direction of even without total success in the lifetime of anyone alive today as aging causes more suffering than anything else. And I view suffering as bad.

#72 cariaso

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Posted 27 May 2009 - 04:56 PM

http://www.medpageto...motherapy/14391
This cancer treatment erases fingerprints. This seems relevant to imminst.

Promethease 0.1.66 recently.

#73 woly

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Posted 31 May 2009 - 03:58 AM

Zoolander or Ben-AUS, Have you guys tried this? I was looking on their website and they now say they ship to Australia!

#74 StrangeAeons

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Posted 04 June 2009 - 05:14 PM

Curious to see if I can get my parents to try this, or help fund me to try this; we're homogenous Ashkenazic Jews, so we come from a very limited gene pool; we also have a high rate of mood disorders, especially on my father's side. I imagine the profile would look very unique.
Actually, now that I think about it, they already had my little sister tested for genetic issues specific to our ethnicity. I doubt it would be that much of a stretch to try this version out, where you get a much more complete picture.

#75 m86

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Posted 09 March 2010 - 10:53 PM

bumping just to spam 23andMe's temporary (exp. 3/31) discount targeted at Oprah viewers (perhaps someone would be interested).

https://www.23andme.com/partner/foa/

the ancestry edition is $199 with the offer, however, you can add the complete edition to the cart (removing the ancestry edition afterwards) and purchase that instead for $299

#76 James Cain

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Posted 10 March 2010 - 01:02 AM

the ancestry edition is $199 with the offer, however, you can add the complete edition to the cart (removing the ancestry edition afterwards) and purchase that instead for $299

Been considering something like 23andme lately, but this really seals the deal. Got two complete tests for me and the woman, $300 each. $200 discount each using this method!

#77 StrangeAeons

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Posted 20 March 2010 - 08:04 AM

bumping just to spam 23andMe's temporary (exp. 3/31) discount targeted at Oprah viewers (perhaps someone would be interested).

https://www.23andme.com/partner/foa/

the ancestry edition is $199 with the offer, however, you can add the complete edition to the cart (removing the ancestry edition afterwards) and purchase that instead for $299


Thanks for the mention, I was about to get 23andme anyways, you just saved me $200!

#78 Apchi

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Posted 26 March 2010 - 02:38 AM

Having recently reviewed the results of my analysis I have to say I'm a bit disappointed.
Mostly interesting stuff like Haplogroup, carrier status for a few things.

No major revelations. Many things I already know like ethnicity, hair and eye color. Acouple of things might be off; I didn't know I was lactose intolerant...(I eat plenty dairy w/o issues).
Having tiny percentage over or under the population for getting certain conditions isn't really useful.
Maybe I'm a bit lucky to have such a boring report but for some reason expected more...

Hopefully new data coming down in the future from further research may be more eye opening. I've noticed that they added new stuff to the analysis withing the first day so this is encouraging.


Would like to hear others' experiences as well.

#79 niner

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Posted 26 March 2010 - 03:00 AM

I'd like to know all of the SNPs that are relevant to nutrigenomics. Would the Ancestry edition tell me the status of all known SNPs or just things that relate to ancestry?

#80 m86

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Posted 26 March 2010 - 06:31 AM

The Ancestry edition is indeed locked into only features pertaining to Ancestry (Relative Finder, haplogroups, Ancestry Painting, etc etc). You can't get any of 23andMe's health related interpretations of the data (of which almost none are nutrigenomically inclined) and only the full version can download and access the raw data (and get 3rd party interpretations thereof).

#81 Apchi

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Posted 26 March 2010 - 03:08 PM

After running 23andMe raw data via the Promethease application(4 hours) and reviewing the results I'm very impressed.

First impressions:

A lot more comprehensive than the 23andme report. On the common items analyzed it's usually in line with the 23andme interpretations. In addition, many more important markers analyzed and seems to be valid based on what I know about myself and family history.

Some few items are reporting opposing results compared to the 23andme report; for example, longevity was typical on 23anmde while it's supposed to be exceptional based Promethease.

Also, the main disease items highlighted in the reports were different.

My first impression is that Promethease analysis is substantially more comprehensive and likely much more useful than the one given to me by 23andMe. At the very least it a different view and interpenetration of your data and it's free.

Strongly recommended for people who have the raw data available.

#82 niner

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Posted 26 March 2010 - 09:54 PM

My first impression is that Promethease analysis is substantially more comprehensive and likely much more useful than the one given to me by 23andMe. At the very least it a different view and interpenetration of your data and it's free.

Strongly recommended for people who have the raw data available.

Well that's interesting, considering that places like 23andMe are mostly selling annotation. A simple SNP scan is probably a commodity item at this point. I'll bet 23andMe farms that out to a lab somewhere, and it's probably pretty cheap in quantity. We just need to find a place that will generate the data in a no-frills manner for a good price.

#83 StrangeAeons

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Posted 27 March 2010 - 04:25 PM

My first impression is that Promethease analysis is substantially more comprehensive and likely much more useful than the one given to me by 23andMe. At the very least it a different view and interpenetration of your data and it's free.

Strongly recommended for people who have the raw data available.

Well that's interesting, considering that places like 23andMe are mostly selling annotation. A simple SNP scan is probably a commodity item at this point. I'll bet 23andMe farms that out to a lab somewhere, and it's probably pretty cheap in quantity. We just need to find a place that will generate the data in a no-frills manner for a good price.


23andme uses LabCorp. Says so right on the website; as per the price, I doubt there's enough leverage amongst us to get a significant saving. Aside from that, I already bought my complete kit (saliva's sitting in my mailbox as we speak) using the Oprah deal for $300 + S&H

#84 1kgcoffee

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Posted 27 March 2010 - 04:51 PM

Thanks for posting that deal m86. Just ordered, can't wait!

#85 AgeVivo

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Posted 27 March 2010 - 05:02 PM

My first impression is that Promethease analysis is substantially more comprehensive and likely much more useful than the one given to me by 23andMe.

I fully agree with Apchi. For those who are still hesitating, here is an example of report from someone who decided to post it online: http://www.snpedia.c...can_pooled.html . 300$ and a few weeks away...

#86 AgeVivo

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Posted 31 March 2010 - 07:16 PM

bumping just to spam 23andMe's temporary (exp. 3/31) discount targeted at Oprah viewers (perhaps someone would be interested).

https://www.23andme.com/partner/foa/

the ancestry edition is $199 with the offer, however, you can add the complete edition to the cart (removing the ancestry edition afterwards) and purchase that instead for $299


Thanks for the mention, I was about to get 23andme anyways, you just saved me $200!

last day for the 200$ discount! March 31st. Hurry up!

Edited by AgeVivo, 31 March 2010 - 07:16 PM.


#87 cariaso

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Posted 13 July 2010 - 12:13 PM

on the contrary, you are very much invited. I hope I didn't somehow imply otherwise? I was only curious when some of us started wondering how to use your tools and then suddenly you were here explaining and updating (which I appreciated).

I'm certainly not remotely sure we'll get it done in the next 80 years either. I happen to think it's a worthy goal to work in the direction of even without total success in the lifetime of anyone alive today as aging causes more suffering than anything else. And I view suffering as bad.




I've registered for the 10-10-10 conference and wanted to use this as a chance to meet other ImmInst members who use Promethase.

#88 AgeVivo

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Posted 08 August 2010 - 11:31 AM

I've registered for the 10-10-10 conference and wanted to use this as a chance to meet other ImmInst members who use Promethase.

Happy to see you there!
Perhaps we can ask if it is not too late for you to make a presentation there, or more simply a series of questions and answers?
I think many persons would here are very interested in what their genes tell in terms of disease and drug sensitivity
And Promethease is just wonderful!

#89 cariaso

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Posted 12 August 2010 - 04:05 PM

I've given Promethease presentations at many conferences, and if there is interest I woud be happy to prepare one for this as well. I'm not sure of the format or venue, but I can squeeze the essentials into 10 minutes, go deep in an hour, or cover anything in between which fits your interest an availability.

cariaso@snpedia.com




I've registered for the 10-10-10 conference and wanted to use this as a chance to meet other ImmInst members who use Promethase.

Happy to see you there!
Perhaps we can ask if it is not too late for you to make a presentation there, or more simply a series of questions and answers?
I think many persons would here are very interested in what their genes tell in terms of disease and drug sensitivity
And Promethease is just wonderful!





Click HERE to rent this GENETICS advertising spot to support LongeCity (this will replace the google ad above).

#90 AgeVivo

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Posted 12 August 2010 - 11:02 PM

Carioso, I transmitted your message, that would be great!!!

Promethease Wins 23andMe "Crystal Ball" Personal Genomics Contest
"Judged by accuracy, creativity, and cleverness, Cariaso's entry was deemed "the clear winner in all three categories".


DNA tests is the type of thing that is transforming the world towards long and healthy lives:
  • people can be aware of their potential diseases and sensitiveness to drugs, they may positively influence their life and towards long and healthy lifespans
  • possibly more importantly, the collective awareness of what is important in health, driven by those DNA tests, may actually change things by a lot:
  • when some biomedical research or clinical trial for important diseases is presented anywhere, many people who have done such tests will be interested and as a result the focus of governments will be better redirected towards important health improvements. Today people often don't even pay attention...
  • in those tests people discover this truth: that the danger is concentrated at high ages and that the leading trouble so far is just... aging.

So, although it first sounded too fast to me, I really hope it will enter supermarkets soon.
Communication about them is key. DNA test should be mandatory for all! (*partly* joking)
Anyway, you surely have your own slides to astonish us!
Posted Imagehttp://www.prweb.com...prweb962884.htm

Edited by AgeVivo, 12 August 2010 - 11:15 PM.


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