90 replies to this topic

[zoolander]

They do add new research findings, but the DNA profiling is incomplete

for the average Joe this is not the case. You get information on 500,000 markers.

Additionally, the pricing has been the biggest hurdle for most. Pointing out that the DNA profiling is not complete for a US$400 price mark is like paying for a $10,000 car and stating that the fit out is not complete because it didn't have rain sensing wipers, a tiptronic gear box or GPS guided auto pilot.

If people are prepared to wait another 2 years then they can more likely get their entire genome sequenced for around $1000 instead of paying the current $350,000 (1)

[Brainbox]

Pointing out that the DNA profiling is not complete for a US$400 price mark is like paying for a $10,000 car and stating that the fit out is not complete because it didn't have rain sensing wipers, a tiptronic gear box or GPS guided auto pilot.

If people are prepared to wait another 2 years then they can more likely get their entire genome sequenced for around $1000 instead of paying the current $350,000 (1)

I guess you're right, but I didn't start participating traffic in a BMW either, but on an old bicycle.
It's fun to know at least something about your background and genetic properties.

Edit:

Actually, thinking of it, this was my first form of motorised biking, lots of fun when you're 14 (if the brakes would function properly, that is). Not exactly health promoting material.

Edited by Brainbox, 24 December 2008 - 01:12 AM.

[drmz]

Hello,

We plan to create additional Health and Traits articles as more research data becomes available and undergoes our review process. Though we cannot predict which topics will be covered in the future, we will make additional information available to you at no additional cost as long as the SNPs related to the genetic associations for the traits and conditions in question are included on the DNA chip used to process your saliva sample. Under these circumstances our existing customers will not need to undergo additional testing or need to provide new saliva samples.

Though many of our current and planned Health and Traits articles deal with medical issues, it is important to remember that the feature is neither a diagnostic tool nor a substitute for a physician's advice.

Regards,
The 23andMe Team

Edited by drmz, 24 December 2008 - 06:18 AM.

[zoolander]

It's fun to know at least something about your background and genetic properties.

I'm assuming you haven't received your results as yet because for a large percentage of the population (one would assume) the results from 23andme (500,000 markers) are more than enough and certainly a lot more than "at least something".

[Brainbox]

It's fun to know at least something about your background and genetic properties.

I'm assuming you haven't received your results as yet because for a large percentage of the population (one would assume) the results from 23andme (500,000 markers) are more than enough and certainly a lot more than "at least something".

I get the feeling this is becoming a lexical language issue. I'm almost certain we agree!

[Brainbox]

I did receive the results the other day. I must say that I'm not disappointed at all.

The health issue of which my risk was elevated by a factor 2 to 3 wrt. the general population is already reality. I'm really stunned about that since this is the only annoying health issue I currently have and the only one with elevated risk according the related SNP's (of the non-research categories).
I'm also prone to becoming obese, but I figure that's going to happen in case I actually start eating to much. I'm at the very low end of the BMI scale at the moment....

I will check the ability to control the information when you set up a share of the information with others. If there's sufficient control over what information you give away and still share a significant part of the genome, it would perhaps be nice to share our genomes to figure out what SNP is responsible for joining imminst. And to discus some more serious aspects. But to be honest, I'm quite hesitant to that at the moment.

[Prometheus]

How did you score on the OCD trait? (I'm an OC and didnt know it.. but perhaps others around me did)

Also, were you breast fed sufficiently?

Anyway, heres my intelligence gene scores:

Measures of intelligence: rs363050 AA (+3 IQ)
Episodic Memory: rs17070145 CC (typical - I wonder if thats why I can never remember peoples names..)
Effect of breastfeeding on IQ: rs174575 CC (+6/7 if breastfed (yeeha - 1 yr))

Now it occurred to me that based on two of the above SNPs is it possible to discriminate genetically for up to 10 IQ points - is that GATTAGAish or what? Imagine what happens when the rest of the intelligence SNPs are identified. Who needs an academic transcript when you can just offer a DNA sample for entry into higher learning.. Or certain jobs.. Genie is out of the bottle.

[eternaltraveler]

Who needs an academic transcript when you can just offer a DNA sample for entry into higher learning

eh

Who needs a transcript when you can administer an IQ test in an interview. Only you can't. Because the supreme court determined that is discriminatory in the 70s. Course that's just america.

I wish they had the SNP to determine apoE4 carrier status. You can check apoE2 status though which has some of the effect of negating the effects of apoE4 if present. I have one copy of apoE2 and one unknown.

[Prometheus]

Who needs an academic transcript when you can just offer a DNA sample for entry into higher learning

eh

Who needs a transcript when you can administer an IQ test in an interview. Only you can't. Because the supreme court determined that is discriminatory in the 70s. Course that's just america.

I wish they had the SNP to determine apoE4 carrier status. You can check apoE2 status though which has some of the effect of negating the effects of apoE4 if present. I have one copy of apoE2 and one unknown.

You can do it yourself. In fact theres a single SNP you can use to test for the epsilon 4 variant. If you tell me the lab gear you have access to at the uni youre at I can suggest suggest reagents and primers/probe.

[kismet]

Who needs an academic transcript when you can just offer a DNA sample for entry into higher learning.. Or certain jobs.. Genie is out of the bottle.

I'd assume IQ is not everything, which is the reason why everyone has the right to attend university in my country.

Does the 23andMe test show Huntington risk? The disease develops due to several repeats of a nucleotide sequence, so it's not an SNP. Wouldn't it be nice to know wether you have a fatal and uncurable disease?

[maestro949]

Does the 23andMe test show Huntington risk?

No Huntington's. I searched for rs17781557 in my SNP data and it didn't show up. Navgenics nor Decode doesn't report on it either according to Eupedia.

There was a lot of hype over a case where a girl found out she had the gene for Huntington's a couple of year's back and was traumatized from the news. I wonder if that's why it is not included.

Edited by maestro949, 10 March 2009 - 11:28 PM.
typo

[eternaltraveler]

Does the 23andMe test show Huntington risk?

if you know who your parents are you already know your huntington's risk

[kismet]

Does the 23andMe test show Huntington risk?

if you know who your parents are you already know your huntington's risk

That would be my guess too, but from the wikipedia article I conclude that there are two exceptions a. de novo mutation (extremely rare) and b. an intermediate/unaffected genotype changes through addition of CAG repeats (not so rare, ~10% according to them).
Unfortunately there's also dozen of other trinucleotide repeat disorders.

There was a lot of hype over a case where a girl found out she had the gene for Huntington's a couple of year's back and was traumatized from the news. I wonder if that's why it is not included.

What a horrible story, how can you not deal with it? It's in your genes and always was there. Pathetic hype is what it really is.

[eternaltraveler]

Its pretty useless to know your huntington trait status anyway

[kismet]

Its pretty useless to know your huntington trait status anyway

That ocurred to me too! But.. but it's better than not knowing. I mean there could be experimental prevention strategies worth trying and one would need to get a cryonics contract ASAP. I don't know if there are any prevention stratgies, though, as I don't have huntington. At least I think so.
Just thought there might be some things that SNP tests are missing, on the other hand, I remember James Watson was quite cynical about his fully sequenced genome not even adding one year to his life expectancy.

[Prometheus]

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.

[Brainbox]

tip.

[Gerald W. Gaston]

Up to $200 in my 23andMe fund... so a few more paychecks and I will join the club.

I have a step-sister who's mother and aunts all had Huntington's. One of the aunts committed suicide after finding out. My step-sister hasn't been tested and says she doesn't want to know. I guess she is more likely to find out soon enough as she is in her 40s now.

On a lighter note, if it were viable now, a cryogenics type service aimed at the physically healthy (instead of dead) like this IceLift 'might' make sense in cases such as these if one started to develop symptoms:

IceLift...leave today and come back after 50 years

Unless it was something like a condition such as this, I couldn't see giving up living your life now for some hope of it being better in the future.

[Brainbox]

tip.

I tried it and it crashed. In addition, security is not optimal if you think that's important. At least use an encrypted folder on your computer to store the data, which makes it a bit safer. But if it's not working that's all of no use.

[eternaltraveler]

tip.

I tried it and it crashed. In addition, security is not optimal if you think that's important. At least use an encrypted folder on your computer to store the data, which makes it a bit safer. But if it's not working that's all of no use.

I couldn't get it to work either

[eternaltraveler]

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.

Edited by eternaltraveler, 06 April 2009 - 06:27 PM.

[Gerald W. Gaston]

I tried it and it crashed. In addition, security is not optimal if you think that's important. At least use an encrypted folder on your computer to store the data, which makes it a bit safer. But if it's not working that's all of no use.

What version did you try? And were you using your own data or the sample?

There is no resource version info in the exe, but the window title apparently shows the version number. Although the screen shots show 1.49, and the text about the download links indicate 1.55, what you get today is shown as 1.29

I see 1.45 is still in their archives.

[Brainbox]

I tried it and it crashed. In addition, security is not optimal if you think that's important. At least use an encrypted folder on your computer to store the data, which makes it a bit safer. But if it's not working that's all of no use.

What version did you try? And were you using your own data or the sample?

There is no resource version info in the exe, but the window title apparently shows the version number. Although the screen shots show 1.49, and the text about the download links indicate 1.55, what you get today is shown as 1.29

I see 1.45 is still in their archives.

Yes, it's all quite "funny". The level of trust that I have went down to below zero. After all, it's sensitive data we're talking about here. I would not recommend it at this moment.

[cariaso]

Yes, it's all quite "funny". The level of trust that I have went down to below zero. After all, it's sensitive data we're talking about here. I would not recommend it at this moment.

Sorry to have squandered your trust. 0.1.55 for windows is now correctly in place.
http://www.snpedia.c...php/Promethease
Perhaps it'll restore some of the faith for a few of you.

[Brainbox]

Yes, it's all quite "funny". The level of trust that I have went down to below zero. After all, it's sensitive data we're talking about here. I would not recommend it at this moment.

Sorry to have squandered your trust. 0.1.55 for windows is now correctly in place.
http://www.snpedia.c...php/Promethease
Perhaps it'll restore some of the faith for a few of you.

I assume you're from the SNPedia site? Great example of the benefits of crowdsourcing! Very much appreciated.
If you're the developer of Promethease, could you explain how the personal data is compared with the info on the site? I assume the general SNP information is downloaded by Promethease from SNPedia and no personal data is transmitted? Would it be possible to give more information about security?

[cariaso]

I assume you're from the SNPedia site? Great example of the benefits of crowdsourcing! Very much appreciated.
If you're the developer of Promethease, could you explain how the personal data is compared with the info on the site? I assume the general SNP information is downloaded by Promethease from SNPedia and no personal data is transmitted? Would it be possible to give more information about security?

I'm the programmer who wrote Promethease, as well as being the guy who setup and maintains the SNPedia webserver. Both exist to help me make sense of my own DNA.

Promethease reads the file formats of the various companies, and checks to see which SNPs are known in SNPedia. It then builds a single .html file report based on what it learns. If your 23andMe file says that you are
rs4680 AA
then Promethease needs to read the page
http://www.snpedia.c...php/Rs4680(A;A)
from SNPedia, just like you would if you were doing this by hand. As a result the webserver logs have a record that you looked at rs4680(A;A). This then implies that you are probably rs4680(A;A) and not rs4680(A;G) or rs4680(G;G). So while no personal information is transmitted per-se, the specific requests you make do 'leak' your genotypes.

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.

In time I hope to ensure that the cache is fully comprehensive (mainly for performance and freshness reasons). I'd also like to scrub the ip/genotypes from my logs. But I'm a strong believer in release early, release often and Promethease wouldn't exist at all if I had to wait until every case was covered.

This has always been documented at
http://www.snpedia.c...ethease/privacy
which is linked to from
http://www.snpedia.c...php/Promethease
where you downloaded Promethease. The recent performance enhancements justify making a few additions to that page, which I'll do shortly. If you have further questions and want to ensure they get addressed, its better to leave them there.

I don't blame you for being security conscious. I am as well, which is why that document has existed since May of 2008
http://www.snpedia.c...;action=history
But I've been amazed at how many people are comfortable sharing their information
http://www.snpedia.c...dex.php/Genomes
and am grateful for the valuable test data they have provided.

If you are fond of tinfoil toques Promethease may not yet be for you. If you can't wait, I'd suggest doctoring a few 23andMe files, and running promethease a few times, from various coffee shops in foreign countries. You alone will know which file was real, and the rest will serve as chaff http://en.wikipedia....g_and_winnowing

[nootrope]

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.

[trumann]

I'm the programmer who wrote Promethease, as well as being the guy who setup and maintains the SNPedia webserver. Both exist to help me make sense of my own DNA.

Wow.. That's a fantastic effort. I remember snpedia's humble beginnings and wondering how long it was going to last for. I've used your program and found it quite informative. If you can web 2-ify it you'll have every 23andme customer cross checking their file on your interpreter. The question that must be in your mind is how to generate some revenue from it..

[cariaso]

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.

[cariaso]

I'm the programmer who wrote Promethease, as well as being the guy who setup and maintains the SNPedia webserver. Both exist to help me make sense of my own DNA.

Wow.. That's a fantastic effort. I remember snpedia's humble beginnings and wondering how long it was going to last for. I've used your program and found it quite informative. If you can web 2-ify it you'll have every 23andme customer cross checking their file on your interpreter. The question that must be in your mind is how to generate some revenue from it..

What does web2.0ify it mean in this context?

SNPedia generates revenue from the google adwords across the bottom of each page. Promethease generates revenue via the $2 click. Both revenue streams are modest, but enough to keep the server up.

The CC license on the site, and the instructions for how to scrape in the FAQ, mean that even if we did, others would be free to rehost the data elsewhere non-commercially. So there is little danger of it going away.