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» LymeNet Flash » Questions and Discussion » Medical Questions » 23andme Raw Data Analysis Fun

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Author Topic: 23andme Raw Data Analysis Fun
Judie
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I just got my raw data and it's been a hoot to plug it in places to see what it all means.

Since 23andme isn't doing the health analysis part anymore, I figured I'd start a thread on where to go now and what people experience.

Here's what I've done so far:

Nutrahacker (free for basic detoxification/methylation report, $37 for in depth)
https://www.nutrahacker.com/

I just did the free report and there was more info than I expected. There is some supplement information offered.

It also said I was slow to metabolize certain drugs (this is also shown on the promethease site with more specific information).

One interesting thing it said was to avoid curcumin. The time I tried to take curcumin for several months it did nothing for me and may have aggravated some problems.

Taurine was another one that seemed to make me worse and it was on the avoid list.

Promethease ($5 paid through amazon)
https://promethease.com/ondemandagreed

Copious amounts of information on EVERYTHING. It divides the genes into good, bad and uncategorized. I suggest watching the how-to video. It also tells you how much the gene is likely to effect you (magnitude of 4 is likely).

The video said the "bad" was more interesting. Wrong for me. I loved reading "good" things about my genes.

It had some very obscure predictions even for personality and eye color that were accurate.

It also covered drugs that my body doesn't metabolize correctly.

Eupedia (free, clunky to navigate but good info)
http://www.eupedia.com/genetics/autoimmune_diseases_snp.shtml

Shows the genes involved for everything from autoimmune illnesses to physical and health-related traits.

I looked up porphyria and celiac which I've always been curious about.

Download the SNPtips add on (only works in firefox) and your gene results will show up right next to each category. You can then click on them to compare your data.

SNPtips instructions:
http://snptips.5amsolutions.com/help/

SNPtips can be enabled to work on ANY webpage too.

GEDmatch (free)
http://gedmatch.com/

It seems more for comparing various kits. There's a section on rare genes. Not much info I could make sense out of except what origin the gene came from.

I found the eye-color predictor interesting. It got the color wrong, but I could submit a picture to help the makers improve their system.

Genetic Genie (free/donation)
http://geneticgenie.org/

It just shows the genes that are homozygous and heterozygous for methylation without any useful health analysis.

I did find this sample report on genova and was able to use the data from genetic genie for further analysis:

***update - unfortunately the drug interaction part of this test has been deleted online.***
http://www.gdx.net/core/sample-reports/Detoxi-Genomics-Sample-Report.pdf

While the information on this page doesn't completely match mine, one of them did.

It was CYP1B1 and it pretty much matched some things I already knew. I had a bad reaction to rifampin and that was actually listed as a possible problem for me on the page.

Here's someone else's report for methylation/detoxification (using yasko info, genetic genie and 23andme). Again, only a couple matched mine, but some useful info:

http://www.gestaltreality.com/2013/03/17/my-nutrigenomic-analysis/

Have fun!

[ 09-06-2014, 05:58 PM: Message edited by: Judie ]

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BuffyFan
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so you were able to plug the raw data using these websites and is that how you get your health info?
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Judie
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Each website has a different set of instructions. Some connect directly to 23andme, while others you need to download your report on to your computer and then direct the site where to go in your files.

The only odd ball was Eupedia. It just wasn't user friendly. Once I followed I found the SNPtips instructions, that helped.

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map1131
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Oh shoot Judie, don't tell me something I'm about to use isn't user friendly.

You got me all excited about getting my 23andme results and then you throw me a curve ball.

I hope this is going to be in English when my tests results come in the mail. Thank you so much for posting what you have to help and prepare me.

Pam

--------------------
"Never, never, never, never, never give up" Winston Churchill

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Judie
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Hey Maps,

Every site provided really great instructions to use their products (except eupedia).

I just needed to slow waaaaaaay down for some and go step by step. Promethease and Eupedia were the most complicated.

Promethease was most in depth (easy to use, but lots of details to follow). I just played the video and paused it several times to imitate what the guy was doing on the screen by following along with my own data.

The only one that was really confusing was eupedia (not straight forward at all if you want to compare your data, but after installing SNPtips it's easier). I downloaded the SNPtips and nothing changed. I had to search for instructions (which I have provided a link for).

After you do this, the other info that was missing was you need to click on your info tab to do the comparisons yourself to see if you have good genes or bad ones.

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Judie
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Bump
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GretaM
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Super fun Judie!

Thanks for bumping.

And just realized how much I miss Pam's sunny personality.

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beck
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Does this mean you can purchase the $99 kit 23andme currently offers and, instead of using it for ancestry purposes, use the data to look up a health analysis on your own?
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AML94
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Yes, beck. My LLMD had me do it. I'm waiting for results!
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beck
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Hey! That's great! I might just do this.
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oceangirlSA
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I have done the 23andme testing as well and have used a number of these sites to interpret the data.

There is another site to interpret your data - MTHFRsupport.com - the cost is $20 I think, and they do a report as well.

You can also go onto SNPedia.com to look up all your SNPs and see what the existing research is on that SNP.

After I got reports from all the online sites, I wanted to explore the SNPs involved in drug metabolism the most, and contacted a couple of private genetic counselors.

As a word of caution, genetic counselors will not use your raw 23andme data UNLESS you have the health report that they generate. This is due to the current FDA investigation that is going on and the many questions geneticists have about the way 23andme are getting their data.

I only did my testing after 23andme stopped generating their health reports, so it was disappointing to me that the private genetic counselors would not use my data.

I hoped I could avoid the expensive costs of genetic testing that my insurance would most likely not pay for, but I was told that a counselor would still have to work with an MD and get more genetic testing done as they are not allowed to use the 23andme raw data.

Both genetic counselors ended up telling me that the area of pharmocogenetics is a very new area of genetics, and that whilst there is some firm data on drugs and genetics, there is a lot more that they don't know.

I was told that even if I do have SNPs that might affect drug metabolism, that they still might not be able to give me an accurate picture of what this means for me personally.

So I decided not to pursue getting any genetic counseling for now as there does not seem to be much point.

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Dekrator48
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Don't miss this:

"How to Read Your 23andme...Without Going Crazy!!" with Dr Jess Armine.

It is a radio show that will air on Monday, Oct 6 at 8 pm Eastern, and you can call in with questions.


http://www.blogtalkradio.com/drjessarmine/2014/10/07/how-to-read-your-23andmewithout-going-crazy

--------------------
The fibromyalgia I've had for 29 years was an undiagnosed Lyme symptom.

"For I know the plans I have for you", declares the Lord, "plans to prosper you and not to harm you, plans to give you hope and a future". -Jeremiah 29:11

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Razzle
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Dr. Yasko's site, http://knowyourgenetics.com/ , also has a SNP calculator for the methylation genes. Once you put in your methylation gene values, the site can give you a whole protocol for compensating for them...for free.

--------------------
-Razzle
Lyme IgM IGeneX Pos. 18+++, 23-25+, 30++, 31+, 34++, 39 IND, 83-93 IND; IgG IGeneX Neg. 30+, 39 IND; Mayo/CDC Pos. IgM 23+, 39+; IgG Mayo/CDC Neg. band 41+; Bart. (clinical dx; Fry Labs neg. for all coinfections), sx >30 yrs.

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anuta
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I've got this e- mail last week. It looks like they produce reports again to Canadian clients.

"We have great news. Today, we are excited to announce that our 23andMe Canadian product will now include health reports.

As a current 23andMe customer, these reports will be available to you at no additional cost. Once your DNA is processed at our lab, your health reports will be loaded into your account.

What will you be able to see?
In addition to your ancestry data and raw genetic data, you will have access to 108 genetic reports including information about inherited conditions, drug response, trait reports and genetic risk factors for various health conditions."

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Lymetoo
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That's great news, anuta!

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Opinions, not medical advice!

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migs
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Thanks for all the links. I am doing 23 and me for the background fun of it but will be looking at this kind of stuff too.
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terv
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For those who have used 23andme, how long did it take to get your results?
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sickntired771
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It takes 3-4 weeks to get results. I just wonder how accurate these sites are and how accurate 23&Me is. Do we take it as a grain or salt or the holy word?
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Judie
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My 23andme results matched me to a T. MTHFR was definitely the same (got the blood test too).

Other specific things were very accurate. I have an unusual eye color pattern and it even got that.

Promothease is always updating itself (you need to pay if you want an updated report). So info WILL change, but your genes won't.

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terv
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I finally received mine and it took 5 weeks. That being said I am not impressed at all with their customer service. They have no phone number and only offer an email option. If they responded to email that would be great but they don't. I did find a phone number for them on the internet and whatever option I picked I got the message to go to their FAQ section.

When my results were ready I received no email from them telling me so which is odd since I received emails all about the ancestry thing. I only knew it because I checked my account.

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Judie
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bumping for newbies....
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Robin123
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Even though I don't like the fact they have no customer service, I have a feeling it might be because they'd be swamped with calls from everyone who's doing the test, and probably they don't want to deal with that.

Very interesting, Judie - I'll look at some of these sites later.

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LisaK
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oceangirl, my genetic person used my 23andme raw data. no problem.

not sure what you are refering to.

but , you are right about no tmany people knowing all there is to know on how this all works in / for the body- BUT.... it is being worked on.

my gene person is one I do consider an expert. he is really qualitfied . no one is perfect, but he knows what he knows and is fuguring a lot more out. he works with a team of scientists to figure it out and then also figure out which suppliments help what.

no one suppliment should be tried alone "to see what happens". it is a complex thing and if you don't take one, but take another it may make you really sick- ie. tons more anxiety, or heart irregularities, depression, etc.

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Be thankful in all things- even difficult times and sickness and trials - because there is something GOOD to be seen

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LisaK
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23andme seems faster now- or at least it was to me- NOW that I see the date on some of these posts, hahaaa

....

my report took about 2 weeks to come back I think. maybe even shorter. and I guess now they do allow genteic ppl to use raw data, as a year or more ago , no?

I think the DNA aspect is accurate . the other fluffy stuff about ancestry can;t be. it relies on people honestly submitting their personal stories. like answering a quesiton: have you had any illnesses? and anyone can say whatever they want, and then 23andme uses that info to make assumptions for that gene pool.

I could have said my relatives were from Japan and we all had cancer and a club foot and then that info gets entered and then it's history.

taking your raw data to someone that knows what they are doing is key. that is if you want to utilizes the new science of 'fixing' your methylation cycle.

Judie, *or anyone* have you looked back at any of those sites to see if they are still running and the same as when you first went? I wonder if much has changed in this time

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Be thankful in all things- even difficult times and sickness and trials - because there is something GOOD to be seen

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Judie
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All the sites are still running except, snp tips and a sample report.
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WPinVA
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I plugged my genetic 23andme info into a bunch of those sites. But a lot of the info was conflicting - if you have x mutation, then y supplement is good for you. But if you have z mutation (I had both) then that same supplement is bad for you.

I ended up not knowing what to do with it and gave all the info to my LLMD. He didn't know what to do with it either.

How have others handled this -- the question of what practically to do with this info?

On the plus side, I have found two blood relatives through 23andme! Super fun to make those connections - which we confirmed through comparison of family tree research. So that's a confirmation that the DNA part is spot on.

We just may need to wait until medicine catches up with science on the health front.

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Lymetoo
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Lisa, the ancestry is based on the DNA, not on the survey.

I don't even recall their asking where my ancestors were from. Not at all. They are not making assumptions.

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LisaK
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Lymetoo, I received a notice that gave me 'guesses ' to my ancestry since I "did not provide information' . some of it was guessese based on *other* people with *similar* DNA, but could not be proven. like it told me I "may" have .02% of native amreican. and "possibly" came from some small tribe in south asia.... stuff like that. that is what I am referring to .

this is a quote from the site on my page under "To Do List" :

"Help us improve the 23andMe ancestry experience. Tell us where you are from"

then it asks things like:
"Do you know anything about the ancestral origins, such as birthplace or ethnicity, of these biological relatives? Please check the ones for whom you do."

then:
"Thank you! This survey is complete. Your answers will contribute confidentially to research efforts to learn more about the relationship between ancestry and genes. "

doesn't this all mean <some> of it is guessing? or relying on what others put in ?

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Be thankful in all things- even difficult times and sickness and trials - because there is something GOOD to be seen

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Lymetoo
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But this was AFTER you received the results, right? DNA is 99% accurate, hence the words "may" or "possibly."

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--Lymetutu--
Opinions, not medical advice!

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LisaK
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this also..

"Countries of Ancestry shows you the country each part of your genome may have come from. This lab is fueled by the 23andMe Community's responses to the "Where Are You From?" ancestry survey. "

ancestry is different than DNA matches suposedly.

the top 6 "guesses" 23andme made included the 4 countries I already knew my ancestors were from- Russia, Lithuania, Germany and Ireland.

it also included Poland, UK (as my top %) which I know of no one admitting they came from there. 2 of my grandparents were born in lithuania and russia. another was 100% irish supposedly and the family name even traces back to a knighted man there. the other , german, although looked totally german, could have been part UK I guess, but who knows since he didn't speak much of his terrible childhood.

I did not complete the survey so this is why it probably isn't accurate and if I did and put fake things anyway, well then.....

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Be thankful in all things- even difficult times and sickness and trials - because there is something GOOD to be seen

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LisaK
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ok, I found what I was talking about . this is why I think if anyone puts in whatever they want on the site for their known ancestry then it just makes it al linvalid. of course I am no expert and I could just be talking out of my you know what, but it all just seems to hokey to me...

from the site:
"

In this feature we combine information from your DNA Relatives matches (regardless of whether you have made contact or revealed your identities to one another) and those matches' answers to the Where Are You From? ancestry survey.

An example is probably the easiest way to explain what's going on:

Say you have a DNA Relatives match who shares a 14.3 cM stretch of chromosome 20 with you. If that person said that all four of their grandparents were born in Sweden, Countries of Ancestry will mark that segment with four green strips (one for each grandparent).

But what does that mean? Well, it can mean that you have Swedish ancestry. Since all four of your match's grandparents were born in Sweden, the chunk of chromosome you share with that match can only have come from Sweden. But (there's always a "but") all we can say right now is that your match's grandparents were born in Sweden, not that they're ancestrally Swedish. So it could be that your match's ancestors moved to Sweden, but are ancestrally from elsewhere. This is commonly the case for those of Ashkenazi Jewish ancestry, where relatives are spread over Russia, Ukraine, Germany, etc., but are ancestrally (as we've said) Ashkenazi. We're working on several ways to clarify where nationality is likely to indicate ancestry, and where it doesn't.

You'll see colored-in chunks of DNA for every one of your DNA Relatives matches who have filled out the Ancestry Survey and indicated that all four grandparents are from the same place.

The contributions of all your Countries of Ancestry matches are summarized in the table, showing you what proportion of your genome is covered by segments from various countries. You can mouse over the different countries in the table to highlight segments of your DNA that match each locale.

The adventurous may wish to try the "Advanced Controls" to explore your matches further. You can decrease the minimum segment length to see matches that might be a little more tenuous. You can also choose to display results from matches who trace their grandparents back to countries that have histories of very recent immigration from other parts of the world -- the United States, Canada, Australia, New Zealand and South Africa.

Using the Advanced Controls you can also decrease the number of grandparents required from a single country in order to be shown. This will allow you to see chunks of DNA that might be traced back to multiple places. The table will reflect the uncertain nature of where each matched segment comes from by displaying a range of percent genome covered. For example, if you had a DNA Relatives match who shared a segment representing 1% of your genome, but that match had grandparents from Sweden, France, England and Scotland, you would see that for each of these countries the amount covered would be 0-1%. This is because we can't be sure which grandparent the segment you inherited actually came from.

Finally, keep in mind that this feature improves the more people take the ancestry survey, so make sure you and your friends have taken the survey, and keep checking back, because your results can improve every day. "

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Be thankful in all things- even difficult times and sickness and trials - because there is something GOOD to be seen

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Lymetoo
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Wow... I never saw any of that. Don't you think they are coupling the DNA results with the survey results to make it more likely to be correct?

The DNA is the biggest factor, but they have to have a starting point too. They have to have some idea where the people with that DNA come from.

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--Lymetutu--
Opinions, not medical advice!

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LisaK
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right. it is kind of weird.

I am so tempted to plug in my personal info, but I don't feel 'safe' doing that. haha. it's probably my anxiety genes getting to me.

[Wink]

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Be thankful in all things- even difficult times and sickness and trials - because there is something GOOD to be seen

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WPinVA
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Poland was part of the Russian Empire for a while. So maybe that's what happened with the Poland part.
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Lymetoo
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True .. the borders are way different now.

Prussia included Germany a long time ago if I'm not mistaken. All I know is that some of my family is from old Prussia and they are German.

http://www.newworldencyclopedia.org/entry/Prussia

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--Lymetutu--
Opinions, not medical advice!

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LisaK
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that is true.... and interesting.

supposedly if you trace my family name all the way back to when names started or something, that my family are descendants of Saint Paul.

at least that is what we were told. hehe

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Be thankful in all things- even difficult times and sickness and trials - because there is something GOOD to be seen

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Lymetoo
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I have to wait a few more weeks to find out more about my ancestry. Should prove to be interesting!

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Opinions, not medical advice!

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sixgoofykids
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I just ordered the test kit a few days ago. I'm looking forward to finding out what it says!

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sixgoofykids.blogspot.com

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mathewcarnage
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I had tried this tool: https://www.xcode.life/product/ftdna-ancestrydna-23andme-raw-data-interpretation-analysis-tools But this also sounds like a good one. Will give it a try for sure. How do I go about doing it?
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Blackstone
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I would highly advise that anyone interested in genetic information and analysis NOT use services like "23andMe" as they are hostile to your privacy.

Information collected by sites like "23AndMe" is subject to their site-based (read as: basically garbage) privacy policy as the full scope of information itself and metadata interpreted from it is NOT considered "protected health information" - PHI.

This is because most common genetic-related labs are not originally registered as medical labs doing healthcare related work , but rather use a loophole that they are for "ancestry" and/or "novelty", which means they don't have to treat your data the same was as your physician or a lab like LabCorp. As time has gone on they've inched further toward pushing the envelope of advertising personalized medical information as the reason for using their services. The FDA and CLIA can certify that their lab is clean and whatnot, but it doesn't necessarily have anything to do with their privacy policy so be wary of that sort of justification.

Thanks to the lax regulations compared to "real" healthcare focused labs - 23AndMe and other sites can basically retain both data and metadata (by nature of your apparent "consent" thanks to submitting your sample and taking advantage of the service - a horrid but common element of all big-data industries when it comes to violation privacy) , sell it to others etc.. that could not be done with protected health information. Here's an article I just pulled up from 2013 and things have only gotten worse - https://www.scientificamerican.com/article/23andme-is-terrifying-but-not-for-the-reasons-the-fda-thinks/

They can laud all of their "research" and "analysis" by virtue of having this data available, but until we have a massive change to our healthcare system and privacy laws, I would not trust the company to have your best interest in mind.

This is not to dissuade anyone from getting genetic testing done to gain more information about their health, but be it 23AndMe or some other operation that has popped up in the last decade, be very aware of their privacy policy, the status of your data (ie if they consider it Protected Health Information under HIPAA), and overall how they operate. Try to choose labs that deal primarily in medical services and treat your data as PHI. Just something to keep in mind.

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map1131
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Quite frankly I really don't care if someone sees my DNA results. What the heck are they going to do with them?

Thank goodness, I finally got into researching my 23&me SNPs & mutations and found vital information on myself and my family.

Genetic info in the future is going to make fools of our traditional medical establishment. First do no harm, when they have been harming us for decades.


Pam

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"Never, never, never, never, never give up" Winston Churchill

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WakeUp
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quote:
Originally posted by map1131:
Quite frankly I really don't care if someone sees my DNA results. What the heck are they going to do with them?

Thank goodness, I finally got into researching my 23&me SNPs & mutations and found vital information on myself and my family.

Genetic info in the future is going to make fools of our traditional medical establishment. First do no harm, when they have been harming us for decades.


Pam

I admire your brave attitude-- but especially for younger people (who have young organs), privacy of one's DNA is potentially an issue.

Worst case is that there are many desperate elderly billionaires out there who would pay handsomely to get healthy young organs from young people whose DNA they match! Unscrupulous dealers could buy the DNA database, and identify those with matching DNA for their billionaire customers who need a new heart or a new lung, or a bone marrow transplant or a liver..

Accidents can be arranged for DNA "matches" to accommodate desperate billionaires....and driver's licenses often give permission for hospitals to extract organs ---without the family's knowledge.

Organ trafficking is potentially the dark side of all of this. And if you think this idea is outlandish, just remember that an aborted child's calvarium (head) sells for at least $100 on the market. Lungs and livers have also been sold by Planned Parenthood.

So strict privacy laws on our DNA are a good idea.

Thanks, OP for this very informative thread.

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