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Reiverroots
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« on: March 05, 2009, 05:37:28 PM »

Hi,
I want to buy either 23andme or DeCodeMe for my Mum to try and find out about her unknown paternal ancestry.
I have heard that I could use the raw data from the 23andme test for her X chromosomes on the X project. Can I do the same thing if I did the DeCodeMe test too? Does that give you the raw data to use?
If so, what could I find out if I submitted the data? Do both her X's need to come from parents of the same ancestry? I'm particularly interested in what her father's X he gave to her could tell us about his mother and whether it maybe possible to find living distant relatives using X chromosomes. I know X testing is in it's early stages but any information would be gratefully received, particuarly at this stage with whether DeCodeMe's data could be submitted and what it would tell us.
Thanks.
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Seán MacGorman Powell
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« Reply #1 on: March 05, 2009, 08:06:27 PM »

Hi,
I want to buy either 23andme or DeCodeMe for my Mum to try and find out about her unknown paternal ancestry.
I have heard that I could use the raw data from the 23andme test for her X chromosomes on the X project. Can I do the same thing if I did the DeCodeMe test too? Does that give you the raw data to use?
If so, what could I find out if I submitted the data? Do both her X's need to come from parents of the same ancestry? I'm particularly interested in what her father's X he gave to her could tell us about his mother and whether it maybe possible to find living distant relatives using X chromosomes. I know X testing is in it's early stages but any information would be gratefully received, particuarly at this stage with whether DeCodeMe's data could be submitted and what it would tell us.
Thanks.

Hi Reiverroots,

Yes, you would get raw data from deCODEme that you could submit to the X-chromosome Project.  It's just more work though because deCODEme does not present their results in the same format as 23andMe, so you've have to do a lot of manual conversions (not a big deal, it just takes some time and patience to do).  The project data is aligned to 23andMe's format because that's the lab that most people are using.  I think I've only had a couple of people submit deCODEme-derived data to the project (to my knowledge), though they are most welcome to do so.  That's not to say that deCODEme isn't a good lab to use--quite the contrary, it is indeed an excellent one.

As for what you could find out by submitting the data... the project results chart is more of a tool for researchers, than something that is going to give you any personally-useful information, unless you are good at interpreting such data.  By submitting your results, you are potentially helping people to figure out where certain blocks of DNA originated, geographically... and at some point down the road, that might help you figure out where some of your ancestors lived in ancient eras (and potentially more recent times, if we are able to refine the meaning of the data).

Your results, once submitted to the project, will show you how various blocks of DNA are related to other people who submitted their data.  You will most likely be perfect matches to other people for some blocks, but be matches to different people for other blocks.  That's because X-DNA recombines nearly every generation, and you have a mixture of DNA from many different people.  You can't really compare the entire X-chromosome as a unit to other people.

No, both of your mother's X's do not need to come from parents of the same ancestry.  However, females tend to have "heterozygous" results for a large proportion of their SNPs (i.e., different letters of genetic code for a given chromosome position), and for those SNPs, it can be very difficult to determine which DNA came from which parent.  Females therefore have less-complete data presented in the results chart, because we only show those data that can be resolved unequivocally.

There's not really any way to tell which portions of your mother's X-DNA came from a particular X-DNA ancestor, except to test additional family members in an attempt to narrow it down.  For example, if you were to test both of your parents, along with yourself, then you'd be able to deduce which portions of your X chromosome(s) came from which parent.  You can't tell which of your mother's X-DNA came from her father though, without also testing her mother--though you may be able to make some educated guesses, if your parents came from very different ethnicities (that's a tricky thing to do though, even for the experts).

As for trying to identify distant relatives using X-DNA results... that's possible, but it's a longshot.  A very few lucky people have had some success doing that, but it's very much the luck of the draw as to whether anybody will show up in your test results who is a partial match to you, and who matches enough of your DNA to share any more than a very ancient common ancestor with you.  I wouldn't do the testing with the express intent of trying to identify such unknown relatives, as you will likely be disappointed with the outcome.  There are plenty of other good reasons to do the testing though (like uncovering your deep ancestry, and getting a picture of your medical risks).

Sean
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Reiverroots
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« Reply #2 on: March 06, 2009, 12:52:58 PM »

Hi Sean,
Many thanks for all your help. I think I'm probably going to do DeCodeMe so I may need some help with converting when the results come back!
I'm hoping I may be able to distinguish which X came from which parent as I know the origins of my maternal Grandmother (every line traced back to 1580 roughly)however I believe things maybe completely different with my maternal Grandfather, so hopefully I maybe able to find out!
Can I ask, what does heterozygous mean?
Thanks for all your help.
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« Reply #3 on: March 06, 2009, 01:29:46 PM »

Hi Sean,
Many thanks for all your help. I think I'm probably going to do DeCodeMe so I may need some help with converting when the results come back!
I'm hoping I may be able to distinguish which X came from which parent as I know the origins of my maternal Grandmother (every line traced back to 1580 roughly)however I believe things maybe completely different with my maternal Grandfather, so hopefully I maybe able to find out!
Can I ask, what does heterozygous mean?
Thanks for all your help.

No problem at all, Reiverroots.  Just send me a message when your data comes in (or post here), and I'll explain to you how to convert your data.

As for the term "heterozygous," my parenthetical comment after I used that term was meant to explain what it means, but I probably didn't explain it very well...

Every chromosome in the human body (excluding sperm and egg cells) has two copies, one from the mother, and one from the father... except for the Y chromosome, and the X in males, each of which have only one copy in normal humans.  If the person inherited the same nucleotide base "letter" from each parent (e.g., his/her test result for that nucleotide is TT, CC, AA, or GG), then (s)he is "homozygous" for that nucleotide.  If the person inherits a different nucleotide from each parent, (e.g., AT, GA, CT, etc), then (s)he is "heterozygous" for that nucleotide.

With respect the X chromosome, females have two copies of that chromosome (one from each parent), so they can be either homozygous or heterozygous for any given nucleotide.  When they are homozygous, there's no interpretation problem.  When they are heterozygous though, there's no immediate way (without further testing, or without running the data through "phasing" software, which has its limitations) to tell which nucleotide came from which parent, so they are reported in the project's results chart with an asterisk (*).

Because males only have one X chromosome (which always comes from his mother), we always know which parent it came from (though we would not always know which grandparent it came from).

Sean
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Reiverroots
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« Reply #4 on: March 08, 2009, 05:21:46 PM »

Hi,
Well just placed my order and really excited about the possibilites of the test I have gone for!
I will certainly be in touch when the results come though.
In the mean time, just to see if my understanding is correct, if I have heterozygous nucleotides and I put them onto your database and discover one is clearly European but the other is of a different ethnicity, then I would know which came from which parent because I know my mother is English and so were her ancestors back to the 1580's? So I could assume the other was from my Dad?
Is the project at a point where certain blocks are associated with certain populations?
Thanks.
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« Reply #5 on: March 08, 2009, 05:51:15 PM »

Hi,
Well just placed my order and really excited about the possibilites of the test I have gone for!
I will certainly be in touch when the results come though.
In the mean time, just to see if my understanding is correct, if I have heterozygous nucleotides and I put them onto your database and discover one is clearly European but the other is of a different ethnicity, then I would know which came from which parent because I know my mother is English and so were her ancestors back to the 1580's? So I could assume the other was from my Dad?
Is the project at a point where certain blocks are associated with certain populations?
Thanks.

Unfortunately, it's not so simple a matter to look at a particular SNP and be able to say with any degree of  certainty where it came from, even in general terms as to a continent.  For any given SNP, we can see that a particular allele tends to occur with greater frequency in a certain population, but it may also occur with lesser (but still common) frequency in a different population.

For example, for the SNP rs4933045 (the very first one shown in the raw data for the X chromosome in 23andMe's browser), the G allele occurs in 69.2% of the Europeans in the dbSNP database.  That same allele occurs in 75-83% of Asians (depending on which Asian population you refer to).  Africans aren't even included as one of the populations in the database for that SNP, so who knows what that allele's frequency is there.  So in this case, having the G allele (instead of the other possibility for the SNP, the A allele) really tells you nothing at all about where it likely came from.

With other SNPs, it can be more definitive, and a particular allele will occur almost exclusively in a certain population.

You can examine a block of the surrounding SNPs though, and if your allele values all seem to consistently point to a particular population with higher frequency than the other populations, then you might be able to come to the conclusion that this particular block of DNA originated in that population.  It's a very tricky matter to identify those blocks though.

Another complicating factor is that even if you know that you know that a particular lineage is, say, English, back to the 1500's, the SNP that you're examining may be far older than that (by hundreds of thousands of years), and may have originated someplace far from Europe (maybe even in Africa, if it's old enough).  So it could show up as likely African, even though all your known ancestors for that lineage lived in Europe.

I don't mean to confuse you (I do appreciate that this stuff can be confusing!), only to point out that there are a lot of complicating complexities involved.  For the average layman testee, it's probably less useful to do any detailed examination of particular SNPs, and instead look for broader patterns (i.e., whether you share any large blocks of DNA with other people, or whether you have any large DNA blocks that are characteristic of a particular geographic population).  Both of the testing labs that you are considering (23andMe and deCODEme) provide tools for that kind of evaluation.
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Reiverroots
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« Reply #6 on: April 04, 2009, 01:01:59 PM »

Hi,
I don't know if you got my PM, but I now have my DeCodeMe data and I'm ready to convert it!!! What do I need to do?!
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Seán MacGorman Powell
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« Reply #7 on: April 07, 2009, 07:54:20 PM »

Hi,
I don't know if you got my PM, but I now have my DeCodeMe data and I'm ready to convert it!!! What do I need to do?!

Sorry for the delayed reply, but I haven't been at my computer much the past few days...  I just checked my PM in-box and don't see any messages from you. 

People who want to submit deCODEme data to the project results chart can PM me with their e-mail address, and I will send you a data submission spreadsheet with instructions for how to convert to 23andMe's format.

Reiverroots, please try sending me another PM and let's see if that one goes through, or you can try clicking the little e-mail icon under my name (e-mails often get intercepted by my spam filter if I don't have you in my address book, so PM's are more reliable, theoretically, but feel free to try).

Your contribution would be most welcome.
« Last Edit: April 07, 2009, 07:54:55 PM by Seán MacGorman Powell » Logged

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Reiverroots
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« Reply #8 on: April 09, 2009, 12:53:14 PM »

PM sent... hope this one gets to you!
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