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Seán MacGorman Powell
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« on: January 26, 2009, 01:26:41 PM »

I just wanted to personally extend an invitation for anybody who has questions about the X chromosome (or X DNA testing) to feel free to post on this board.  I hope people are not intimidated by the sometimes-advanced topics that are often being discussed here. 

People of all levels, from the brand new X DNA testee with no science background, to the professional geneticist, are all welcome here.  I think you'll find that the members with more expertise here are more than happy to answer questions posed by the more novice members.  We're all here to learn.

There's no such thing here as a dumb question, as far as I am concerned.
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susanrosine
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« Reply #1 on: January 26, 2009, 02:02:12 PM »

Ok, I'll jump in. I'm new to the world of X, but not new to Y or mtDNA testing. I received my 23andme kit and will be sending that in soon.

Since I'm female, would my next best step be to have my father also do the 23andme testing? He is 80, so if that is truly my next best step, I'd like to do it as soon as I gather the funds together.

Would it be helpful to also have my mother and my sister do it? I can only afford so much at a time, so I really can't be ordering these kits right and left!! My dad has one sister, she is 85. My mom has several sisters and one brother. Could anyone tell me the best order in which to try and get each of these people tested, so as to get the most meaningful information???

Also, I have thought regarding X STR testing, which FTDNA does. FTDNA already has DNA samples for my dad, my mom, my sister, and my mom's brother. If I ordered X STR tests for all of us, would that work in tandem with X SNP testing? I know SNP is deep ancestry and STR is not, but couldn't I still get meaningful blocks from STR testing?

Susan
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Dad: JAMES:  Ysearch QSCQ3;  R-P312, L21+ (R1b1b2a1b5*)
Dad: mitosearch QSCQ3; T1a; no matches HVR2 or FGS
Mom's brother: LEWTER: Ysearch FYFDA;  R-U106, L48+ (R1b1b2a1a*)
Mom's brother: mitosearch FYFDA, U5b2; 1 exac
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« Reply #2 on: January 26, 2009, 02:20:05 PM »


Hi Susan
Take a look at the thread on "X-STR Results Chart  and link on the XSTRs here now..( Just 3 of us so far)
It is a very economical way to preserve and test the markers you have done at FTDNA.. it would only cost you about $30 to test the DXS10074,10075,10079 haploblock for each of you..
Thomas Krahn's site at DNA Fingerprint has a lot more folks X markers tested right now. I did my X STRS in 2006 and HAVE found some matches.I did mine and my Sister's which gave us what our Dad's Haploblcok is ( which he in turn inherited from his Mother's line)

I am very excited that Sean/GhostX has done this for us..the more we know... the more we know.
I DO expect to test at 23andme in the not too distant furture however.
Kathleen
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Kathlingram

X chromosome ancestry % 62.50 Irish,Colonial Admixture of Eng/Irish/Welsh 37.50%.Father 25% Irish,25 % Colonial admix.Mother 37.50% Irish 12.50% Colonial Admix
tomcat
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« Reply #3 on: January 26, 2009, 05:06:38 PM »

... I received my 23andme kit and will be sending that in soon...would my next best step be to have my father also do the 23andme testing? ... Would it be helpful to also have my mother and my sister do it? ...Could anyone tell me the best order in which to try and get each of these people tested, so as to get the most meaningful information???... If I ordered X STR tests for all of us, would that work in tandem with X SNP testing? I know SNP is deep ancestry and STR is not, but couldn't I still get meaningful blocks from STR testing?

For the semi-autosmal X and the 22 autosomal chromosomes it is ALWAYS best to test as far back up the family lines as possible - family elders. So yes to a 23andMe test of your father and mother. Aunts or uncles are fair stand-ins for parents, but a test of your sister would be duplicative.
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Paternal X: 100% Ukrainian Ashkenazi. Maternal X: 50% Upper Midwest Native American, 50% European.
susanrosine
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« Reply #4 on: January 26, 2009, 05:22:09 PM »

I thought I remembered somewhere that someone told me that my sister would not be the same as me, because she would have received at least some different X haploblocks than I did. Or maybe that is STR, and not SNP?
So on that same note, wouldn't each of my aunts receive a different mix of X haploblocks from their parents? My uncle and my dad of course would receive just one X chromosome. But wouldn't I get a better view of deep ancestry by testing as many aunts, uncles as possible, in addition to my parents? Perhaps I am misunderstanding how X works. 
With my dad having just one sister, wouldn't I see more X deep ancestry by getting her XX results, rather than JUST my dad's X results?
In the regular autosomal (DNA Tribes testing) my sister and I are not identical. We each received some the same, but some different, from our parents.  Wouldn't that be somewhat similar for XX semi-autosomal?
I am definitely a newbie to this "X stuff", so bear with me! Susan
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Dad: JAMES:  Ysearch QSCQ3;  R-P312, L21+ (R1b1b2a1b5*)
Dad: mitosearch QSCQ3; T1a; no matches HVR2 or FGS
Mom's brother: LEWTER: Ysearch FYFDA;  R-U106, L48+ (R1b1b2a1a*)
Mom's brother: mitosearch FYFDA, U5b2; 1 exac
susanrosine
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« Reply #5 on: January 26, 2009, 05:26:30 PM »


Hi Susan
Take a look at the thread on "X-STR Results Chart  and link on the XSTRs here now..( Just 3 of us so far)
It is a very economical way to preserve and test the markers you have done at FTDNA.. it would only cost you about $30 to test the DXS10074,10075,10079 haploblock for each of you..
Thomas Krahn's site at DNA Fingerprint has a lot more folks X markers tested right now. I did my X STRS in 2006 and HAVE found some matches.I did mine and my Sister's which gave us what our Dad's Haploblcok is ( which he in turn inherited from his Mother's line)

I am very excited that Sean/GhostX has done this for us..the more we know... the more we know.
I DO expect to test at 23andme in the not too distant furture however.
Kathleen

Ok, so it is STR testing where me and my sister will differ. So we would be able to figure out our father's haploblock just from that. So maybe I don't need to test my dad's STR? Or just test my mom and dad's and no need for me and my sister? I'm talking about as far as X STR testing through FTDNA. Not talking about the 23andme now. Although the FTDNA is much cheaper, I still don't want to pay for totally unnecessary testing. I could use that money towards other tests LOL!
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Dad: JAMES:  Ysearch QSCQ3;  R-P312, L21+ (R1b1b2a1b5*)
Dad: mitosearch QSCQ3; T1a; no matches HVR2 or FGS
Mom's brother: LEWTER: Ysearch FYFDA;  R-U106, L48+ (R1b1b2a1a*)
Mom's brother: mitosearch FYFDA, U5b2; 1 exac
Seán MacGorman Powell
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« Reply #6 on: January 26, 2009, 05:43:29 PM »

Ok, I'll jump in. I'm new to the world of X, but not new to Y or mtDNA testing. I received my 23andme kit and will be sending that in soon.

Since I'm female, would my next best step be to have my father also do the 23andme testing? He is 80, so if that is truly my next best step, I'd like to do it as soon as I gather the funds together.

Would it be helpful to also have my mother and my sister do it? I can only afford so much at a time, so I really can't be ordering these kits right and left!! My dad has one sister, she is 85. My mom has several sisters and one brother. Could anyone tell me the best order in which to try and get each of these people tested, so as to get the most meaningful information???

Also, I have thought regarding X STR testing, which FTDNA does. FTDNA already has DNA samples for my dad, my mom, my sister, and my mom's brother. If I ordered X STR tests for all of us, would that work in tandem with X SNP testing? I know SNP is deep ancestry and STR is not, but couldn't I still get meaningful blocks from STR testing?

Susan

Welcome to the forum, Susan!

Tomcat and Kathleen both gave you some good advice, and I'll add a few of my own thoughts here...

I've been debating myself whether to get one of my elders tested--she is 91 years old now, so it's probably now or never!  As for which family member is best to test, I suppose that depends on your goals.  If health-related info is a priority, then it would be sensible to test your mother and/or your father.  If you have a gene that puts you at high risk for a condition, and a tested parent doesn't have it, then you'll know that your other parent is the carrier.  Testing a sister wouldn't give you the same level of specificity.

If genealogy is your main focus, testing either your mother or your father would give you information about your X chromosomes (as you appear to be female), so take your pick between those two people.  An advantage of testing your father would be that you'd get information on your family's Y-DNA lineage (i.e., your father's surname).  You'll get less-useful information about your mother's mother... lineage from the mtDNA that 23andMe scans.  So from that perspective, and given your father's age, he'd be a priority for me.

You'll undoubtedly get different (and perfectly valid, from different perspectives) answers from different people, but if it were me, here's the order I would test additional family members:

1) Father
2) Mother
3) Grandparents (take your pick)
4) Siblings

If I had to pick just one family member to test, for genealogical purposes, and assuming he was still alive, I'd pick my paternal grandfather.  If he's not still alive (as yours presumably can't be), I'd pick my father (as I did--he's the only other family member who I have had tested so far).  That's assuming that you don't have some overriding reason for wanting to test a particular lineage.
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Seán MacGorman Powell
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« Reply #7 on: January 26, 2009, 05:59:43 PM »

if you had to pick only one type of test or the other, I would only pick an X-STR test if you're really trying to figure out a particular question about your immediate family, or trying to confirm a very recent ancestry.

Just to clarify what I meant when I wrote that... I do not mean to suggest that X-STRs have no other use than for studying recent ancestry/immediate family.  Quite the contrary, they could potentially turn out to be very useful for deeper-ancestry studies, in ways that we have not even figured out yet.  I was just trying to point out the currently-known uses of one type of test versus the other, if you can only pick one and are trying to decide which type of test better suits your immediate interests.
« Last Edit: January 26, 2009, 08:27:09 PM by GhostX » Logged

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« Reply #8 on: January 27, 2009, 10:16:30 AM »

Since I'm female, would my next best step be to have my father also do the 23andme testing? He is 80, so if that is truly my next best step, I'd like to do it as soon as I gather the funds together.

To have your fathers X may be an advantage as he has only 1 x-chromsome and as he is a male his X-chr data is phased meaning his X is directly comparable to other males.
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tomcat
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« Reply #9 on: January 27, 2009, 11:46:12 AM »

I thought I remembered somewhere that someone told me that my sister would not be the same as me, because she would have received at least some different X haploblocks than I did...
So on that same note, wouldn't each of my aunts receive a different mix of X haploblocks from their parents? My uncle and my dad of course would receive just one X chromosome. But wouldn't I get a better view of deep ancestry by testing as many aunts, uncles as possible, in addition to my parents?...
With my dad having just one sister, wouldn't I see more X deep ancestry by getting her XX results, rather than JUST my dad's X results? ...

Susan,
It is true that you and your sister most likely received differing assortments of X markers from your mother, but testing your mother would yield ALL the X markers she had to pass on. Testing your mother's sister would expand the list of X markers attributable to the maternal lines AND allow you to deduce the X markers attributable to their father, your maternal grandfather.

Both you and your sister got the same X assortment from your father.

Testing your father's sister, in addition to your father, would yield the X markers from your paternal grandfather and another assortment of X markers from the paternal grandmother. Although you will not, in all instances, be able to deduce which grandparent contributed which markers.

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tomcat
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« Reply #10 on: January 27, 2009, 12:01:36 PM »

...
 An advantage of testing your father would be that you'd get information on your family's Y-DNA lineage (i.e., your father's surname).  You'll get less-useful information about your mother's mother... lineage from the mtDNA that 23andMe scans.  So from that perspective, and given your father's age, he'd be a priority for me...

This is slightly off-topic, but I wondered how useful SNP scans are in determining Y and Mt haplogroup and clade? Especially if one already has a basic assignment via a 25-marker Y and/or HVR Mt tests.
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« Reply #11 on: January 27, 2009, 12:31:52 PM »

[quote author=susanrosine link=topic=8450.msg109191#msg109191 date=1233005190
Ok, so it is STR testing where me and my sister will differ. So we would be able to figure out our father's haploblock just from that. So maybe I don't need to test my dad's STR? Or just test my mom and dad's and no need for me and my sister? I'm talking about as far as X STR testing through FTDNA. Not talking about the 23andme now. Although the FTDNA is much cheaper, I still don't want to pay for totally unnecessary testing. I could use that money towards other tests LOL!
[/quote]

If you are talking the cost of two tests for X STR's, you and your sister versus your father and mother, you would be better served by testing the parents. As it is entirely possible that both you and your sister got the same haploblock from your mother, which would leave one of the maternal haploblocks unknown. Whereas a test of your mother would disclose both her haploblocks.

There is a reason, however, to test either your self or sister in addition to the parents, and that is to isolate maternal haploblocks from one another. In example; your mother's 3 linked markers might read 10,11-12,10-13,12, but without a test of one of her children one would not know whether the blocks were 10,11,13 or 10, 12,12 or any of the other possible combinations. If your mother had several sisters one might accomplish the same by testing them all.
« Last Edit: January 27, 2009, 12:47:07 PM by tomcat » Logged

Paternal X: 100% Ukrainian Ashkenazi. Maternal X: 50% Upper Midwest Native American, 50% European.
Seán MacGorman Powell
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« Reply #12 on: January 27, 2009, 02:50:49 PM »

This is slightly off-topic, but I wondered how useful SNP scans are in determining Y and Mt haplogroup and clade? Especially if one already has a basic assignment via a 25-marker Y and/or HVR Mt tests.

For Y haplogroups, SNP scans are very useful--in fact even more useful than the Deep Clade tests done by the other testing labs, because they have the potential to identify new subclades defined by markers that aren't even known to the other testing labs to define subclades (so they aren't yet part of those labs' deep-clade SNP panels).

It's possible that the deep-clade tests at FTDNA include some SNPs, for certain haplogroups, that aren't part of the genome scanners' chips, but I'll let others speak to that point, as I'm not aware of any.

For mtDNA haplogroups, the genome scans are very useful in most cases, though potentially less so than a FGS test from a lab like FTDNA, because FTDNA tests all the mtDNA nucleotides, whereas the genome scanners only scan a subset of them.

In either case (Y-DNA vs mtDNA), the genome scanners will occasionally missreport values (either errors, or no-calls), and if one of those happens to be for a marker that defines a subclade (statistically highly unlikely, but possible), then they won't tell you what you need to know.

If you're interested in getting a highly-specific mtDNA subclade assignment, I'd get the FGS test at FTDNA, though a genome scan may tell you what you need to know (depending on what haplogroup you end up being in).  If you're more interested in a Y-DNA haplogroup assignment, either FTDNA, 23andMe, or DeCODEme will serve you well.
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