Haploblocks for STRS

[kathlingram]

What will be available here ( if anything) for those of us who have tested our X haploblocks at FTDNA or at DNA-FP and have our blocks listed there?

Tomcat and I already posted yesterday with where our Haploblocks are to be found and what they are called?
Simply put mine are at Kathlingram and Kathlingram2 at DNA-FP..
I have some matches and we are comparing ethnicity and surnames..

There are many of us who have these blocks..hundreds I guess..
are there as many of folks who will post here who also have their full genome scan?

That was the main reason I am here was for more information on the testing I have done already..
Tom Krahn had indicated to us that these haploblocks do not recombine and are virtualy unchanged for more than 1000 years..

I DO appreciate your inviting me here..
I just have not yet decided if the full genome scan is all  everyone thinks it is as I have not heard any great or even firm conclusions yet..

Please remember that X marker testing comes in more than one flavor..
Kathleen

[Seán MacGorman Powell]

What will be available here ( if anything) for those of us who have tested our X haploblocks at FTDNA or at DNA-FP and have our blocks listed there?

Tomcat and I already posted yesterday with where our Haploblocks are to be found and what they are called?
Simply put mine are at Kathlingram and Kathlingram2 at DNA-FP..
I have some matches and we are comparing ethnicity and surnames..

There are many of us who have these blocks..hundreds I guess..
are there as many of folks who will post here who also have their full genome scan?

That was the main reason I am here was for more information on the testing I have done already..
Tom Krahn had indicated to us that these haploblocks do not recombine and are virtualy unchanged for more than 1000 years..

I DO appreciate your inviting me here..
I just have not yet decided if the full genome scan is all  everyone thinks it is as I have not heard any great or even firm conclusions yet..

Please remember that X marker testing comes in more than one flavor..
Kathleen

Kathleen,

X-STR results are something that I've actually been pondering including here, and I was actually working on something that has to do with that very matter at the moment you posted.

At present we don't have enough spreadsheet slots available on the project website to have a separate spreadsheet for STR results (the two slots available to me are already in use), but that may change shortly, as the WorldFamiles site is currently being redesigned.

In the meantime, I have added the locations of a few STRs to the X DNA results spreadsheet (the few for which I know their position on the chromosome), and I can easily add your results there.  I haven't decided yet if I should do this as an opt-in basis, only including the results for people who choose to specifically send their results to me, or if I should just reproduce the data from DNA-Fingerprint, and would welcome people's opinions about that (particularly Thomas Krahn, if he reads this).

Please stay tuned for a better way to display more comprehensive STR results--there's a lot of work left to be done on this new project, and I can only focus on so much of it at a time.

Thanks for the suggestion, Kathleen!

[kathlingram]

Why thank you! Sounds exciting!
It would be great if Thomas joined us in this endeavor..one of the folks I match slightly is Astrid.
:)
I am intrigued with the Danish and German matches X matches..on my maternal line my Grandmother's father was of Swedish descent ( possibly Danish)..Swanson.
and My Grandmother's mother was German politically but possibly from Alsace by birth..Rementer aka Regimenter.
Again thank you for being so helpful
Kathleen

[Seán MacGorman Powell]

Why thank you! Sounds exciting!
It would be great if Thomas joined us in this endeavor..one of the folks I match slightly is Astrid.
:)
I am intrigued with the Danish and German matches X matches..on my maternal line my Grandmother's father was of Swedish descent ( possibly Danish)..Swanson.
and My Grandmother's mother was German politically but possibly from Alsace by birth..Rementer aka Regimenter.
Again thank you for being so helpful
Kathleen

No problem, Kathleen. 

X-STR data is actually considerably more complicated to deal with than Y-STR data.  Y-DNA isn't subject to recombination (for the most part), so it's no big deal to examine Y-STR markers separately from the positions of the Y-SNP markers on the chromosome... but on the X chromosome, the two types of markers can't really be dealt with independently, as the positions of X-STR markers relative to X-SNP haploblocks could be very important, and recombination rates need to be considered.  So it might not be a fruitful exercise to simply examine X-STR markers by themselves, but rather in conjunction somehow with SNP data.  That's sort of the idea behind my including the STR markers on the same spreadsheet with the SNP markers.

Anyway, that's just some of the kind of stuff that's going to need to be worked out before we can decide on the best way to proceed, and on the the final form that such data presentation is going to take, whether it be here or elsewhere.

[kathlingram]

Well I know that I am missing something in the translation here but I believe that the X markers DXS10074, DXS10075 and DXS 10079 are considered to be an X haploblock when together ..Tom K. had indicated that they were small linked markers.. those three together and another one DXS 10066,10067,10068 I think?

I may also be very behind the times as the full genome had not yet come out..

I am not/do not explain it well.. here is a quote from him late in 2005..seems to me I tested late in 2006?

" However, the XSTR markers can bring us even several generations ahead,
if we use the technology of linked STR "quasi haplotypes" on the X
chromosome. XSTR markers are linked, if they are located close together
at nearly the same position of the X chromosome. It is very unlikely,
that a crossing over event will exactly hapen in between two linked
markers, so they can be considered as "haplotypes" that are transferred
from one generation to the next as a complete block. If you find a very
unique haplotype block in two different individuals, then you can be
quite sure, that they share a common ancestor. However, if they don't
share the same haploblock, you can still say nothing. They may be
related anyway.
On my website I have started the first public STR database that also
contains XSTR data. We hope that we can collect linked XSTR haplotypes
from all over the world and that we may find haploblocks that are
characteristic for a certain geographical region."

That is what I refer to..possibly only those linked STRs that are considered to be a haploblock but it is also very possible that more is needed than the linked STRS..

Hopefully I will do a full genome test in the Spring..
Kathleen

[Seán MacGorman Powell]

Well I know that I am missing something in the translation here but I believe that the X markers DXS10074, DXS10075 and DXS 10079 are considered to be an X haploblock when together ..Tom K. had indicated that they were small linked markers.. those three together and another one DXS 10066,10067,10068 I think?

I may also be very behind the times as the full genome had not yet come out..

I am not/do not explain it well.. here is a quote from him late in 2005..seems to me I tested late in 2006?

" However, the XSTR markers can bring us even several generations ahead,
if we use the technology of linked STR "quasi haplotypes" on the X
chromosome. XSTR markers are linked, if they are located close together
at nearly the same position of the X chromosome. It is very unlikely,
that a crossing over event will exactly hapen in between two linked
markers, so they can be considered as "haplotypes" that are transferred
from one generation to the next as a complete block. If you find a very
unique haplotype block in two different individuals, then you can be
quite sure, that they share a common ancestor. However, if they don't
share the same haploblock, you can still say nothing. They may be
related anyway.
On my website I have started the first public STR database that also
contains XSTR data. We hope that we can collect linked XSTR haplotypes
from all over the world and that we may find haploblocks that are
characteristic for a certain geographical region."

That is what I refer to..possibly only those linked STRs that are considered to be a haploblock but it is also very possible that more is needed than the linked STRS..

Hopefully I will do a full genome test in the Spring..
Kathleen

Thomas' quote sums up the situation nicely.  Thanks for posting that, Kathleen.

So yeah, if X-STR markers are close enough together, they are effectively linked, but just how close together they need to be to exhibit linkage (and how strong the linkage is) varies, depending on the highly variable recombination rates among various parts of the chromosome.  For example, if two STRs are fairly far apart (say several hundred thousand base pairs separating them), but they're in they're in the middle of a haploblock that shows strong linkage disequilibrium (and low recombination rates), they would be considered strongly linked.   Two STRs in a similarly-sized region that has a high recombination rate, however, would not be as strongly linked, and might easily be broken up by recombination over a number of generations.

That's why it's important to consider the position of the STR's on the chromosome (and relative to SNPs), rather than simply considering strings of STR values.  You probably already know all of this... I'm just saying it so that others can understand the complexity of the situation compared to Y-chromosome markers.

[kathlingram]

Actually no I did not know all of that but am trying to learn..Thanks for that information as I do think I understand that..

I saw this post from Thomas Krahn today at Rootsweb
http://archiver.rootsweb.ancestry.com/th/read/GENEALOGY-DNA/2009-1/1232558976

Kathleen

[PDHOTLEN]

The main reason I would be at all interested in having my  single X chromosome tested is to give an insight to my Austrian lineage, which (I assume) would be one half of that X. Austrian genetic info would seem to be limited in the USA. I don't have any reason to have my X tested for my family tree, since I already know who my maternal grandfather was. As to which test would accomplish that, what lab, and what cost, I still haven't done any research.

U5b2 & R1a1

[Seán MacGorman Powell]

What will be available here ( if anything) for those of us who have tested our X haploblocks at FTDNA or at DNA-FP and have our blocks listed there?

Ask and ye shall receive:

http://www.worldfamilies.net/forum/index.php?topic=8448.0

[kathlingram]

WOW.Thanks..Let me read it, figure it out and get it done.
Ask and you shall receive,indeed!
Kathleen

[tomcat]

Well I know that I am missing something in the translation here but I believe that the X markers DXS10074, DXS10075 and DXS 10079 are considered to be an X haploblock when together ..Tom K. had indicated that they were small linked markers.. those three together and another one DXS 10066,10067,10068 I think?

Has anyone identified any haploblocks for 10066, 67, 68, 69?

[kathlingram]

TOM
Do you mean Haploblocks or Haploblock matches..??

I have THIS:
Dad  15,15,21,14
Mom 14,14,19,19
Mom 13,16,22,17

But I do not match anyone..if I displayed them differently I DO Match someone BUT than Sister and I would not share Dad's block so that cannot be correct..

It would be a LOT EASIER here if they were displayed together:
10066, 10067,10068,10069
What do you think?
Sean, What do you think?
Kathleen

[kathlingram]

I just went and did a comparison..it was a bit difficult but it worked..I am off on 1 marker on Dad's haplotype..

It would be easier if they were close together..
By The Way..it is an ethnicity that would work for Dad's father..
;)
Kathleen

[kathlingram]

OF COURSE I forgot yet again that Dad's X markers are NOT from his father but from his Maternal Grandfather or Grandmother..
Dumb me!
Kathleen

[Seán MacGorman Powell]

Has anyone identified any haploblocks for 10066, 67, 68, 69?

People tend to use the word "haploblock" loosely in different ways depending on what they are trying to compare.  In this case, I am guessing that Tomcat is asking if there are any X-SNP haploblocks that have been identified that bracket the X-STR markers that he mentioned (feel free to correct me if I misunderstood, Tomcat).  I'm not aware of any that have been, but that doesn't mean there aren't any. 

There is still some confusion about where exactly some of those STR markers are located on the chromosome.  The numbers shown underneath the marker numbers appear to be chromosome position numbers (base pair counts), but at least one of them doesn't correspond to a position that was published in the scientific literature.  I haven't really been studying X-STR markers enough personally to look into this yet, so maybe somebody else can answer that question for us.

As for why they are not displayed together (to respond to Kathleen's comment), it is presumably because those particular markers are not located anywhere near each other on the X chromosome.

[kathlingram]

Hi Sean
I THOUGHT he meant had anyone matched anyone else on that group of STRS that Tom Krahn had indicated were also a microsatellite haploblock only  a more minor one than 10074,10075,10079..

Anyway that was what I was answering.. it has actually been a long time since I had that discussion with Thomas K. so maybe I am incorrect..

anyway..the only person  I match is my Sister..and that only because we share the one from Dad..


Any insight on this is helpful..so we all can learn..
Kathleen

[kathlingram]

Sean and Tomcat
You know I am really really confused about that set of markers..I was led to believe or thought I was that they together formed a "Minor haploblock" which POSSIBLY could someday with enough folks testing be as informational and identifiable as a Y haplotype..

I just am not at all sure..maybe I moved them around to make a block? Was that wrong?Since I am female I got 2 sets of numbers and so did my Sister..so in my mind I have 3 separate "Blocks" but am I wrong? Is there an order to them like a the Kittler protocol?

Help...
Kath

[geneticgenie]

Has anyone identified any haploblocks for 10066, 67, 68, 69?

People tend to use the word "haploblock" loosely in different ways depending on what they are trying to compare.  In this case, I am guessing that Tomcat is asking if there are any X-SNP haploblocks that have been identified that bracket the X-STR markers that he mentioned (feel free to correct me if I misunderstood, Tomcat).  I'm not aware of any that have been, but that doesn't mean there aren't any. 

There is still some confusion about where exactly some of those STR markers are located on the chromosome.  The numbers shown underneath the marker numbers appear to be chromosome position numbers (base pair counts), but at least one of them doesn't correspond to a position that was published in the scientific literature.  I haven't really been studying X-STR markers enough personally to look into this yet, so maybe somebody else can answer that question for us.

As for why they are not displayed together (to respond to Kathleen's comment), it is presumably because those particular markers are not located anywhere near each other on the X chromosome.

According to the table by the Forensic ChrX research Board

http://www.med.uni-magdeburg.de/chrx/linkagde_tabelle.htm

the locations line up with our STRs but I am still confused about DXS10074, DXS10075 and
DXS10079 that are not present at this site. It is still worth visiting this German site that has an international following. At least somebody is doing ChrX research.

I am asking Thomas about the above STRs. Could there have been a mistake? Maybe more than one STR got the same label?

Kathy J.

[Seán MacGorman Powell]

According to the table by the Forensic ChrX research Board

http://www.med.uni-magdeburg.de/chrx/linkagde_tabelle.htm

the locations line up with our STRs but I am still confused about DXS10074, DXS10075 and
DXS10079 that are not present at this site. It is still worth visiting this German site that has an international following. At least somebody is doing ChrX research.

I am asking Thomas about the above STRs. Could there have been a mistake? Maybe more than one STR got the same label?

Kathy J.

Thanks for posting that link, Kathy, that definitely makes the cut for "URL of the Month" for me!  I'm very glad that you're asking Thomas what's going on with the position numbering, as I really haven't got a clue what's behind the discrepancies.

Kathleen, I'm as much in the dark about these STR positions as you are.  If the numbers at the bottom of the Xmatch search form are indeed correct base-pair position numbers, then the 4 markers that Tomcat asked about (DXS10066, 10067, 10068, and 10069) can't possibly all be linked as a block, as they are way too far apart on the X-chromosome.  Even the two of them that are closest-together (DXS01166 & DXS10068) are so far apart that it would be quite a stretch to call them linked.

If those numbers mean something different that I am assuming they are, then it might be a different story.  I just haven't been digging into X-STR research enough to be any sort of authority on this matter, as I've mainly been focusing on X-SNP's to date.

I think we'll just have to wait and see what Thomas says before we can analyze this any further, unless anybody else has any insight.

[tomcat]

Getting ahead of the important clarification of Xmatch numbering from TK, I call your attention to DXS8377 and DXS7423 both of which are numbered 149237039 and seem 'linked' as it is easy to find patterns across results in Xmatch. Don't know how informative they may as to ancestry as some patterns appear in ethnically diverse posters (try DXS8377-44 with DXS7423-15).

[Seán MacGorman Powell]

Getting ahead of the important clarification of Xmatch numbering from TK, I call your attention to DXS8377 and DXS7423 both of which are numbered 149237039 and seem 'linked' as it is easy to find patterns across results in Xmatch. Don't know how informative they may as to ancestry as some patterns appear in ethnically diverse posters (try DXS8377-44 with DXS7423-15).

Yeah, I have often noticed that those particular markers seem to share the same position number, and if that notation is accurate, then they are surely effectively linked.  Three other markers that share that characteristic are DXS10074, 10075, and 10079.  The position number for those three (120700000) seems to be much too round a figure to be an exact position number, and I suspect that they are simply shown as being present somewhere in that region.

[geneticgenie]

Yeah, I have often noticed that those particular markers seem to share the same position number, and if that notation is accurate, then they are surely effectively linked.  Three other markers that share that characteristic are DXS10074, 10075, and 10079.  The position number for those three (120700000) seems to be much too round a figure to be an exact position number, and I suspect that they are simply shown as being present somewhere in that region.

I think we need to call into serious question the accuracy of the locations of any STR marker that is listed at a rounded-off one thousandth position, namely the following:

DXS 10129, 10131, 10067, 10069, 10078. 10077, 10076, 10130, 10132, 10075, 10079, 10074, 10133, 10068, 10066 

[Seán MacGorman Powell]

I think we need to call into serious question the accuracy of the locations of any STR marker that is listed at a rounded-off one thousandth position, namely the following:

DXS 10129, 10131, 10067, 10069, 10078. 10077, 10076, 10130, 10132, 10075, 10079, 10074, 10133, 10068, 10066 

Yeah, it certainly does make one wonder how those positions were determined (or estimated) in the first place.  I'm sure Thomas will have a good explanation, as he always does.

[geneticgenie]

I think we need to call into serious question the accuracy of the locations of any STR marker that is listed at a rounded-off one thousandth position, namely the following:

DXS 10129, 10131, 10067, 10069, 10078. 10077, 10076, 10130, 10132, 10075, 10079, 10074, 10133, 10068, 10066 

Yeah, it certainly does make one wonder how those positions were determined (or estimated) in the first place.  I'm sure Thomas will have a good explanation, as he always does.

I don't know if you noticed, Thomas must have discretely corrected the 10075, 10079 and 10074 mistakes. See:
http://www.dna-fingerprint.com/modules.php?op=modload&name=xmatch
A gremlin must have been at work overnight to rearrange the X.

[geneticgenie]

Getting ahead of the important clarification of Xmatch numbering from TK, I call your attention to DXS8377 and DXS7423 both of which are numbered 149237039 and seem 'linked' as it is easy to find patterns across results in Xmatch. Don't know how informative they may as to ancestry as some patterns appear in ethnically diverse posters (try DXS8377-44 with DXS7423-15).

The position of two STR sequences will also have to be corrected.  There is no physical way two sets of STRs can occupy the same space at the same time.