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Author Topic: Haploblocks for STRS  (Read 4466 times)
Seán MacGorman Powell
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« Reply #25 on: February 03, 2009, 10:35:39 AM »

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.

Ahhh, good catch, Kathy!  Now we're getting somewhere.

I see that DXS10076 has been moved too.  Also, the order of DXS10077 and 10078 have been reversed (though the position numbers haven't changed).

I just rearranged the project results chart to reflect these changes:

http://www.worldfamilies.net/geo/xdna/pats/raw
« Last Edit: February 03, 2009, 10:38:00 AM by GhostX » Logged

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tomcat
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« Reply #26 on: February 03, 2009, 10:58:47 AM »

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).

'Contradictory results' regarding these markers is the subject of a Szibor paper referenced on the ChrX site and For Sale online.
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Paternal X: 100% Ukrainian Ashkenazi. Maternal X: 50% Upper Midwest Native American, 50% European.
Seán MacGorman Powell
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« Reply #27 on: February 03, 2009, 11:10:20 AM »

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).

'Contradictory results' regarding these markers is the subject of a Szibor paper referenced on the ChrX site and For Sale online.

Hmm, interesting, Tomcat.  Are the contradictory positions at least located in the same general locus on the chromosome, or are they widely separated?
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geneticgenie
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« Reply #28 on: February 03, 2009, 11:20:03 AM »

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).

'Contradictory results' regarding these markers is the subject of a Szibor paper referenced on the ChrX site and For Sale online.

It sounds like there are many contradictory results. But if we can get the primer sequences,
we should be able to double check the results at the UCSC genome site by using BLAT.
FTDNA has always said it would abide by NIST standards.
Perhaps the standards have not been set by NIST yet, but surely FTDNA wants to report results that at least make sense. As the corrections are made in the literature, we are going to need to stay on top of the changes. We can't continue to do these kinds of comparisons with each other if the locations on the X chromosome are not clear.
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Kathy J.
X Chromosomes: 75% English, 12.5% German, 6.25% Dutch, 3.125% Irish, 3.125% Scottish;
from Father's X: 43.75% English, 6.25% Dutch;
from Mother's X: 31.25% English, 12.5% German, 3.125% Irish, 3.125% Scottish
Seán MacGorman Powell
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« Reply #29 on: February 03, 2009, 11:53:18 AM »

As the corrections are made in the literature, we are going to need to stay on top of the changes. We can't continue to do these kinds of comparisons with each other if the locations on the X chromosome are not clear.

Yeah, that very thought occurred to me earlier today, and it's going to be a challenge to keep things updated.  We'll just have to rely on each other to post changes here as we discover them.  I'll be sure to promptly change the results chart anytime anybody brings a revision to my attention, and I'll certainly post here anytime I discover one.
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tomcat
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« Reply #30 on: February 03, 2009, 12:35:21 PM »

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).

'Contradictory results' regarding these markers is the subject of a Szibor paper referenced on the ChrX site and For Sale online.

Hmm, interesting, Tomcat.  Are the contradictory positions at least located in the same general locus on the chromosome, or are they widely separated?
Think they are located close-by but I can't afford the paper. Also please note the 200,000bp  spread between HPRTB and DXS10066 and the patterning of results that suggest they may be linked in some cases.
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Paternal X: 100% Ukrainian Ashkenazi. Maternal X: 50% Upper Midwest Native American, 50% European.
tomcat
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« Reply #31 on: February 03, 2009, 12:38:10 PM »

Sorry, DXS10068 in within 200kbp of HPRTB.
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Paternal X: 100% Ukrainian Ashkenazi. Maternal X: 50% Upper Midwest Native American, 50% European.
Seán MacGorman Powell
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« Reply #32 on: February 03, 2009, 07:21:29 PM »

In case anybody misses this in the other thread (these threads are starting to overlap now, so it's hard to know the best place to post announcements like this!):

I added a new haploblock candidate to the X-chromosome Project's SNP results chart, between positions 66,573,001 (rs2497931) and 67,018,756 (rs2781516).  This one is of particular relevance because it includes 3 of the linked STR markers that we have been discussing (DXS10079, 10074, and 10075), so we can begin to compare SNP and STR blocks.  These are clearly part of a well-conserved SNP block, and this could be a very useful set of markers to study.

SNP results chart:

http://www.worldfamilies.net/geo/xdna/results/raw
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