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DKF
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« on: January 22, 2009, 03:03:13 PM »

Hello fellow X-philes (pun intended).

It occurs that some of us may already have taken a haploblock and examined it from head to toe.  Perhaps we can use this thread to report our successes.

At this point, we are all at different stages in the learning curve but over time each of us can build a skill set to enable us to get the most from a probing of any particular block.  I am including the analysis of my "Xibo Block" (it helps to name blocks).  This level of analysis will probably be outside the scope of many at this point in time, but it will give folks an idea of what can and will happen down the road. 

I take little credit (other than persistence) for the work here.  If it was not for Anders Palsen I would have little more than a general awarness of the characteristics of "my block".  His expertise in the use of sophisticated programs to explore haploblocks is what allowed me to develop an understanding of the block and offer an interpretation in keeping with the weight of data.  Also, although I did test with 23andme, they have not to date even painted the X let alone offered any tools for analysis.  My work is based on the decodeme data which can be directly compared to the huge HGDP-CEPH worldwide database.  I suspect that it won't be long before 23andme offers this capability (with a few modifications that may need to be made by genetic genealogists).

The information can be found at http://davidkfaux.org/X_Chromosome_NA_Haploblock.html

Hopefully it will inspire others to delve into a block in as great a depth as circumstances permt.

Thanks to Anders Palsen without whose help none of this analysis would have been completed.
« Last Edit: January 30, 2009, 04:00:03 AM by DKF » Logged

X-chromosome:  56.25% England; 12.5% Scotland; 12.5% Ireland; 12.5% Germany; 6.25% North America (Lower Mohawk, Six Nations)
Maria_W
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« Reply #1 on: January 26, 2009, 12:49:02 PM »

DKF,

I am very impressed with the work you have done.  I went to your website and it is absolutely amazing... Haven't had a chance to read most of it but I will be comming back to it later...I admit I know nothing about the X chromosome but I am willing to learn. I intend to monitor this site every day...I am happy to be a part of the X-files!  Hope you or someone else can help me out! Have a great day!

Maria
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DeCodeMe: Autosomal: African 2%, Asian 6%,  European 92%.  X: African 4%, Asian 9%, European 87%.
23andme: pending.
United States (Native American: Potowomecke from Virginia and European(Ireland, Scotland, Wales, England, Germany, Switzerland and France)
DKF
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« Reply #2 on: January 26, 2009, 02:15:57 PM »

DKF,

I am very impressed with the work you have done.  I went to your website and it is absolutely amazing... Haven't had a chance to read most of it but I will be comming back to it later...I admit I know nothing about the X chromosome but I am willing to learn. I intend to monitor this site every day...I am happy to be a part of the X-files!  Hope you or someone else can help me out! Have a great day!

Maria
Hello Maria, the only reason I have made as much progress as I have is thanks to the assistance of so many people with the same interests.  I made a big change in the website last night to include the analysis of autosomes to complement what had been done with the X.  Once we are through with the X (of course that will never happen) we will want to turn our attention to what is written on the autosomes.  I have found in reading the literature that other than the unique inheritance pattern of the X, the same basic principles apply such as linkage disequilibrium (SNPs that hitchhike along together for untold generations and are unlikely to be separated by a recombination event).

It is mind boggling that only two months ago I had never seriously considered that the X chromosome might have any particular ancestral significance.  It is like a light went on and now it is evident that there is an overwhelming amount of ancestral data written on it - it just needs decoding.  I hadn't even ordered any of the X STR markers from FTDNA - just a few autosomal markers.  That has all changed.

Perhaps the most important aspect that I have learned recently is that the output of both decodeme and 23andme is virtually useless unless you are from Utah, a member of the Yourba tribe in Africa, or Japanese.  The depth of the analysis offered to customers is at the amateur level, but worse, could be very misleading.  Not having Japanese ancestors, and there being little evidence that Japanese match Native Americans in genetic structure, it is now clear that there are serious gaps, ones that could be misleading.  I have tried to show in my analysis that unless one matches groups known via other sources to have the same ancestors as Native Americans (i.e., the Yakut of Siberia) then a match to say a Japanese is likely noise.  I am going to see if decodeme and 23andme are open to the creation of better tools for customers.  Right now we only see mist that may or may not have substance.

What is really needed Maria is enthusiasm and a dog with a bone attitude.  At this point in time the testing companies can offer little more than the data to work with.  We need to club together to understand some of the basic principles and then how to apply concepts such as centriMorgan to our own work.  Concering the latter we need to find out the rate of recombination in a particular region of the X before we can fully interpret out findings.  This is all far removed from Y and mtDNA work, but I find that actually seeing a series of say three million nuceotide bases, and being able to link this pattern to a specific ancestor and region of the world, as something entirely unique.  There is something very special about this sort of work, and we haven't even seen the tip of the tip of the iceberg yet.  What a great ride this is going to be for genetic genealogists.

I do hope everyone realizes that we are all rather new to this and that there will be a lot of head scratching and gnashing of teeth over the terms and concepts; but at least there are no seasoned veterans at this point, just a few who got an early start, and we can assist each other in the learning process.   
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X-chromosome:  56.25% England; 12.5% Scotland; 12.5% Ireland; 12.5% Germany; 6.25% North America (Lower Mohawk, Six Nations)
kathlingram
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« Reply #3 on: January 26, 2009, 02:28:21 PM »

DKF,

I am very impressed with the work you have done.  I went to your website and it is absolutely amazing... Haven't had a chance to read most of it but I will be comming back to it later...I admit I know nothing about the X chromosome but I am willing to learn. I intend to monitor this site every day...I am happy to be a part of the X-files!  Hope you or someone else can help me out! Have a great day!

Maria

Maria
Send the X STRS that you have tested ( FTDNA) to Sean/GhostX, the moderator and he will post them here for you..we have a few there already at this thread: "X-STR Results Chart "

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
DKF
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« Reply #4 on: January 30, 2009, 04:06:09 AM »

I have changed the URL in the first posting of this thread since I removed all of the autosomal work so that the focus would be entirely on the X (removing distractions and all).  A lot more detail has been added over the past few days.  It seems that every time I talk to Anders there is new information to include.  With each revision we appear to be getting closer to the sort of individualized analysis that some day, perhaps, decodeme and 23andme will include as a routine part of their analysis.  I am not holding my breath but perhaps we need to contact them to outline specifically what we would like to have.  Hopefully a conference call, arranged for early February, to the scientists to one of the companies will prove fruitful.
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X-chromosome:  56.25% England; 12.5% Scotland; 12.5% Ireland; 12.5% Germany; 6.25% North America (Lower Mohawk, Six Nations)
Svaale
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« Reply #5 on: January 30, 2009, 05:40:04 AM »

... perhaps, decodeme and 23andme will include as a routine part of their analysis.  I am not holding my breath but perhaps we need to contact them to outline specifically what we would like to have.  Hopefully a conference call, arranged for early February, to the scientists to one of the companies will prove fruitful.

I think deCODEme have the underlying engine already remember the key word "high-sharing" I think it is more or less the same thing. What deCODEme need is a webapplication that is able to let the user compare all the matching blocks in a user friendly way to the whole panel instead of one individual per population as presently in the genome browser.
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