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Author Topic: Haploblock Analyses Using the Worldwide HGDP-CEPH Panel  (Read 1034 times)
DKF
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« on: January 22, 2009, 03:20:17 PM »
The following is an analysis of 1045 individuals (673 males and 371 females) with 5249 SNPs using the PLINK program.  Anders set the bar at a minimum block of 1 Mb and 100 SNPs.

What is interesting is to see the individuals from various regions and who they match and at what location on the X (and who they don't match). 

There is a great deal of information about population history embeded in this analysis.  I have gone over it line by line (over 23,000 comparisons) and have taken notes.  I am hoping that a fresh set of eyes will notice things here that I might have missed so will wait for some time before I add my two cents.  I really hope that people do comment on their observations.  Observations are the first step toward hypothesis generation so lets see what we can see.

I also hope that this URL will "work".  It should open to a zip file which can easily be unzipped into Excel (automatcally with most computers).  I am including this analysis with the permission of Anders Palsen.

Here is the link:  http://www.davidkfaux.org/X-Segment-FauxV2.zip.  Enjoy.
« Last Edit: January 26, 2009, 01:45:08 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)
DKF
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« Reply #1 on: January 26, 2009, 01:53:44 AM »
I edited the above posting to include an amended link. 

http://www.davidkfaux.org/X-Segment-FauxV2.zip

Some minor errors were corrected and the comparisons expanded.  All credit goes to Anders who has developed true expertise in the use of complex phasing programs.

David.
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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)
Maria_W
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« Reply #2 on: January 28, 2009, 06:01:29 PM »
DKF,

When I try to open up your link it gives me an invalid or currupt warning...Could you please check it out or is it on my end....

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)
Svaale
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« Reply #3 on: January 28, 2009, 06:36:43 PM »
Quote from: Maria_W on January 28, 2009, 06:01:29 PM
DKF,

When I try to open up your link it gives me an invalid or currupt warning...Could you please check it out or is it on my end....

Maria

Works fine for me, just tried.
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JimT
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« Reply #4 on: January 30, 2009, 07:20:26 PM »
It worked for me.  Are you trying to open the zip file with Excel rather than unzipping it first?
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X chromosome 100% Halländsk (Danish before 1645; Swedish after 1645)
Maria_W
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« Reply #5 on: January 31, 2009, 01:43:00 AM »
Just wanted to let you know that now I can open it up.  Not sure what happened!

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 #6 on: January 31, 2009, 04:18:30 AM »
Quote from: Maria_W on January 31, 2009, 01:43:00 AM
Just wanted to let you know that now I can open it up.  Not sure what happened!

Maria
Great!  There is a huge amount of useful information in this file.  As long as one has Excel (even 2000) installed on the computer the zip file should open.  It could open in other formats for all I know.  Glad it worked out.  Just think, there will come a day when all of us can be included in this massive dataset.  At present it lacks a good reprsentative group of northwest Europeans.  Things are now happening at a lightening pace so we will see what is next to come down the pike.  I expect that the program PLINK will be around for a long time.  It is quite new and already has a lot of population and medical geneticists who are using it.
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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)
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