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Author Topic: Haploblock Candidates Datasets (X-SNP results)  (Read 28074 times)
Seán MacGorman Powell
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« Reply #25 on: February 09, 2009, 05:26:32 PM »

You mean you are not ready to quit your day job?
Anthro-X-genetic genealogy  pays so well.

If I could get paid by the hour for how much time I have spent doing genetic genealogy work (including all my personal Y-DNA analyses) over the past year alone, I would probably be a very rich man!

I would so love to do this as my primary job.
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« Reply #26 on: February 15, 2009, 09:40:13 PM »

I've just added a new person's data to the X-SNP results chart.  This is testee ID #35, an anonymous contributor from Ben's spreadsheet, with reported ancestry from Ukraine, Belarus, and Lithuania:

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

I've also renumbered most of the testee ID numbers, to make room for this contributor and other future contributors from Ben's spreadsheet, so be sure to check the blue legend box on the far right of the chart for your current ID number.

Also, I would like to again urge everybody to make sure that the ancestry that they reported is for their X chromosome only, as discussed in this thread:

http://www.worldfamilies.net/forum/index.php?topic=8498.0

If you need to make any changes, please send me a PM.
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« Reply #27 on: February 22, 2009, 04:26:20 PM »

I've just added a new person's data to the X-SNP results chart.  This is testee ID #36, an anonymous contributor from Ben's spreadsheet, with reported ancestry mostly from the British Isles:

http://www.worldfamilies.net/geo/xdna/results/raw
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« Reply #28 on: February 27, 2009, 10:30:33 PM »

The URL for the X-SNP results chart has changed:

http://www.worldfamilies.net/geo/xdna/results?raw=1
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« Reply #29 on: March 02, 2009, 11:29:12 AM »

The glitch that has been preventing me from uploading updates to the X-SNP results chart has been fixed.  I've just uploaded the following additions:

1) Added a new block between positions 145,556,600 - 145,724,581, containing the X-STR DXS10066.

2) Added a new contributor, Cofgene2, with 100% German ancestry.

3) Testee ID numbers have been renumbered to make room for the new contributor.  Check the legend on the right margin of the results chart for your current ID number.

http://www.worldfamilies.net/geo/xdna/results?raw=1
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« Reply #30 on: March 02, 2009, 02:39:54 PM »

Here's another addition that I didn't get in time for my earlier update today:

Added a new contributor, name "Rollefson," with ancestry 75% Colonial America, 25% Irish.

The testee ID numbers have been renumbered again since my earlier post today, so be sure to check the legend.

This seems like a productive week for the testing labs--this is good to see!
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« Reply #31 on: March 03, 2009, 11:33:29 AM »

I made the following additions to the X-SNP results chart today:

1) Added results for new contributor "ID037," with 100% German ancestry
2) Added results for new contributor "Nevelainen," with 100% Finnish ancestry
3) Added some incomplete data for previous contributor "ID006," with British Isles ancestry.

As usual, I've renumbered the testee ID numbers, so check the legend.

http://www.worldfamilies.net/geo/xdna/results?raw=1
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« Reply #32 on: March 03, 2009, 08:12:06 PM »

I made the following additions to the X-SNP results chart today:

1) Added results for new contributor "ID037," with 100% German ancestry
2) Added results for new contributor "Nevelainen," with 100% Finnish ancestry
3) Added some incomplete data for previous contributor "ID006," with British Isles ancestry.

As usual, I've renumbered the testee ID numbers, so check the legend.

http://www.worldfamilies.net/geo/xdna/results?raw=1

This new Finn "Nevelainen" is interesting in my favorite slow-moving ancient block between 66,228,526 and 66,564,941.  My parents could be a combination of  two uncommon haplotypes, this Finn in one X block and also the X that has the nice crossover recombination, Italian/Ashkenazi “Warwick”.  So if you will permit me to (again) engage in seemingly senseless unscientific speculation, that could mean a couple of ancient founders since I have neither Finnish nor Italian nor Ashkenazi in my background.  So we will have to be on the lookout for more people falling into these two haplotypes to see if we can find the X founders in some likely geographical area.
Kathy J.
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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
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« Reply #33 on: March 03, 2009, 08:35:18 PM »

I made the following additions to the X-SNP results chart today:

1) Added results for new contributor "ID037," with 100% German ancestry
2) Added results for new contributor "Nevelainen," with 100% Finnish ancestry
3) Added some incomplete data for previous contributor "ID006," with British Isles ancestry.

As usual, I've renumbered the testee ID numbers, so check the legend.

http://www.worldfamilies.net/geo/xdna/results?raw=1

This new Finn "Nevelainen" is interesting in my favorite slow-moving ancient block between 66,228,526 and 66,564,941.  My parents could be a combination of  two uncommon haplotypes, this Finn in one X block and also the X that has the nice crossover recombination, Italian/Ashkenazi “Warwick”.  So if you will permit me to (again) engage in seemingly senseless unscientific speculation, that could mean a couple of ancient founders since I have neither Finnish nor Italian nor Ashkenazi in my background.  So we will have to be on the lookout for more people falling into these two haplotypes to see if we can find the X founders in some likely geographical area.
Kathy J.

That's probably my favorite haploblock too.  It's so stable, and such a long block to be so well-conserved.  It really impresses me that over 336,000 base pairs could be that preserved (with just a bit of variation) over what is obviously a very ancient span of time.

I love it when a new project contributor shows up who is 100% of any ethnicity.  I think I actually uttered out loud, "Yessss, another one!" when I saw the latest contributor.
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« Reply #34 on: March 04, 2009, 05:29:52 PM »

I made the following additions to the X-SNP results chart today:

1) Added results for new contributor "ID037," with 100% German ancestry
2) Added results for new contributor "Nevelainen," with 100% Finnish ancestry
3) Added some incomplete data for previous contributor "ID006," with British Isles ancestry.

As usual, I've renumbered the testee ID numbers, so check the legend.

http://www.worldfamilies.net/geo/xdna/results?raw=1

This new Finn "Nevelainen" is interesting in my favorite slow-moving ancient block between 66,228,526 and 66,564,941.  My parents could be a combination of  two uncommon haplotypes, this Finn in one X block and also the X that has the nice crossover recombination, Italian/Ashkenazi “Warwick”.  So if you will permit me to (again) engage in seemingly senseless unscientific speculation, that could mean a couple of ancient founders since I have neither Finnish nor Italian nor Ashkenazi in my background.  So we will have to be on the lookout for more people falling into these two haplotypes to see if we can find the X founders in some likely geographical area.
Kathy J.

I checked the HapMap group to see if I could find European matches with our more unusual haplotypes in this block and it looks like in the Utah group, NA07022, NA10837 and NA12752 match our #12, NA11891, NA11930 and NA12413 match Nevelainen and NA07349 and NA11839 match Warwick. I think most of the others fit into our main haplotypes but I was only eyeballing the results so I could have missed something.

So the prize goes to the person who can figure out who these founder X-eves could have been.  When and where did each one live? Were they Europeans?
Kathy J.
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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
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« Reply #35 on: March 05, 2009, 04:30:23 PM »

I added two more contributors to the X-SNP results chart today, labeled as follows:

1) "Wehba," with 50% Lebanese / 50% unspecified Colonial American ancestry.  That Lebanese part is a very welcome contribution to the project!  This is a female, so her results are presented as usual in as an "a" and "b" column, with asterisks replacing the heterozygous SNPs.

2) "Heffernan," with British Isles ancestry.

I've renumbered the testee ID numbers as usual, to make room for the new contributors.

http://www.worldfamilies.net/geo/xdna/results?raw=1
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« Reply #36 on: March 08, 2009, 08:55:21 PM »

I added a new contributor today, labeled ID039, from Ben's spreadsheet.  He is 100% Norwegian (75% Rogaland / 25% Nordland).


EDIT: I had previously wrote "ID038" here by mistake.
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« Reply #37 on: March 11, 2009, 05:37:39 PM »

I added a new contributor's results today, labeled ID040, from Ben's spreadsheet.  He is 100% Finnish.
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« Reply #38 on: March 14, 2009, 07:27:58 PM »

I added a new contributor's results today, labeled "Schmeer."  His X-ancestry is German and French.

http://www.worldfamilies.net/geo/xdna/results?raw=1
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« Reply #39 on: March 21, 2009, 11:15:55 PM »

I added a new contributor's results today, labeled "MacGorman (father)."  His X-ancestry (in descending order of prevalence) is French / Amerind (mtDNA A2) / British Isles / Spanish.

http://www.worldfamilies.net/geo/xdna/results?raw=1
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« Reply #40 on: March 22, 2009, 08:12:27 PM »

I added two additional contributor's results today, one labeled "Cofgene2 (father)," with 100% German ancestry, and the other adding some previously-incomplete data for member "Haegen" (Belgian ancestry).

http://www.worldfamilies.net/geo/xdna/results?raw=1
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« Reply #41 on: March 28, 2009, 10:08:01 AM »

I just added a column to the legend (the blue box at the far left margin of the results chart) for contributors to note their mtDNA haplogroup.

Note that the mtDNA lineage is only a small proportion of a person's X-DNA (a very small proportion, after going back several generations), but this information may be helpful to some researchers.

If you've already contributed data to the results chart, I encourage you to send me a PM with your mtDNA haplogroup, and I will add it to the chart.  While you're at it, please make sure that your ancestry percentages are only for your X-chromosome lineages, not your overall ancestry.  There are links on the bottom of the results chart explaining how to calculate this ancestry.

http://www.worldfamilies.net/geo/xdna/results?raw=1

When you reply, please let me know which chart(s) you have data submitted to (X-STR and/or X-SNP), and how you are identified in the chart(s).  Please do not refer to the "Testee ID" number on the X-SNP chart, because those numbers change frequently, but it's okay to refer to an ID number on the X-STR chart, because those numbers are relatively fixed.
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« Reply #42 on: March 29, 2009, 12:25:29 PM »

I added the results for the four anonymous males who just contributed to Ben's spreadsheet:

1) ID041 - German / British / Irish ancestry
2) ID043 - Irish / minor Spanish ancestry
3) ID044 - Finnish ancestry
4) ID045 - German ancestry

Please note that I am no longer extracting data for female contributors from Ben's spreadsheet, because it is too time-consuming to manually phase the data and delete all the heterozygous SNPs (i.e., SNPs for which you have two different nucleotide base letters in your results, indicating a different nucleotide inherited from each parent), and because presenting such incomplete data adds little useful information to the results chart.  However, any women who wish to be included can send me a PM with their e-mail address, and I will send you a data submission form with instructions on how you can report just your homozygous results to me, after which I would be happy to add it to the chart.  Your results will be presented anonymously unless you choose to be shown otherwise.

Results chart:
http://www.worldfamilies.net/geo/xdna/results?raw=1


EDIT: Removed comment that was based on a glitch in the data.
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« Reply #43 on: March 29, 2009, 03:55:23 PM »

I added the results for the four anonymous males who just contributed to Ben's spreadsheet:

1) ID041 - German / British / Irish ancestry
2) ID043 - Irish / minor Spanish ancestry
3) ID044 - Finnish ancestry
4) ID045 - German ancestry

Please note that I am no longer extracting data for female contributors from Ben's spreadsheet, because it is too time-consuming to manually phase the data and delete all the heterozygous SNPs (i.e., SNPs for which you have two different nucleotide base letters in your results, indicating a different nucleotide inherited from each parent), and because presenting such incomplete data adds little useful information to the results chart.  However, any women who wish to be included can send me a PM with their e-mail address, and I will send you a data submission form with instructions on how you can report just your homozygous results to me, after which I would be happy to add it to the chart.  Your results will be presented anonymously unless you choose to be shown otherwise.

Results chart:
http://www.worldfamilies.net/geo/xdna/results?raw=1

The chart didn't get uploaded properly for some reason earlier today.  It should be visible now.

Sean
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« Reply #44 on: March 29, 2009, 06:42:53 PM »

I added the results for the four anonymous males who just contributed to Ben's spreadsheet:

1) ID041 - German / British / Irish ancestry
2) ID043 - Irish / minor Spanish ancestry
3) ID044 - Finnish ancestry
4) ID045 - German ancestry

There are some interesting new haplotypes contributed by some of these people for the haploblock candidate that runs from position #66,228,526 - 66,564,941.  Specifically, see the new sub-block shown in green between positions 66,456-836 - 66,484,467.  Interestingly, the two people who show that new green block do not have any reported common recent ancestral origins.

Please note that I am no longer extracting data for female contributors from Ben's spreadsheet, because it is too time-consuming to manually phase the data and delete all the heterozygous SNPs (i.e., SNPs for which you have two different nucleotide base letters in your results, indicating a different nucleotide inherited from each parent), and because presenting such incomplete data adds little useful information to the results chart.  However, any women who wish to be included can send me a PM with their e-mail address, and I will send you a data submission form with instructions on how you can report just your homozygous results to me, after which I would be happy to add it to the chart.  Your results will be presented anonymously unless you choose to be shown otherwise.

Results chart:
http://www.worldfamilies.net/geo/xdna/results?raw=1

The chart didn't get uploaded properly for some reason earlier today.  It should be visible now.

Sean

Check your data.  I sent in number ID043 who should match the yellow group. There was a frameshift in the data.  Thanks for all your help.
Kathy
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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
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« Reply #45 on: March 29, 2009, 10:03:34 PM »

Quote from: geneticgenie link=topic=8437.msg110396#msg110396
Check your data.  I sent in number ID043 who should match the yellow group. There was a frameshift in the data.  Thanks for all your help.
Kathy

Thanks Kathy, you're right.  There appears to have been a bug in the program I wrote to convert the data from Ben's spreadsheet to the format of the project results chart.  Why that only affected two of the datasets I added today, and not the others, is a mystery to me, but I set it so that it shouldn't happen again.  No wonder the data looked so strange for those two people!  The fact that two different people shared the same odd recombination should have tipped me off.  I'm glad you were paying attention.

Hopefully there are no other frameshifts with any of the other data.  It should stand out very clearly if it happened elsewhere, and I don't see any such standouts.

Sean
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« Reply #46 on: April 11, 2009, 08:13:01 AM »

I added a new contributor's results today, labeled "ASmith."  Her X-ancestry is 100% English.  Note that because she is female, all of her heterozygous results have been replaced with asterisks, as they could not be resolved between her two X chromosomes.

http://www.worldfamilies.net/geo/xdna/results?raw=1
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« Reply #47 on: April 19, 2009, 05:31:11 PM »

I added a new contributor's results today, labeled "ID046," with 100% Greek ancestry.

http://www.worldfamilies.net/geo/xdna/results?raw=1
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« Reply #48 on: April 29, 2009, 05:24:04 PM »

I added two new contributors' results today, labeled "ID047" and "ID048."  Neither of them unfortunately provided any X-chromosome ancestry information.

http://www.worldfamilies.net/geo/xdna/results?raw=1

ID047 has a very interesting and rather unique haplotype in the block (actually a subsection of one of the haploblock candidates) that runs from positions 75,322,143 to 76,202,684.  Parts of that block have never been seen before in the dataset, and parts of it are similar to Currie's results, and I therefore wonder if they might represent African or Native American (or possibly earlier Asian) ancestry.  I'd have to examine the SNPs one-by-one in dbSNP before I could really come to that conclusion, but it is interesting.

Hopefully we can get the ancestry info for these contributors, as it could be particularly enlightening in this case.
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« Reply #49 on: May 01, 2009, 07:08:26 PM »

I added two new contributors' results today, labeled "ID047" and "ID048."  Neither of them unfortunately provided any X-chromosome ancestry information.

http://www.worldfamilies.net/geo/xdna/results?raw=1

ID047 has a very interesting and rather unique haplotype in the block (actually a subsection of one of the haploblock candidates) that runs from positions 75,322,143 to 76,202,684.  Parts of that block have never been seen before in the dataset, and parts of it are similar to Currie's results, and I therefore wonder if they might represent African or Native American (or possibly earlier Asian) ancestry.  I'd have to examine the SNPs one-by-one in dbSNP before I could really come to that conclusion, but it is interesting.

Hopefully we can get the ancestry info for these contributors, as it could be particularly enlightening in this case.
Some of the SNPs could have had a founder in Asia (or Native American?) such as rs6648142 (75844970) and rs958410 (76143152) but his 66 million block sure looks like the sub-Saharan African founder. So as you say, perhaps a mixture (why not African, Native American + European or similar heritage?) but I know better than to rule out anything. It would sure be interesting to see where these ancestors have been in the ancient past, or could there be a more recent ancestor in common between the two, ID047 and Currie?
Such secrets are hidden in our genes.

Kathy
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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
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