World Families Forums - Haploblock Candidates Datasets (X-SNP results)

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Author Topic: Haploblock Candidates Datasets (X-SNP results)  (Read 28040 times)
Seán MacGorman Powell
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« on: January 20, 2009, 02:19:55 AM »

I am starting to play around with the data uploading functionality of the X-chromosome Project website.  I've created a sample of one possible way that I envision X haploblock data being tabulated.  This is just a very rough "alpha version" of the table, but I wanted to post it for opinions before I proceed any farther with adding additional haploblock candidates.

The project website is adopted from the WorldFamilies Y-DNA projects, so is not really optimal for X DNA data yet.  Please ignore the "Notes for understanding results" below the spreadsheet, as that is the standard language posted on all Y-DNA results pages, and at present cannot be deleted (we're working on that).

Here are some things to note when you look at the results spreadsheet:

1) I have colorized all SNP values that have the same nucleotide among all the testees, with the same color.  This should facilitate the identification of different haplotypes within the blocks.  The more uniform the color is across a block, the better-conserved the block is over time (and the more pronounced is the linkage disequilibrium for that region of the chromosome).

2) You will notice that the rows and columns are transposed on this spreadsheet compared with the way that these haploblocks were presented over at dna-forums.org (so you read down a column for any given person here, not across).  This was necessary for several reasons, but primarily because we only currently have the capability to add a total of two spreadsheets to the project.  I therefore decided to include all haploblocks on the same spreadsheet, to be ordered in the same order as their position on the chromosome. 

Excel has many more rows than columns that can hold data, so it will be necessary to put the SNPs in rows, and the less-numerous testees in columns.  People who have been studying Adriano Squecco's Y-DNA spreadsheet and Ben Moscia's X-DNA spreadsheet will be used to this format, but people who are used to the horizontal format we've been using at dna-forums may find that they need to mentally adjust the way they look at this data.

If anybody has trouble visualizing things in this orientation, you can easily tranpose the rows and columns into an Excel spreadsheet of your own.  Feel free to ask me how to do this if you're not familiar with that function.  If we eventually gain the ability to post multiple spreadsheets on this website, such that we can have a separate spreadsheet for each haploblock, then we can decide if it would be more informative to go back to a horizontal layout.  In the meantime, I'd be interested in hearing your thoughts about which way works better for you, and also whether you feel it would be better to have all the data in one spreadsheet, versus broken out into separate spreadsheets by haploblock.

3) I originally had the names/ID numbers of the testees spelled out sideways in a top row of this spreadsheet, but the forum apparently can't handle that kind of formatting (or at least I haven't figured out how to make it work in the project's text editor).  I therefore replaced everybody's names with a shorter "Testee ID" code, with a legend near the top right showing which code corresponds with which testee.

4) There is an invisible column on the left margin of the spreadsheet that I will later use to mark the position of the centromere relative to the SNP sequences.

5) Using this spreadsheet format, with various haploblocks arranged all on the same page, I am not able to separately group different "Types" for each haploblock the way we have been doing at dna-forums (due to the fact that the order of the testees must always be the same from one haploblock to the next, in order for the columns to line up properly).  Hopefully the colorization will make this grouping unnecessary, as the groupings should be readily visible at a glance.

6) Underneath each haploblock candidate are some statistics that I calculated for that block.  I discussed some of the assumptions for these calculations on this post over at dna-forums:

http://dna-forums.org/index.php?s=&showtopic=5756&view=findpost&p=80449

If anybody feels that these calculations are invalid or uninformative as stated, I would welcome any discussions here about a better way to summarize information about the recombination rates of the various haploblocks.

So please take a look and let me know if you think this format will be useful to you.  There are several more haploblocks that I can then add to the spreadsheet (as we've been posting over at dna-forums), but it requires quite a lot of work to set up this spreadsheet, so please bear with me as I add them one or two haploblocks at a time.

Here's the URL to the non-frames version of this spreadsheet:

http://www.worldfamilies.net/geo/xdna/results?raw=1
« Last Edit: February 27, 2009, 10:40:58 PM by GhostX » Logged

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« Reply #1 on: January 21, 2009, 11:30:07 AM »

I've just added a third haploblock candidate to the project results page, again copied from what was previously posted at dna-forums.org, but converted to the new project format.

As I noted earlier, it is quite a lot of work to convert from the dna-forums.org format to what is being posted here (mainly due to all the colorization and the rearranging of all the columns to the same order for each block), so please bear with me while I add these blocks one at a time.  I am starting with the blocks that I contributed, simply because they are easier for me to deal with, but I'll get around to adding everybody else's blocks too.

I've also done some minor reformatting of the spreadsheet, and I've renumbered the testee ID numbers.  I may periodically reorder the columns in the spreadsheet, so please don't assume that the ID number that is currently assigned to you will be the same in the next iteration of the spreadsheet.  Always check the legend on the right margin of the spreadsheet for the current testee ID assignments.

If anybody would like their name listed in a different way, just let me know.

Again, please note that these blocks are being arranged on the spreadsheet in the order of their relative positions on the X chromosome (not in the order that they are added to the spreadsheet).  The latest block is the one that's in between the other two.
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« Reply #2 on: January 21, 2009, 01:55:23 PM »

I've just added a fourth haploblock to the spreadsheet, again extracted from dna-forums.org:

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

I've also started adding X-STR marker locations to the spreadsheet, in the appropriate positions in the chromosome sequence (as they've been getting posted on the Rootsweb list).  If I miss any, or if anybody knows where the remaining STRs that are currently being tested are located in the nucleotide sequence, please let me know and I'll add them.

I'm trying to come up with a better way to present X-STR test results given the limited number of spreadsheet slots that I have available on the project website, so stay tuned.
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« Reply #3 on: January 21, 2009, 10:04:17 PM »

I've just added a couple more haploblock candidates to the spreadsheet, extracted from the posts at dna-forums.org:

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

I'm discovering that it's no easy matter to consolidate all the haploblocks that people have been posting, such that they are all formatted the same way!  Also, people's names are listed in different ways from one source to another, so it's proving to be a challenge at times to figure out who is whom.  People are listed by Ben's spreadsheet codes in some places, but by name in others, so it is possible that I have you listed by name in one of the right-hand columns of the spreadsheet for one haploblock, whereas I have you listed by ID number for a different haploblock.  This makes no difference at all to any data analyses, but if you would prefer that I list you in a different way or consolidate your entries into a single column, just let me know.  Otherwise, it's no big deal to have you listed in two different ways.

I'm adding researchers' haploblock contributions one at a time now in the order that they occur on the chromosome as I work my way down the chromosome (not in the order that they were discovered), so please bear with me if I haven't posted yours yet--it's going to take me a while to get to them all.
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« Reply #4 on: January 22, 2009, 12:16:55 PM »

What criteria is used for selecting interesting haploblocks?
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« Reply #5 on: January 22, 2009, 12:36:20 PM »

What criteria is used for selecting interesting haploblocks?

That's really up to the person who identified the haploblock candidate.  In some cases, they started out simply as a female testee noticing that she was completely homozygous (i.e., the same nucleotide value duplicated at any given SNP position for both of her X chromosomes) for a long sequence of SNPs (indicating that both of her parents had exactly the same SNP values for that block), so she invited other people to post their results for that block to see if they too shared those values.  Chances are excellent that if a female is homozygous for a stretch of SNPs, then many other people will turn out to be too, and a new haploblock is born.

Speaking for myself, I visually scanned Ben Moscia's spreadsheet of X DNA testees (with the aid of some conditional formatting) and looked for blocks where most people (if not everyone) had the same SNP values as me.  I ignored any no-calls and treated them as "wildcards" (as Jim Turner put it).  Then I subjectively decided on upper and lower bounds for the sequence, to bracket a block that demonstrated minimal-to-no evidence of recombination.  So the haploblocks that I contributed were visualized by comparing several different people simultaneously.  It's effectively the same technique as a female looking for homozygous blocks in her own test results, but expanded to more than just two people being compared at a time.

Note that I am calling these blocks "haploblock candidates," because we don't really know at the time of their discovery how well-conserved they are across everybody, and different people have different definitions for the population that a block has to be conserved across (and for the length of the sequences) for it to be defined as a "haploblock."  So people can decide for themselves if it really is a haploblock.

The trick is finding haploblocks that don't contain any genes though, because we don't want to include any of those, for privacy reasons.
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« Reply #6 on: January 22, 2009, 12:52:00 PM »

One more haploblock candidate added, extracted from dna-forums.org:

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

I've rearranged the columns so that the testees are in alphabetical order, and reassigned new ID numbers to everyone.
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« Reply #7 on: January 22, 2009, 01:58:35 PM »

One more haploblock candidate added, extracted from dna-forums.org:

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

I've rearranged the columns so that the testees are in alphabetical order, and reassigned new ID numbers to everyone.
In the words of Jim Carey, "smokin".  What an amazing amount of info is now, thanks to your tireless efforts GhostX, availble for consideration.  We are well and truly underway.  Hopefully Terry will be able to add a bit more "X specificity" and functional space for what we hope to do.  I expect that this will happen in due course, and in the meanwhile we have plenty to explore.  I have a few things to add today.
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« Reply #8 on: January 22, 2009, 02:22:12 PM »

In the words of Jim Carey, "smokin".  What an amazing amount of info is now, thanks to your tireless efforts GhostX, availble for consideration.  We are well and truly underway.  Hopefully Terry will be able to add a bit more "X specificity" and functional space for what we hope to do.  I expect that this will happen in due course, and in the meanwhile we have plenty to explore.  I have a few things to add today.

Thanks for the comments, David.  The thanks really deserve to be spread around among all of us enthusiastic amateur genetic genealogists who take the trouble to look for these haploblocks (and other kinds of data), and the testing lab customers who contribute their test results.  It's obvious that it's not the sole domain of professional geneticists to advance this field of study (though their contributions are invaluable, and we wouldn't be where we are without them).
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« Reply #9 on: January 22, 2009, 05:13:41 PM »

I agree with David, this is good work GhostX! This method is good for smaller interesting blocks, but I dont see how comparing several hundred SNP would fit so well using this method.
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« Reply #10 on: January 22, 2009, 05:40:34 PM »

I agree with David, this is good work GhostX! This method is good for smaller interesting blocks, but I dont see how comparing several hundred SNP would fit so well using this method.

Thanks for the comment, Svaale.  I agree with you that this wouldn't work so well for really large blocks of several hundred SNPs, but blocks that large would be much more specific to smaller subset of the population of testees, and would be outside of the scope of what we are able to present here on the results page (indeed, it would probably exceed the size of the spreadsheet slot available to us!).  It's going to be up to specific researchers who have interest in those large blocks to analyze them on their own, and hopefully report their findings here.

My goals with the spreadsheet that's posted here, at least for the present, is to identify haploblock candidates that are extremely well-conserved across most people, which most people would therefore have common interest in, and to consolidate the blocks that have been examined so far into a single place, with a common format.  These blocks appear to be largely in the range of about 20-60 SNPs or so (judging from the contributions so far).

I'm actually beginning to wonder how much bigger the spreadsheet can get before we run out of space available to us at the website...
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« Reply #11 on: January 22, 2009, 05:55:26 PM »

One more haploblock candidate added, extracted from dna-forums.org:

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

It starts at position #68455063.

This one was by far the hardest one for me to colorize, and some of the color groupings are largely arbitrary, with various possible recombination and mutation events producing them.  There's quite a lot of recombination that obviously happened in this block, though there are still some sub-segments that are well-conserved.

It seems to me that blocks like this one might be more useful for separating out subgroups and identifying more recent lineage splits (relatively speaking--we're still potentially talking about many thousands of years between crossover events), whereas blocks that are more uniformly-colored might be more useful for reconstructing very ancient ancestry, and for determining what the earliest versions of the human X chromosome looked like--at least as far as is possible to trace through the X chromosome.
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« Reply #12 on: January 23, 2009, 09:06:44 PM »

Two more haploblock candidates added, extracted from dna-forums.org:

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

I've also recolorized some of the sequences in a few of the blocks.  The more I stare at a given haploblock, the more the patterns of recombination seem to rearrange themselves in my mind!  There are several different ways that the recombination events could have been indicated (and on many occasions it is not clear whether a recombination or a mutation was the cause of a variant), so this is just my interpretation.

I think that's the last of the haploblocks that's been discussed on the "X-DNA Haploblocks" sub-forum at dna-forums.  If I missed any, or if anybody has any corrections or data additions, please feel free to send me a PM and I'll be happy to fix them.

If anybody has a new haploblock that they've discovered, please feel free to start a new topic thread on this forum board, and I'll post it to the spreadsheet if it looks like a lot of people share the sequence.  Again, for privacy reasons, please be careful not to post any sequences that contain genes.
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« Reply #13 on: January 24, 2009, 06:45:04 PM »

Hi Sean,
I am in the spreadsheet under some haploblocks as testee 55 "Eldon" and under some other haploblocks as testee 125 "Wade".   That was not your mistake but maybe you could fix it.
There are six haploblocks for which I have not yet provided any information.  I have that information in an Excel spreadsheet.  How may I get that spreadsheet to you?
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Y-DNA:  R1b1a2a1a1a4b1 (R1b-L148).
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« Reply #14 on: January 24, 2009, 06:56:13 PM »

Hi Sean,
I am in the spreadsheet under some haploblocks as testee 55 "Eldon" and under some other haploblocks as testee 125 "Wade".   That was not your mistake but maybe you could fix it.
There are six haploblocks for which I have not yet provided any information.  I have that information in an Excel spreadsheet.  How may I get that spreadsheet to you?
Regards,
Eldon Wade
ewade@cfl.rr.com


Hi Eldon,

I'll be happy to make those corrections for you.  I'll send you a PM with some details in a minute.
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« Reply #15 on: January 27, 2009, 08:05:15 PM »

One more member's data has been added to the X-SNP results chart.  He is currently Testee ID#72, but that number may change as new people get added:

http://www.worldfamilies.net/geo/xdna/results/raw
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« Reply #16 on: January 28, 2009, 04:21:40 PM »

Testee ID#83 has been updated with additional data:

http://www.worldfamilies.net/geo/xdna/results/raw
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« Reply #17 on: January 28, 2009, 11:24:44 PM »

I've just posted a major revision of the X-SNP results spreadsheet:

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

Changes include:

1) Added data from Ben Moscia's spreadsheet for all haploblocks for which this data was incomplete. This updates the haploblock data by over 30 new testees for several haploblocks.

2) Renumbered the Testee ID numbers, due to new members having been inserted into various places in the spreadsheet.  Please check the legend for your current ID number each time you visit the results page.

3) Added ancestry information to testees, where available (info taken from Ben Moscia's spreadsheet and David Faux's spreadsheets).  See the legend in the right margin of the spreadsheet, and please let me know if anything is incorrect or missing.

When reporting ancestry, please make sure you are reporting your X-DNA lineages only.  X-DNA ancestor contributors can be determined from charts found on the following websites:

http://www.thegeneticgenealogist.com/2008/12/21/unlocking-the-genealogical-secrets-of-the-x-chromosome/

http://www.thegeneticgenealogist.com/2009/01/12/more-x-chromosome-charts/

I would prefer to show actual percentage contributions for all X-DNA ancestors by major ethnic group/country, if known (see the spreadsheet's legend for some examples--look for the entries showing percentages).  These percentages can be calculated from the above charts.
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« Reply #18 on: January 28, 2009, 11:49:30 PM »

I've just posted a major revision of the X-SNP results spreadsheet...

Oops, I didn't upload it properly a few minutes ago.  The revision should be there now.
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« Reply #19 on: February 02, 2009, 11:15:16 PM »

A new haploblock candidate has just been posted on the project's X-SNP results page.  It's between position numbers 105,197,873 and 105,712,333 (SNPs rs5916968 thru rs5917009):

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

This is an intergenic region, as far as I am able to determine.

I have only posted the results for people who have given me explicit permission for this particular block, even if they had previously told me that they no longer care to be anonymous in Ben's spreadsheet.  I have also posted the results of all people from Ben's spreadsheet who are still completely anonymous.  If you are one of the people who is in Ben's spreadsheet, but who I had previously removed from the anonymous section, I have your data all ready to add to the results page, so just send me a PM and let me know that I have your permission to do so (check the project results page to see if your data is there first).

Anybody who is not on Ben's spreadsheet can also PM me with their e-mail address if they want to be included, and I will send you a data submission form on which you can enter your data.  This also applies to any other haploblock candidates for which you want to submit data.
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« Reply #20 on: February 03, 2009, 11:13:56 AM »

A new haploblock candidate has just been posted on the project's X-SNP results page.  It's between position numbers 105,197,873 and 105,712,333 (SNPs rs5916968 thru rs5917009):

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

I just made a few corrections to that latest block.  I had neglected to delete the results for heterozygous SNPs for females and replace them with asterisks.
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« Reply #21 on: February 03, 2009, 07:07:42 PM »

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

1) Added a new project member, currently assigned Testee ID#35 (ID numbers subject to change, so always consult the legend on the right margin of the results chart).

2) Added a new haploblock candidate, between positions 66,573,001 (rs2497931) and 67,018,756 (rs2781516)

3) Began adding X-STR positions to the results chart to show their locations relative to the SNP's.  So far I have only done this to the new block mentioned above, but I will continue to add more as they are found to be relevant to a particular haploblock candidate.

Results chart:

http://www.worldfamilies.net/geo/xdna/results/raw
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« Reply #22 on: February 08, 2009, 05:31:54 PM »

It would not be difficult to gather all the SNP results from the HapMap Utah residents and put these
in our Haploblocks.  It is task to go through all the batches of results, but it can be done.

This is the group I am talking about:
“30 mother-father-child trios from the CEPH collection (Utah residents with ancestry from northern and western Europe), representing one of the populations studied in the International HapMap project ( http://www.hapmap.org). See http://www.hapmap.org/citinghapmap.html.en for further information about this population and others studied in the project. http://www.hapmap.org/hapmappopulations.html.en also has relevant information.”

But I don’t think we can find STR results on any of these individuals.  Maybe they are all LDS members who have extensive pedigrees, and some of them would not mind at least giving us their X percentages and would be willing to run their DNA for STR testing. Well you never know, some of them may read this forum some day and want to participate by allowing us to use their intergenic results in order to push genetic genealogy forward.
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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 #23 on: February 08, 2009, 10:12:17 PM »

It would not be difficult to gather all the SNP results from the HapMap Utah residents and put these
in our Haploblocks.  It is task to go through all the batches of results, but it can be done.

That's a really good idea, Kathy.  I'm rather bogged down with some data analysis issues at my "real job" right now, and may not have time to look into that for a while, but if anybody else cares to do that and submit the data to me, then I'll be happy to add it to the project results chart (assuming there are no restrictions on reproducing such data).  I have a data submission form already prepared (for use for new members to submit their data) that would work very nicely for such a purpose.
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« Reply #24 on: February 09, 2009, 05:21:30 PM »

It would not be difficult to gather all the SNP results from the HapMap Utah residents and put these
in our Haploblocks.  It is task to go through all the batches of results, but it can be done.

That's a really good idea, Kathy.  I'm rather bogged down with some data analysis issues at my "real job" right now, and may not have time to look into that for a while, but if anybody else cares to do that and submit the data to me, then I'll be happy to add it to the project results chart (assuming there are no restrictions on reproducing such data).  I have a data submission form already prepared (for use for new members to submit their data) that would work very nicely for such a purpose.

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