Showing posts with label Big Y. Show all posts
Showing posts with label Big Y. Show all posts

Saturday, August 9, 2014

Unraveling BIG Y Test Results: R-S1026


For a long time I have been stymied in my efforts to trace my SNP trail through the most recent three or four millennia down to genealogical time. Now we are beginning to make some headway due largely to the herculean efforts of the citizen scientists of the R-L21 and subclades project. The BIG Y, Full Y, Chromo2 and other discovery tests are providing multiples of the numbers of SNPs that had been identified prior to the beginning of 2014. 

R-L21 is the most prevalent male haplogroup along the western coast of Europe. In some areas it approaches 80% of the male population. Therefore, knowing that one is part of this mega clan is interesting but not very useful genealogically speaking. I had tested positive for DF13 which is a SNP just below L21. This still is not that useful as the vast majority of R-L21 men also belong to this subdivision. A dozen subclans of DF13 have been discovered in recent years but one by one I had tested negative for all of them prior to getting my BIG Y results. Now I know that I belong to the newly identified S1026 subclan. Below are the results of nine of us who have BIG Y results: 
This chart lists the SNPs for each of us that have been discovered downstream (toward the present) from S1026. At least six men have been identified by the Chromo2 project at ScotlandsDNA. 

My results are those in the middle column above. The man whose results are my closest match in the SNP chart above (just to the right of mine) is a sixth cousin-once removed. He and I share 105 of the 111 short tandem repeats (STRs) over which we previously had been tested. We appear to share five SNPs that so far separate our migration trail from that of any of the other members of this emerging group. He and I share a common ancestor who died in Southern Maryland in 1733. Even more recently I have four additional SNPs and he has seven.

The McDaniel man represented by the SNP trail in the column to my left above is my next nearest relative in this grouping. He and I previously had discovered we shared 35 of 37, 64 of 67 and 102 of 111 STR markers. He has seven identified SNP mutations since his ancestral DNA trail separated from mine and that of my Dowell cousin. The three of us share nineteen additional so far identified SNPs in common before our common trail merges with that of the three men in the columns to our right. Then the six of us share five earlier SNPs before we converge with others with whom we share SNP R-S1026.

It is going to take test results from additional men to sort out the exact sequence in which all these SNPs should be arranged chronologically. For example, we know that the five SNPs recently named (see chart above):
Z16886 Z16887 Z16888 Z16889 Z16890
are grouped together but we don't know in what chronological sequence they occurred. Only as more are tested and some are positive and others are negative will this more precise arrangement be possible. This sorting of other SNPs which are lumped together above will follow a similar process. As a result the SNPs will appear to be out of sequence as their correct ages and thus their actual locations along the migration path of our paternal DNA begin to appear. This will result in the nice orderly naming progressions to be scrambled.

Isn't genetic genealogy fun? The more we discover the more we have yet to learn. 

Monday, December 16, 2013

When will you see BIG Y results?



When will we see the beginning of the SNP Tsunami from the large number of BIG Y tests many of you have ordered? 

Got a calendar on the wall for the first quarter of 2014? Got a dart? ;-)

I'm in batch 542 (see blog earlier post) which was originally predicted to be returned 12/31/2013. What great fun it would have been to decode Y-SNPs on New Years Eve!  This predicted date on my FTDNA page -- as many of you probably know -- has now eroded to 2/28/2014. The FAQ on FTDNA’s site has always said a less specific February, 2014.

On December 6th Janine Cloud, Customer Service Manager @ FTDNA wrote:
FYI: When a kit is batched it automatically gets an expected results date. Unfortunately, it is batch-specific, not test specific. There's not currently a mechanism to set that message by test type until AFTER it's been batched.

 For example, everyone knows that a Y-12 will get results faster than a Y-111, yet both get the same expected results date if they're batched at the same time.

 Since everyone who ordered Big Y already had testing done with us, the orders batched each Wednesday as usual, even though the test has not begun running yet. Consequently, those Big Y tests got the same expected results date as all the other tests in the batch. With regular tests, we don't know that the whole group of tests will not be ready at the end of that expected results dates, but with the Big Y we did, so rather than wait until the end of the block of time, we arranged for those dates to be changed up front to help mitigate some of the potential for frustration over the test not being completed by that initial date.

 Normally those dates are updated the day after the expected date, but in this case there was reason to wait until Jan 1st, etc. to make the change. 

Then a few days later from Thomas Krahn who used to manage the SNP testing in the FTDNA lab but now runs his own company:

Good news for Big Y! I was at FTDNA yesterday and Max has told me that they have the first successful runs in house completed. He didn't say on which machine they were running (MiSeq or HiSeq) and he didn't comment on possible barcoding problems, but this gives us hope that some customers may not need to wait until next year to see their results.

We have also discussed the transfer of customer samples. It is important that those who want their samples transferred need to contact Max directly (max@genebygene.com) because apparently a commitment from the FTDNA customer support is not sufficient. However if Max approves them himself, then there doesn't seem to be a problem that samples can get transferred. Usually 50ul are sufficient. However if there is a way to get a new sample, then both companies would prefer that method instead of a sample transfer. Only samples that cannot be re-done or where laws prohibit taking a new sample should consider the transfer.

Also good news for FGC customers: YSEQ has returned the first results to our customers today. Most of the FGC markers could be confirmed right away with Sanger sequencing. It seems that Greg has done a very good job with analyzing the data. In addition to that we have kicked out a bunch of SNP candidates on repetitive and X homologue sequences during the primer design phase, so that the remaining FGC markers were almost all a hit on the first try. Especially I'd like to point out the FGC5496 marker for R1b-DF13 researchers because it has also been confirmed in another sample of the 1000 genomes project. This marker is available at http://shop.yseq.net/ already.


If you aren't confused yet, you haven’t been paying attention! Let me know when you get your results.


Happy Holidays!!

Friday, November 15, 2013

BIG Y Tests Begin Processing


At the moment I'm riding the crest of the BIG Y-SNP tsunami. Both my kit and that of my deceased father-in-law are showing on our respective personal pages at FTDNA as: 



So we seem to have made it into a batch that started processing on Wednesday. IF all goes well, I should have my results available to contemplate as I watch the ball drop on New Years Eve. 

It would be unusual if a project as "big" as BIG Y actually came off without a hitch and on schedule. However, miracles do happen. As some of you have heard me say, I was born in Missouri, the "Show-Me" state, and l an a slow learner. Therefore I believe most things two weeks after I see them. 

So the first batch may or may not come back on time. I'm not sure how often batches will be started. That depends on how many orders are received. So the second batch of BIG Y tests may be a decent interval behind the first.

With Y STRs my Dowell DNA project has been able to reconstruct the exact 111 marker results of my 6th great-grandfather Philip Dowell who died in 1733 in Southern Maryland. Where was he or his ancestors before he showed up as an established tobacco planter in the 1690s and where did he get all his "guY DNA?" My voyage of discovery takes on a new leg -- surfing the BIG-Y. 


UPDATE: FTDNA has posted this FAQ:

How soon will I have my BIG Y results?
We plan to release the first set of BIG Y results in February 2014.

Does anyone want to start a pool to predict the date I'll actually get my results?

Wednesday, November 13, 2013

ISOGG Group Gears Up For SNP Tsunami


The International Society of Genetic Genealogists (ISOOG) is a totally voluntary organization that does not charge dues. However, since 2006 it has been responsible for maintaining the Y-DNA Haplogroup Tree 2013 for researchers and testing labs around the world. The number of SNPs being discovered has been exploding since the end of 2010 and this is just the beginning. The recent wave of newly discovered SNPs have resulted from the Walk the Y, GENO 2.0 and 1,000 Genomes projects as well as the normal discovery processes of investigation by academics and citizen scientists.

End of year
Cumulative # of SNPs in tree
2006
436
2008
790
2010
935
2012
2067
Sept, 2013
3610


The tsunami has yet to come. Geno 2.0 has not yet published all its SNPs. Treasure troves of additional SNPs from FullGenomes and FTDNA’s Big Y tests loom just over the horizon. These have the potential to identify and place thousands of here-to-fore unknown SNPs. Many of these will be leaves toward the ends of branches on the Y-DNA Haplogroup Tree. They will be recent enough to connect with the documented trees by genealogists. 

In anticipation of this bounty and the chaos that may accompany it, those members of the ISOOG group who maintain this tree who were able to gather in Houston on Saturday planned for this event.  

Alice Fairhurst (center) leads the discussion. Members of her group in attendance (clockwise from Alice) are Richard Kenyon, Marja Pirttivaara, Michael Herbert, Sue Berry, Dr. D. (in red), Tim Janzen, Astrid Krahn and Thomas Krahn. (Photo courtesy of Katherine Borges)
It is clear that our processes need to be reorganized and streamlined if we are going to be able to continue to serve the genetic genealogy community and researchers in related disciplines in a timely basis.