What's Your ySNP Testing Strategy?

In my last post Tested 67 ySTR Markers? Now What?, I discussed how you could get some idea of what your more recent ySNPs might be than the ones estimated by FTDNA. This knowledge can be useful whether or not you want to pursue further SNP chasing aggressively or not.

To build on the example in that last post, it looks like most if not all of those who had ySTR matches in that group actually belong to the R-S1026 haplogroup. This is a small clan that is now thought to have split from DF13 about 3,500 years ago. S1026 was just added to the FTDNA SNP Tree about a month ago. It still has not been added to the ISOGG yTree although the L21-DF13-S1026: R-S1026 and Subclades Project is linked from there. Our mechanisms for organizing new findings have been overwhelmed by the SNP tsunami of the last two years. 

If you have gone through the process of finding the project for your matches who have done extensive SNP chasing, you can get a general idea of where your personal ySNP trail was located. For example, in the example I have been following, S1026 is the pale pink group of boxes in the bottom right-center of the following diagram created by volunteer super SNP chaser Mike Walsh:

Only a small fraction of these SNPs were known two years ago. We are still in the early days of understanding SNPs. We are about where we were about 10 years ago in our understanding of STRs. 

Even more specific information can be found by following the SNP trails of our STR matches. The group of pink boxes associated with S1026 above have been expanded by another volunteer super SNP chaser Alex Williamson:

Now I must introduce the concept of a block of SNPs. In Alex's chart above most of the SNPs between S1026 at the top and the individuals tested at the bottom are located in blocks (or boxes). These blocks may contain only a couple of SNPs or as many as 30. We know that these SNPs in a given box are located contiguously but we are still working to determine their exact sequence chronologically. In addition it is thought that these SNP mutations occur at random but about once ever 150 years. That number will be refined as more individuals are tested and our knowledge base grows.

In the chart above some of the men listed at the bottom would be the ones that are likely to have been your 67 marker STR matches in my previous post. In this case they are the ones under the large fat SNP block in the center of the chart. Your results will differ. This example is a little skewed because several of us encouraged our closest ySTR matches to take the BIG Y test -- a strategy you may wish to employ if you do decide to take the BIG Y test.

If you are fortunate enough to be chasing a SNP that is below R-L21, you will be able to use the tools created by Mike and Alex to learn more about your own SNP path. If you are a member of a different haplogroup, hopefully there will be an experienced SNP chaser in your group who can guide your search. These volunteers are absolutely the most knowledgeable individuals about your haplogroup. 

ySNP TESTING STRATEGIES
I am going to continue to use my own haplogroup for illustration purposes. Of course your situation will differ. 

Within our haplogroup project we have proved that those with close ySTR matches also appear to have relatively close (pun intended) ySNP paths of descent down through the eons.
The three strategies from which you can choose going forward depend on your genealogical goals and the amount of disposable cash you can use to feed this addiction. This is clearly not the case where one strategy is the best fit for all.

Those three strategies are: 

1. to test one SNP at a time and hope, by lucky guess or the process of elimination, to document one's actual SNP trail;
2. to take one of the NextGen comprehensive ySNP tests such as FTDNA's BIG Y or Full Genomes Y Elite 2.0; or
3. to test with one of the bundled panels that are being assembled by various labs.

Of course you can choose a 4th option -- none of the below. That would be to travel through ySNP-land vicariously as we have been doing in this post and the post that preceded it. However, if you wish to further explore your own situation, I would encourage you to chose ONE of the strategies below and not to flip-flop back and forth between them.


Testing individual SNPs

1. The strategy that appears to be the least expensive at the beginning can become the most expensive over the long term. Both FTDNA and YSEQ offer single SNP tests for thousands of SNPs. To employ this strategy you choose a SNP to be tested from a catalog list of those offered. If you choose wisely, you may be able to advance your search for a modest cost. However, if you are ordering single SNP tests at random you can easily spend more, over time, than you would by starting with a more comprehensive test in the beginning. Ordering single tests in sequence is also time consuming because you really should order one at at time, wait weeks for the results and then decide whether another single SNP test would be useful. Single tests are currently $39 at FTDNA and about half that at YSEQ. Both are legitimate labs. FTDNA is in Houston, TX, and YSEQ is in Berlin, Germany. YSEQ is a nimble two person operation that specializes in yDNA. FTDNA offers more comprehensive DNA testing products and services including easy integration into thousands of volunteer led projects.                                                                            
2. Your needs may better by hanging on to the money you have available now and waiting until you can afford a more comprehensive test. While the single SNP testing above is somewhat like dispatching a census taker to a specific location to see in a given SNP is negative or positive, the more comprehensive testing is more similar to taking satellite photographs of the 58 million or so SNPs along your Y chromosome. Many passes are made and stitched together by a computer algorithm. While it may not be as exact in every case as the individually targeted SNP testing (Sanger), it is certainly more cost effective and gives results for locations which at present have no single SNP test yet available. At this writing the listed price for BIG Y is $575 and Y Elite 2.0 is $775. The latter is more comprehensive although both will give most genetic genealogists more data than they can process. FTDNA will not sell such advanced tests to anyone who does not yet have STR test results or Geno 2.0 results. Full Genomes has no such entry requirement. These comprehensive tests have the added advantage of yielding not only a haplogroup designation but providing a list of unique SNPs that may be approaching offering a terminal SNP that could serve the same family identifying function that did the coats of arms of old.                                                                                         
3. The newest commercial offerings to ySNP chasers are a wide variety of "panels". These are bundles that offer many tests of individual SNPs in one or two steps to narrow in on a specific haplogroup. These are offered by both YSEQ and FTDNA and generally are priced about $88 to $120. While these can screen many SNPs at one time, they generally only identify only one or two SNPs along your migratory path. Buyers should beware that such offerings actually have potential benefit for them.  

In the last analysis the advice posted in the FTDNA learning center:

Please order SNPs with the help of an expert, if you aren’t sure which SNP(s) will benefit your research.

Before ordering, you should ask the advice of an expert on your haplogroup and subclade. We recommend joining an appropiate [sic.] Y-DNA Haplogroup group project. You may then consult the administrators. 

Happy SNPing, but let the buyer beware!

Holiday DNA Sales -- Part 2

FTDNA sure came up with a way to entertain for the next 5 weeks those of us who are DNA junkies. The introduction of the Mystery Reward to the sale is a game changer. If gives us a chance to open our presents (Mystery Reward) discount codes before Christmas -- actually every week. Now the tactical planning can begin. The currently available Mystery Rewards expire Sunday night. 

Apparently they come in 11 categories as Angela Robertson reported on the ISOGG Facebook site: "There are supposed to be 11 kinds of coupon codes. I have identified 10 of those 11 so far. (I don't have all these, but have been tabulating from posts I've seen.) Anyone know which one is missing?"

Now the tactics for a winning holiday genetic genealogy season quickly are coming to the fore. Since you will be offered a new Mystery Reward each week until the end of December, should you wait and hope for a "better" discount? Should you use the discount code you have before it expires on Sunday night? Should you give it to a family member or friend? Should you offer it to a fellow genetic genealogist? The codes are transferable but have a limited life. A secondary marked has already erupted on Facebook. 

If your Mystery Reward is not showing up on your MyFTDNA page you probably need to clear the cache of your browser and try again. That worked for me.

ySEQ

Another holiday sale appeared yesterday from Thomas and Astrid Krahn:

YSeq has also announced that all its extensive catalog of tests for individual yDNA SNPs are on sale for $19 per test. This sale is scheduled to end on December 3rd.


Join in the fun. No Black Friday sale has excited me like this in years.

NextGen Sequencing and yDNA: Part 2

This post is a continuation of my post two days ago.

Within the last week several events have occurred to flesh out our small project. This is exciting but it also will take a while to absorb this influx of new data and make sense out of it all. However, relationships are emerging among project members -- some of whom had previously appeared to be living alone on almost deserted ySNP islands.

The results of an additional BIG Y kit has come back. This connected two men with at least several recent generations of documented French descent. Although they still may not have a common ancestor in genealogical times, their match appears to be within the last millennium. For one of these men whose father was adopted, this is encouragement that he is on the right track in pursuing some ySTR matches who are also of French ancestry.

One member has received Sanger confirmation through ySeq that his S1026 result from NextGen sequencing was correct. Although this analogy is very crude, NextGen sequencing is the equivalent to taking images from a space satellite. On the other hand, Sanger technology would be like driving to a specific location on earth and recording an image. 

NextGen sequencing is much faster for scanning large areas particularly those which may be almost inaccessible or those which have coordinates which were previously inexact or even unknown. It is great for discovery. 

On the other hand Sanger technology can be targeted precisely to one specific location (SNP or STR) and is considered to be much more reliable. The down side it is much more expensive drive around on the surface of our genomes and record a series of images that could be stitched together to form a coherent map. It is much faster and cost effective to start with satellite images. 

Two men who previously had close ySTR matches with others who had previous BIG Y results have tested a single downstream SNP through Sanger technology through FTDNA and confirmed they belong in this project. These men were able to target a specific SNP that had been identified by the BIG Y results of someone with whom STR results had previously suggested a distant relationship did exist. Thus at the cost of a single SNP test, these two men were able to confirm that their SNP trail takes time down into historical times and perhaps to the beginning of the genealogical era. 

One project member got this week, after a wait of three and a half months, his Chromo2 results from ScotlandsDNA. The early examination of the results confirmed that he did belong to R1b-S1026. It was in fact this test that identified and named a SNP at location 19201991 as being S1026. That is where the "S" came from in the naming protocol.

All of these results coming back within the same week has energized our tiny project which now only has a baker's dozen of confirmed members. However, it will take us a while to puzzle over what it all means and what our next steps should be to continue to trace our diverging trails down into genealogical time and hopefully connect with the documented genealogies of specific families.  

But now I must tear myself away from all this and fly to Houston today for Family Tree DNA's 10th Annual Conference on Genetic Genealogy. Don't you just hate it when your opportunities to learn more about genetic genealogy compete for your time to actually do genetic genealogy? I know, I know. I should just be grateful for my opportunities. And I am. 

Sales on DNA Tests

Several companies that test DNA for genealogical purposes are currently offering sales or will be by this weekend.

atDNA Tests

23andMe is currently offering 20% discounts on ADDITIONAL kits after the first when multiple kits are ordered at the same time. This sale is good for those who wish to test several family members. This is an atDNA test.

AncestryDNA is offering a Mothers' Day Sale. It may be a little hard to find but clicking on the link in this paragraph should get you there. It is not clear how long the sale price of $89 will be available for this atDNA test. Buyers are told if they order before May 1st, the kit should be delivered by Mothers' Day.

yDNA Tests

FTDNA is offering two separate sales for a tightly defined period. The sale begins at 12:01 AM CDT on DNA Day, Friday April 25th and ends on 11:59 PM on April 29th. Y-DNA SNPs will be 20% off from April 25 - 29. In addition, the Y-DNA 37 test will be 20% off the retail price. As usual with kits ordered from FTDNA, you may qualify for additional discounts by ordering through a surname or geographic project. Please note that there are two separate tests here. Because these two tests are aimed at different audiences, it is likely that one customer will not be ordering both at the same time. The yDNA 37 STR marker test is a good entry level test for men. It is to test the paternal line which usually corresponds with the surname. On the other hand the individual SNP tests are for more advanced testers who already have some idea about their deep ancestry haplogroup and want to define it more precisely.

YSEQ is also offering individual SNP tests in direct competition with the sale of such tests at FTDNA. Again let me remind you that these tests are not generally for beginners to genetic genealogy testing. The price of $25 per marker "will be in effect until (including) Father's Day (June 15th 2014)."  Thomas & and Astrid Krahn, formerly yDNA experts at FTDNA, are the principals in YSEQ. This price is cheaper per SNP than the sale price of FTDNA. Free shipping is offered on orders of 4 SNPs or more. Buyers will have to consider whether the cost and time of securing new saliva samples for YSEG will offset the difference in the SNP prices. For unusual SNPs one, both or neither lab may currently offer the desired test. There is no simple single solution that will be the best choice for everyone. 


 
So we have two sales for atDNA, two for yDNA SNPs and one for yDNA STRs. Have fun and enjoy the sales.