Big Y “Backbone Tests”

I recently noticed that a Backbone Test had been ordered for my late father-in-law. This surprised me as it was a bit dated.

I mentioned this at the BigY Facebook group and got an interesting answer from Bob:

I think you will find that this Y-HAP-Backbone was ordered as a part of a manual review process triggered by another user’s test results.
Originally, the Y-HAP-Backbone test was performed if FTDNA was unable to unambiguously predict a person’s high-level haplogroup from their STR test results. They would actually perform enough SNP testing to resolve the ambiguity.
In the case of somebody who has actually done a BigY test, there should be no necessity to predict a haplogroup from the STRs.
Normally, the automated caller will consider a result to be a no-call if there are not at least ten reads for that position. If a new kit has a result that might affect the haplogroup definitions, a manual review of the other kits assigned to the haplogroup may occur. The analyst doing the review will look at the raw data and may decide to override the no-call reported by the automated caller. To do this override, the analyst orders the Y-HAP-Backbone procedure. In this case, no actual lab work is involved. It is simply a database operation to report the new result for that SNP.
If you display the user’s Private Haplotree, you can scroll to the top of the page and click on the “SNP Results” link, you will see a list of SNPs. If there are any overridden SNP results, they should be sorted to the top of the list. The test type will be shown as Y-HAP-Backbone. The result may be positive or negative.
If you scroll down through the pages of this report, in addition to any BigY test results, if the user has done any other SNP testing, you will see those results listed. In the case of BigY test results only positive results are shown. (After all, you are negative for several hundred thousand SNPs.)
In my own surname project, until recently our haplogroup had one subclade. We had three men assigned to the main haplogroup and six men assigned to the subclade. Even though our BigY test results actually showed the three of us to be negative for the SNP defining the subclade, these negative results were not being shown in the SNP Results list in our Private Haplotree. During an early manual review, the analyst ordered the Y-HAP-Backbone procedure for the three of us. The result is that we now are shown as negative for this SNP. The color coding in the tree now indicates that we are “Tested Negative” instead of being indicated as “Downstream”. Since that time, a new kit was found to share an additional SNP with one of the three. This resulted in a second subclade being defined. The analyst creating the subclade did not bother to override the calls for the two men remaining in the main haplogroup, so we show “Downstream” for the new subclade.
By the way, the order status for the three of us with negative results for the Y-HAP-Backbone procedures for the SNP defining the original subclade still shows that order as pending. Apparently because no lab work was performed, they failed to mark the order as completed. We have other Y-HAP-Backbone procedures (with positive results) that did get reported as completed.
Does the entry in the SNP Results list for your member’s kit show negative results, or are they all positive?
I was happy to get this reply as it answered many questions I had for my Butler father-in-law’s test as well as a Frazer project I am working on. I posted this image of my father-in-law’s SNP results at the BigY Facebook  Page:
I asked Bob this clarifying question:
Sorry, though, still a bit confused. Are you saying an override does not involve SNP testing? So in this case, the Backbone means no test and the tested negative means that a test was done?
Bob’s response:
While it may be a little confusing, the answer to both is yes. FTDNA does not offer a single-SNP test for FT241245, so the backbone procedure did not involve a laboratory test. They just looked at the raw data from the BigY test. You should be able to do something similar using the chromosome browser. When looking at this user’s BigY Results (Named Variants tabs, change the Derived? filter to Show All and enter the SNP name in the SNP Name Search box.
I suspect that it will show a ? In the Derived? And Genotype columns. Click on the SNP name to bring up the chromosome browser. I suspect that you will have fewer than ten reads shown, resulting in a no-call.
By the way, the Y-HAP-Backbone procedure results in the line being added to your SNP Results list. However, it does not actually result in a change to your raw data or what is shown in the Named Variants tab.
In response, I posted this image of my father-in-law’s results for FT241245:
I wanted to memorialize Bob’s comments as they were so helpful. I have been looking at “Backbone Test” results in a Frazer YDNA Project that I am involved in and Bob’s response answered so many of my questions.

Butler and S23612

As alluded to above, S23612 shows on the SNP results as ‘tested negative’. Let’s look for those results:

 

Just as Bob predicted, this shows up as tested negative. However, I’m not sure why this particular SNP was chosen. I would think that I-S23907 would have made more sense or perhaps BY115420.

Here are my father-in-law Richard’s results for S23612:

He is already clearly negative. Plus this SNP appears to be about 4 or 5,000 years old.

Speaking of S23897

I see that I mentioned S23897 in a previous Blog on Butler YDNA.

This is for a Butler relative with common Irish roots, but we have not yet established a genealogical connection. Now, thanks to Bob, I know where to find this Butler’s secret testing results:

Well, perhaps not secret, but they were to me previously. This Butler has a surprising 7 Negative SNP results. What I am seeing is that this Butler relative must have ordered these SNP separately before he did his BigY:

Frazer Backbone Tests

I have been waiting for Frazer ‘backbone tests’ to complete. However, according to Bob, these could be manual overrides instead of actual tests. Also, confusingly, these tests may not have an end date if the reviewer forgot to put in a date.

Here is a view of the Frazer BigY testers from the view of one of the testers from the James Frazer Line who took the BigY500 test:

My labels didn’t come out too well. The first column represents the James Frazer line and the ‘Your Branch’ represents the BigY500 tester on that line. At the top of his SNP results, we see this:

From the comments from Bob, the Y-HAP-Backbone should represent a manual override for Y151390 which is the defining Haplogroup for the James Frazer Line. Here is the order history for that same tester:

This is confusing because of the batched designation which shows after the ‘completed’ designation. However, I assume that these three entries were for the one override for Y151390. Here are his test results:

Here, he only has 7 positive reads where FTDNA would like to see 10. However, the manual review said they were all positive, so let’s say he is Y151390.

BigY700 on the James Line

The same thing apparently happened for the BigY700 tester.

Here is the James Line BigY700 order history:

This takes some interpretation. I assume that the Backbone got entered twice by mistake and that only the one entry that was actually done shows as completed. Keep in mind here that ‘backbone’ means manual override of inconclusive test results. Here are the BigY700 test results for Y151390:

This is a bit surprising as the results show positive for Y151390, so there were no questionable results to override.

My guess is that the manual review took a look at these results and agreed with them.

Archibald Line Results and Frazier BigY results

The BigY500 tester had no overrides in his SNP results. The same for the BigY700 tester. That must mean that FTDNA had no questions about their results.

That leaves the Frazier BigY results. He also has no unusual results on his list of SNPs. That means that the review was completed for Frazer/Frazier BigY’s some time in early February.

Summary and Conclusions

  • It was a help for Bob from the BigY Facebook Page to show me where to find the SNP Results link at the top of the BigY Haplotree view
  • This gave more clarification to the manual review which FTDNA performed and explained why it looked like a Backbone test was outstanding
  • FTDNA has a confusing array of places where they store information and show the results of the work they have done. They also seem to do things inconsistently. However, with perserverence and help from others who have gone through the process, it is possible to get an idea of how one’s BigY test was reviewed and processed.

 

 

 

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