439=Null; R1b-L1

Leo Little would be gnashing his teeth if he were still with us.  I support the Little Surname project by compiling and posting the results.  When I updated the project last night, I contacted Jane Murtishaw Lindsey, lead admin for the project and suggested that she follow up about the most recent member of the Little Haplogroup R1b, Lineage II - where their 439=Null men are congregated - as he matched the Lineage, but did not have a Null at 439.  The Little project had already followed up.  Here is the reply:

"Hello Mr. Lyttle,

Thank you for your reply. Here is the breakdown for DYS 439 and how it correlates with the L1 SNP:

The L1 SNP causes a null DYS439 readout because the SNP occurs in the sequence that the test is looking at in order to locate and read the marker. If the SNP is present, the test does not find that sequence and a null value is reported. That is the case if the test is designed to locate DYS439 by that portion of the sequence; however, the test can be redesigned to look for a slightly different sequence, not including L1, so that it will find the DYS439 result regardless.

Family Tree DNA has had a longstanding partnership with the University of Arizona, which has been a testing partner with FTDNA for nearly 12 years. However, this partnership has recently come to a close, as we have decided to move all of our testing into our in-house lab. The University of Arizona's (UA) test does NOT adjust for L1, so someone who is L1+ may receive a null value for DYS439.

Family Tree DNA's in-house lab, called the GRC , DOES adjust for L1, and will obtain a result for the marker regardless of the state of L1.

J__ Little's sample was tested at the GRC and not at UA, and therefore a value of 12 was found at this location of his sequence due to the adjustment.

Your sample, for example, was tested at UA, and therefore the adjustment was not made for the L1 SNP condition, and a null value was found.

There are some other caveats. First, if the DNA produces a particularly strong result, then the UA might see the value for DYS439 despite the presence of the L1 SNP. Second, other mutations might cause a DYS439 null on either the UA or the GRC test.

Ultimately, what this means for interpretation is: the DYS439 result is not a firm indicator of a person's L1 result. A DYS439 null result is indicative, but not definitive proof, of a positive L1 SNP. A non-null DYS439 value may be obtained even from someone with a positive L1 SNP, and as we run more of these tests at the GRC this will become more the norm. The only definitive test for whether someone has the L1 SNP is to test L1 directly. If a man is a match with other men (same surname or at a high number of markers) who are known to be L1+, you may infer that he is L1+ regardless of the results of his DYS439."

So - if your project also has 439=Null or men with the L1+ SNP, you need to be aware of this.

Terry

FTDNA deals with the issue

FTDNA steps up!   Info is from Little Project:

Hello Mr. Lyttle,
 
I wanted to reach out to you and let you know that we have been discussing the process of updating the NULL values on 439.  We will not be assuming that all the NULL values will be a 12, however, we do expect about 96% of them to be.  The other 4% will be either an 11 or 13.  The plan is to do a kit by kit analysis to determine the correct value and make the necessary changes. 
 
 Best regards,
 
Jon Manning
Family Tree DNA
IT - Quality Assurance