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Cottonmouth
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« on: August 07, 2012, 01:51:17 AM »

Does anyone know if FTDNA has changed their procedure for determining the value of the marker DYS439? I have contacted their customer service several times but can't get a straight answer.

The Cotton DNA project has one family with ten members who have tested with FTDNA. The first nine all were reported as null 439 indicating the L1 SNP. The most recent participant received a value of 11. The paper trail says we have a common ancestor four generations back and we match on 36 of 37 markers. That would be a remarkable coincidence if we are looking at an NPE.

Is there another company where he could get an SNP test for L1 alone?
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stoneman
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« Reply #1 on: August 07, 2012, 06:56:40 AM »

It could be a lab error.
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vineviz
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« Reply #2 on: August 07, 2012, 10:02:34 AM »

Is the new participant is actually an old customer (i.e. low kit number)?

For a time, FTDNA reported nulls as "11" intentionally.
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Cottonmouth
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« Reply #3 on: August 08, 2012, 02:08:02 AM »

Doesn't appear to be a lab error. They have rechecked the marker and still report an 11. Also not a low kit number (238539). He has never had a DNA test before.

I have a low kit number myself and FTDNA did originally report me as an 11. I contacted them on the recommendation of Leo Little and they admitted that I actually received a null value. Oddly while the other members of our family who tested with Relative Genetics/Ancestry have a 12 at DYS439, I tested with the Sorenson Foundation and actually am an 11. The new member and I share a common ancestor four generations back while the others connect with us nine generations ago so the fact that we share a mutation at DYS439 is not surprising.
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Cottonmouth
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« Reply #4 on: September 02, 2012, 03:14:42 PM »

In case anyone else is interested, I finally got a reply from FTDNA -

I heard back from our lab contact regarding the 439 null. With the advent of new testing technology for many markers the lab has begun to obtain results for people at this marker who may have previously tested as null. We are working on transitioning to new testing methods and hope to have them completed some time later this fall, at which point we will be solving this issue across the database. We are committed to the data always being correct for the customer which is why we created a null system before it was know that many actually had the L1 SNP. We will not be able to go back and retest every sample though since some of the DNA samples are no longer available and participants deceased.
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stoneman
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« Reply #5 on: September 03, 2012, 01:27:57 PM »

Are you saying that you dont belong to the L1 subclade? You must be Z156.
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Cottonmouth
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« Reply #6 on: September 03, 2012, 04:45:23 PM »

No I have a null value for DYS439 which indicates that I belong to the L1 subclade. However in the future, FTDNA will be able to obtain actual values for 439 even if the participant is L1 so the only way to know if you're L1 will be through an SNP test.
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stoneman
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« Reply #7 on: September 05, 2012, 02:15:23 PM »

FTDNA thought that I was L1 but I told them I had a value of 13 at 439. I think 11 is ancestral at this marker for R1b so I have two mutations at this marker.
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Terry Barton
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« Reply #8 on: October 16, 2012, 11:08:13 AM »

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. 

http://www.worldfamilies.net/surnames/little/results 

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
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Jane Murtishaw Lindsey
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« Reply #9 on: October 16, 2012, 06:50:26 PM »

So it is still not clear to me whether those men who tested some time ago and have the null value should now test DYS439.  Is it possible/probable that those who have null will have different values for DYS439 or are they all going to be 12? 

I checked the cost of the test and is nominal - $10 plus one-time charge for transferring sample to Houston if you haven't already had an advanced test.
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jane

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« Reply #10 on: October 16, 2012, 08:48:37 PM »

So it is still not clear to me whether those men who tested some time ago and have the null value should now test DYS439.  Is it possible/probable that those who have null will have different values for DYS439 or are they all going to be 12? 

I checked the cost of the test and is nominal - $10 plus one-time charge for transferring sample to Houston if you haven't already had an advanced test.

I would. The null just meant they couldn't read the value at location DSY439. They could be 13 or 11 or anything. You can't assume anything. The only question is who should pay because one lab can't read something another lab can.  For $10, I don't know if it is worth the time of the argument though.
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df.reynolds
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« Reply #11 on: October 16, 2012, 09:35:53 PM »

I would. The null just meant they couldn't read the value at location DSY439. They could be 13 or 11 or anything. You can't assume anything. The only question is who should pay because one lab can't read something another lab can.  For $10, I don't know if it is worth the time of the argument though.

That's kind of a classic high-tech situation, though. Always something bigger or better on the horizon. You pay your money and take a chance on the current state of technology. :)

I agree, there is no reason to assume all  the previously null results will be DYS439=12. Having a inconsistent database seems like a really bad idea, making a mess out of genetic distance, etc. Re-testing previous DYS439 null results would simply be good hygiene.

--david
« Last Edit: October 16, 2012, 09:36:11 PM by df.reynolds » Logged
Mike Walsh
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« Reply #12 on: October 16, 2012, 09:40:48 PM »

I would. The null just meant they couldn't read the value at location DSY439. They could be 13 or 11 or anything. You can't assume anything. The only question is who should pay because one lab can't read something another lab can.  For $10, I don't know if it is worth the time of the argument though.

That's kind of a classic high-tech situation, though. Always something bigger or better on the horizon. You pay your money and take a chance on the current state of technology. :) ...

I am very supportive of commercial testing laboratories. I want them to be successful and make a good profit. In fact, I hope they receive great profits and reward their investors handsomely.  Good for them and good for the consumers.  We need strong companies for consumers to have good service and choices.

I'm not so kind to putting the risks on the consumer. I am a businessman, but businesses need to produce results. A reliable test report is not beyond the realm of consumer expectation.

When one lab produces one result and another a different one, I'm not so forgiving. However, for $10, I don't care. I'd pick a better battle.
« Last Edit: October 17, 2012, 11:22:35 AM by Mikewww » Logged

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stoneman
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« Reply #13 on: October 17, 2012, 03:42:12 AM »

It is not important what value a person has at 439.What is important is whether or not they are L1+.
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Mike Walsh
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« Reply #14 on: October 17, 2012, 11:21:35 AM »

It is not important what value a person has at 439.What is important is whether or not they are L1+.

I agree that L1+ or L1- is a more important factor and I definitely recommend testing for L1 if you think you fit.

However, I think that if you have a 67 STR length haplotype you want all 67 markers' values correctly tested. 439 might help separate out clusters within L1. I don't know, but I don't think it should discarded. It sure messes up comparative GD calculations and could have an impact on TMRCA calculations... not having the correct data.
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stoneman
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« Reply #15 on: October 18, 2012, 10:05:22 AM »

When I  find the eight SNPS downstream of my present position I will not be making them public. I will advise my friends to do the same.
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Mike Walsh
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« Reply #16 on: October 18, 2012, 10:42:38 AM »

When I  find the eight SNPS downstream of my present position I will not be making them public. I will advise my friends to do the same.

You might consider removing yourself from projects because most do have those Y DNA SNP reports now.
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R1b-L21>L513(DF1)>S6365>L705.2(&CTS11744,CTS6621)
stoneman
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« Reply #17 on: October 18, 2012, 05:06:52 PM »

That is strange as I havent tested positive for any of them.
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Terry Barton
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« Reply #18 on: October 31, 2012, 10:44:14 AM »

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
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Mike Walsh
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« Reply #19 on: October 31, 2012, 11:33:39 AM »

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


Very good. FTDNA is stepping up here and should be complimented.
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R1b-L21>L513(DF1)>S6365>L705.2(&CTS11744,CTS6621)
Joseph David Lyttle
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« Reply #20 on: November 26, 2012, 02:25:51 PM »

November 26, and still waiting for FTDNA to get back with me on the null439 retest.

D Lyttle
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