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Family Finder Advanced Topics Advanced discussion about Family Tree DNA's Family Finder Product.

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Old 23rd March 2011, 10:13 PM
LSSmith LSSmith is offline
FTDNA Customer
Join Date: Nov 2010
Posts: 143
what to do gedmatch matchs

I have started to have people who tested with 23andme contact me and I'm not sure what to say to them. So far they all match my Affy results and none of them match my Illumina results. I have to say that I am a bit perplexed. DNA is science and there is a scientific method for determining if someone is an ancestor or not. I am having trouble comprehending that conversion to a new chip results in the loss of so many FF matches or that the old chip produced so many false positives. I certainly expected some adjustments. However, I did not understand that there was so much left to interpretation. I manage 3 kits and have begun to realize how many of our FF matches have been converted and how most are no longer family. (If only it was this easy to get rid of annoying relatives). Kidding aside what is really going on? Are my Affy matches still matches or not?

me 49 AFFY 15 Illumina
mother 25 AFFY 2 Illumina
husband 42 AFFY 11 Illumina
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Old 24th March 2011, 03:25 AM
k.o.gran k.o.gran is offline
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Join Date: Feb 2011
Location: Oslo, Norway
Posts: 281
Hi LSSmith.

This is how I understand it: Affy does not test exactly the same parts of the DNA as Illumina does. Think of that and look at the chances for a relative to be a match when 6th cousin and beyond: http://www.familytreedna.com/faq/ans...x?faqid=17#628

My theory is that you matched on some of the parts of the DNA that Illumina does not test. That does not mean you're "no longer related" or the matches were wrong.

I also read somewhere that FTDNA is considering adding the Affy results for the people who have done an Affy test, but we'll probably not hear too much about that until the conversion to Illumina is complete.

Hope this helps... This is my layman's understanding anyways.
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Old 24th March 2011, 06:34 AM
JOlson JOlson is offline
FTDNA Customer
Join Date: May 2010
Location: Texas
Posts: 354
Originally Posted by LSSmith View Post
I am having trouble comprehending that conversion to a new chip results in the loss of so many FF matches or that the old chip produced so many false positives.

I have gained a new appreciation for what the guys at FTDNA are faced with.

One example that I've seen is where a new 993 SNP segment on chromosome 3 showed up on the Illumina results. When I made a detailed examination of the Affymetrix results, I found that the same segment was only 349 SNPs because the Affymetrix chip tested far fewer SNPs in that region. This put that segment below the 500 SNP threshold, so it did not show up in those results.

The reverse also happens (shows up in Affymetrix, but not in Illumina). In the same comparison, a 594 Affymetrix segment did not show up in the Illumina results because it only showed 357 SNPs. This time, the Illumina chip tested fewer SNPs in that region than the Affymetrix chip.

Cross-platform comparisons add a whole new level of complexity. Because of all the variability between the different testing platforms (Affymetrix, V2, V3, etc.), GEDmatch.Com has had to make significant software modifications to apply different evaluation parameters to each comparison combination. Each time a new platform is added, it doubles the number of possible comparison parameters that must be developed and evaluated. When changes are made to one set of parameters, it takes about a day to calculate a new matrix for those results. Then, if they don't look right, we get to do it all over again.

Many times, erroneous results are not apparent until they are posted and many people start looking at them. I assure you, nobody is more frustrated by the process than me. ...except maybe the guys at FTDNA.

Everybody wants accurate results. Everybody wants their results ASAP. Somewhere, there's a balance between when those 2 things will happen. For what it's worth, I do think the results are improving as the process gets refined. It's just taking a LOT longer than anybody expected.

Last edited by JOlson; 24th March 2011 at 06:44 AM.
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Old 24th March 2011, 05:11 PM
royfarnol royfarnol is offline
mtDNA: none | Y-DNA: R-L448+CTS4279-
Join Date: Mar 2010
Location: Dunedin, NZ
Posts: 317
Interpreting combined results from different procedures.

Can not some clever stick see a way of doing this successfully?

Seems a logical proposition.
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