Affy to Illumina conversions complete?

[swimmingly]

I haven't checked yet with my cousin to see if his conversion is complete. I will do so. I had read here that all conversions had been done. Apparently not? If some are still not done, then I will assume/hope that match is one of those.

[Ann Turner]

Also, I have one unrelated question that I need to ask. Why would I have some high snps numbers (over 5,000) when the cM is low in that chromosone (2-3 cM)? What is the significance of the snps being high and the cM low?

This probably occurred in the HLA region of chromosome 6. It's a region of tremendous variability (lots of SNPs) but a low recombination rate (low cM). My last 'Satiable Curiosity column for JoGG has more background:

http://www.jogg.info/62/files/SatiableCuriosity.pdf

Please note that I am no longer collecting data because of the switch to Illumina.

[Ann Turner]

Yes, we (my cousin and I) had 4 segments in Affy with over 10 in common. We are a good match. But do not match on Illlumina. It does kind of look like I lost entire parts of my ancestry. Before I had diversity in the matches, and now it is fairly homogenous, and so is my PF, which before was more diverse as well.

You've confirmed that your cousin has been converted? I received a father/mother/child trio yesterday where two close cousins had been lost, but they were part of a family project managed by one person, and he knew that those samples had to be done over. Two cases for one person is higher than I'd expect based on comments that about 100 samples have not been converted.

This is a long shot, but you could check that the Illumina results are actually yours by looking for differences in your Affy and Illumina raw data files:

http://www.math.mun.ca/~dapike/FF23utils/diffs.php

You can expect a few hundred differences, but I think the utility gags with too many differences to report if the files are for different people. Bar coding reduces errors of this type tremendously, though.

[rod]

My Illumina results appeared this morning (along with the last two other waiting project members).

I have 107 matches that appear in Affy only, 28 that appear in Illumina only and 34 that appear in both.

With Affy I had over 40 people that matched me in one segment of chromosome 1. With illumina they're gone.

[JohnG]

If you call, or contact by email, you should be prepared to send your Affy match file, or both match files. I combined mine and added column for source (Affy or Illumina) so it could be easily sorted to see the missing matches.

If you have a couple of examples and can provide kit numbers of clearly related lost matches that might also help.

[gtc]

have lost all my Affy matches.

<snip>

If my 70+ Affy matches were legitimate, then why didn't ANY carry over to Illumina?

I think your 100% loss may be the record so far.

I suggest you call FTDNA with a "please explain".

None of my Affy matches carried over to Illumina

Hi everyone,

Excuse me for butting in! I'm new to this forum and have lost all my Affy matches. I had only been able to confirm two of the Affy matches as cousins: one a 7th cousin, 2x removed (9.72 cM) and the other was a 6th cousin (7.81 cM).

If my 70+ Affy matches were legitimate, then why didn't ANY carry over to Illumina?

Also, I have one unrelated question that I need to ask. Why would I have some high snps numbers (over 5,000) when the cM is low in that chromosone (2-3 cM)? What is the significance of the snps being high and the cM low?

Thanks for any help you can provide. Now that I'm registered I'll be reading the boards to try to increase my knowledge.

Linda Rogers Grinnell
Paternal Haplo r1b1b2
Maternal Haplo X2b

[gtc]

Today I received some email from Bennett Greenspan and he did tell me they are looking into this missing Affy question.

Seems this issue has become the proverbial mirror ... everybody's looking into it.

[swimmingly]

yes, over 10

Yes, we (my cousin and I) had 4 segments in Affy with over 10 in common. We are a good match. But do not match on Illlumina. It does kind of look like I lost entire parts of my ancestry. Before I had diversity in the matches, and now it is fairly homogenous, and so is my PF, which before was more diverse as well.

[djparlette]

I lost two Affy cousins who shared over 10 cM.
50.01 cM shared and 12.2 cM longest block
31.15 cm shared and 10.59 cM longest block
The first match is deceased, but that shouldn't have anything to do with losing him in Illumina.

[rivergirl]

While some matches have dropped off in longst segment they still appear as a match in Illumina.
Affy vs Illumina
3rd Cousin - 5th Cou 36.06 /14.25 vs 4th Cousin - 34.47 12.28
4th Cousin - Distant 35.70 /14.89 vs 5th Cousin - 30.29 8.81
4th Cousin - Distant 31.01/10.15 vs 5th Cousin - 32.21 8.51
5th Cousin - Distant 29.87/9.68 vs 5th Cousin - 27.79 8.31


Others picked up a bit in longest length
Affy vs Illumina

5th Cousin - Distant 24.08 8.17 vs 5th Cousin - 21.79 8.52
5th Cousin - Distant 35.6 8.46 vs 5th Cousin - 33.97 9.92
5th Cousin - Distant 29.56 9.12 vs 5th Cousin - 33.41 9.86
5th Cousin - Distant 29.57 8.54 vs 5th Cousin - 29.18 9.66
5th Cousin - Distant 29.89 8.54 vs 5th Cousin - 34.68 9.63


I can only guess that my old Affy matches dropped too much to be considered.

But I dont consider them to be "barely matches" at FTDNA puts it. A match is a match.

[rivergirl]

Two of my 4th to distant Affy matches that were not picked up by Illumina each had longest shared segments over 10 cM.

#1 30.91 shared cM, 10.15 cM longest shared segment, 7 shared segments
#2 27.18 shared cM, 13.54 cM longest shared segment, 7 shared segments

Has anyone else lost matches in the 10 cM + range? Isn't 10 cM+ over the threshold for IBD vs IBS? I'm looking for an educational assist if anyone has an explanation.

Yes I have lost three Affy matches with over 10cM
3rd Cousin - 5th Cousin 36.57 shared, 12.71 longest block
4th Cousin - Distant Cousin 34.29 shared, 11.67 longest block
4th Cousin - Distant Cousin 33.76 shared, 10.04 longest block

19/28 of my illumina matches are below 10.0 cM longest block

[mkdexter]

FTDNA says they are looking into this

Today I received some email from Bennett Greenspan and he did tell me they are looking into this missing Affy question.

I think they will need a few more days to look at some data.

I'm also finding a few things myself but I need a few more days as well to confirm my tests and findings.

[mkdexter]

Swimmingly I sent you a private message note.. Please check it and reply if you are ok with answering.

[Ann Turner]

Yes, I did lose my confirmed third cousin. We know we are third cousins, and had recently determined that on paper before being matched on Affy. He was my closest match overall. All those SNPs must have been in the Affy spots and not in the Illumina.

Third cousins typically have several segments > 5 cM in length (usually longer, in fact). Did that hold true for you? Even if one segment doesn't make it through, other segments should still have a chance. Have you checked that your cousin has actually been converted?