Was ist das? Primer binding region insertion/deletion?

[Clochaire]

HELP!

Can somebody, in layman's language, explain to me the meaning of:

"An insertion or deletion in the primer binding region"?

I've been trying for 2+ months now to reconcile apparent discrepancies among 3 lab reports for Y STR testing done. I can't get 2 out of 20- some markers tested at 3 labs to agree. I think that's about a 9% discrepancy rate.

These labs have made it quite clear that the issue is NOT a nomenclature issue, but are otherwise unable or unwilling to reconcile their results.

However, I have recently spoken to an academic in my area. And to the best of my understanding, he has posited that the observed discrepancies may be the combined result of "an insertion or deletion in the primer binding region" and the use of different primers at each of these labs.

I think this gentleman is suggesting that there is something weird about my DNA, different from the general population, which invalidates the otherwise useful assumptions that the labs make when selecting primers.

Am I even in the right ballpark here?

Thanks.

Jack

[Nagelfar]

Yes, you've got it. When they look for a certain marker, say with me my DYS
425, they're looking for a "T" nucleotide. So they use that primer. If there's a SNP there which isn't accounted for, it can make them not find the STR with the common primer that they use to find that allele value.

[Clochaire]

Insertion / Deletion May Indicate Presence of Specific SNP?

So . . . let me see if I've got this here . . . It's possible that:
1. These labs are using primers that bind at different sites
2. The 'non-congruent' values reported by some of the labs are due to an SNP insertion at the binding site specific to the primer used by a given lab

So, if that is true, and I were able to somehow identify the primer binding site for the labs reporting 'non-congruent' values, might I be able to infer the presence of a specific SNP? See the link below for a listing of identified SNP's and locations in bp.

http://www.human-evol.cam.ac.uk/Members/Lahr/pubs/AHG-65-01.pdf

Based on some lab tracings I've received from one lab, the table at the link above, and the STR Base fact sheets, maybe I would test positive for M154 or M202?



I know that I could only be certain by purchasing an SNP test for these, if it commercially available. But I think I'll do a little tooling around the web as well.


Jack

[Clochaire]

Okay, my idea re: SNP's may not work . . .

Just did a quick search for SNP's associated with suspected primer binding sites for DYS458 and DYS389ii . . .

http://www.isogg.org/tree/ISOGG_YDNA_SNP_Index.html

So I guess my idea will not work very well. These SNP's are associated with VERY different haplogroups -- E3b, A, I1b, etc. Definitely NOT R1b1c.

So either my idea was not valid, or my discrepancies at these DYS's are NOT due to the SNP thing.

Jack