Archiver > GENEALOGY-DNA > 2005-06 > 1118201971

From: (David Faux)
Subject: Re: [DNA] Re: Genographic Project Upload Tab - Now Available!
Date: Wed, 08 Jun 2005 03:39:31 +0000

I am not so sure Bonnie. The rate of uncertainty is probably comparable for mtDNA and Y-STR haplotypes.

I have just gone through the lengthy task of taking a string of nucleotide bases for 503 Shetland samples, locating those that deviated from the CRS and then using the best set of algorithms available (my contacts are the top mt researchers in the field). I was able to assign haplogroups to about 80% of the sequences, some were entirely impervious since they have apparently not been seen in the literature before or are ambiguous (could be either one haplogroup or another).

Simoni et al. (2000) found precisely the same problem in the attempt to assign 2619 European sequences to a haplogroup. They observed that "78% of the sequences of our database could be unambiguously assigned to one haplogroup". Of these 17% total were assigned to "Other" and the rest to macro groups such as IWX which I would argue is questionable.

Nothing much has changed, I found about the same figures but my approach was to just leave them as "unknown" although most were probably H. I therefore wonder where NGS is going to obtain a foolproof way to pigeon hole all sequences - frankly it is not possible without testing the coding region which adds immensely to the expense unless there is a new development about which I am unfamiliar (entirely possible), but I would like them to describe how they derived these Y and mt algorithms (now that I uploaded 4 to GenoGraphic and am pleased to be officially part of this landmark study).

David F.

-------------- Original message --------------
> All along, FTDNA has been willing to perform further testing of mtDNA
> beyond analyzing HVR1 and 2, when necessary, without charge, to
> determine haplogroups. Their system for determining haplogroups and
> deciding who needs further testing has now been renovated (personal
> communication, Bennett Greenspan). In general their philosophy is that
> they feel sure of everyone's reported mtDNA haplogroup, either through
> analysis of HVR mutations or further testing. I have found errors in
> their system in the past, but I believe that things will be improving
> now, with their Genographic Project involvement, which is bringing in
> new scientists. The point is that they don't consider your reported
> mtDNA haplogroup an "estimate" the way the Y-DNA haplogroup can be.
> Bonnie Schrack

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