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Archiver > GENEALOGY-DNA > 2010-02 > 1265276458


From: Thomas Krahn <>
Subject: Re: [DNA] FTDNA admits to errors in many mtDNA sequences
Date: Thu, 04 Feb 2010 03:40:58 -0600
References: <574B3DDE46B74CB688150F9E310E33DF@IanPC>
In-Reply-To: <574B3DDE46B74CB688150F9E310E33DF@IanPC>


Dear Jan,

It is important that you need to distinguish "erroneous" from reporting
in non- standard format.
The sequences didn't have errors (since FTDNA also supplied the correct
FASTA sequence files), but they were just reported in a way that doesn't
comply the current nomenclature. By the time these sequences were
reported the current standard wasn't even fully established.

This is of course no excuse for keeping the wrong nomenclature in
searchable databases. That's why FTDNA has invested a lot of time to
re-investigate old sequences to bring them up to date to the current
nomenclature.

It is also important that you realize that the current mtDNA
nomenclature is definitely still not the ultimate solution. There are
still some "opinion" related loci that are inconsistently reported so
that you need to force software algorithms to make exceptions so that
they are called like the nomenclature standard requires it. The
nomenclature standard is from a evolutionary standpoint (relating to the
actual biochemical mutation pathway) sometimes complete nonsense. Future
developments will not use any nomenclature system for comparison but
they will simply compare full sequences (e.g. in FASTA format) with each
other. This will soon make nomenclature discussions obsolete.

Like in every kindergarten the tiny small mtDNA molecule is highly
discussed with strong emotional attitude. Maybe when the mtDNA
researchers grow up and start understanding the global scope of total
genomic context they will learn that the nomenclature is not the only
interesting issue that can be learned from the mitochondrial genome ;)

I hope this helps,

Thomas


Ian Logan wrote:
> List
>
> Last autumn FTDNA realised that the string of mutations '524.1C, 524.2A, etc.'
> that started to appear in its mtDNA sequences in 2007 are all erroneous.
> But the extent of the problem has only now been appreciated
>
> The mutations string should always be '523.1C, 523.2A, etc.'.
> We have now been told that the error was due to a software fault
> - and affected hundreds, if not thousands, of results.
>
> As I understand it, all the personal pages for mtDNA customers have now
> been corrected, but customers have not been notified individually.
>
> In respect of GenBank there are 38 affected sequences, with accession numbers:
>
> EF363686 EF428259 EF452295 EF485042 EU089747 EU130551 EU135973
> EU140898 EU156036 EU170361 EU232008 EU256375 EU330213 EU428753
> EU564851 EU573192 EU616820 EU621708 EU677750 EU682394 EU682506
> EU714298 EU715237 EU719115 EU746658 EU849002 EU855118 EU869314
> EU926618 FJ194437 FJ449703 FJ490554 FJ605154 GQ149510 GQ200592
> GQ281051 GQ891957 GU004259
>
> I am very happy to provide any of the submitters of the above sequence with
> a revised submission file (.sqn file) if they would like to get in touch with me.
>
> This applies to all of the GenBank sequences and not just to the submissions
> for which I prepared the original files.
>
> Ian
> www.ianlogan.co.uk
>
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