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Archiver > GENEALOGY-DNA > 2005-10 > 1129397072


From: charles <>
Subject: Re: [DNA] DYF markers and marker naming standards
Date: Sat, 15 Oct 2005 13:24:32 -0400
References: <434F3DDA.9000108@kerchner.com> <434FDD2D.4050104@kerchner.com> <op.syn17imfpqnhvj@localhost> <010901c5d19e$71f189e0$8998893e@Masterbedroom> <200510151703.j9FH3sd0002627@mail.rootsweb.com>
In-Reply-To: <200510151703.j9FH3sd0002627@mail.rootsweb.com>


Thomas:

Thank you very much. I'll have to add something to my next dictionary
edition explaining the difference between DYS and DYF marker names. I
may get back to you later this year for some assistance with the
descriptions and wording. Thanks again for the information and help you
share with this list.

Charles Kerchner
http://www.geneticgenealogydictionary.org/

Thomas Krahn wrote:
> David,
> The authority that should manage the nomenclature issues of DNA segments
> is the HUGO Gene nomenclature committee:
> http://www.gene.ucl.ac.uk/nomenclature/
>
> They mainly cope with gene names. The nomenclature of DNA segments is
> only briefly mentioned in the appendix of "Guidelines for Human Gene
> Nomenclature".
> http://www.gene.ucl.ac.uk/nomenclature/guidelines.html
>
> Scroll down on that page until you find "App 1.1 DNA segments"
>
> The original text says:
> App 1.1 DNA segments
>
> These symbols can be obtained from The Genome Database (GDB) and are
> assigned automatically to arbitrary DNA fragments and loci. Please email
> requests to . These symbols comprise five parts e.g.
> DXS9879E, described by the following guidelines
>
> a) D for DNA
> b) 0, 1, 2,...22, X, Y, XY for the chromosomal assignment, where XY
> is for segments homologous on the X and Y chromosomes, and 0 is for
> unknown chromosomal assignment.
> c) S, Z or F indicating the complexity of the DNA segment detected by
> the probe; with S for a unique DNA segment, Z for repetitive DNA
> segments found at a single chromosome site and F for small undefined
> families of homologous sequences found on multiple chromosomes.
> d) 1, 2, 3,..., a sequential number to give uniqueness to the above
> concatenated characters.
> e) When the DNA segment is known to be an expressed sequence the
> suffix E can be added to indicate this.
>
> If theese guidelines would be followed consequently, many markers that
> we use would have wrong names:
> DYS385,
> DYS413,
> DYS459,
> DYS464 would be a DYZ-number.
>
> DYF385S1,
> DYF399S1 would be a DYZ-number, too.
>
> There do exist STR markers that are located on the X- and on the
> Y-chromosome. They are not male specific.
> One interesting marker is DYXS156, where the Y allele is nearly allways
> larger than the X allele.
> http://www.cmj.hr/2001/42/3/11387645.pdf
>
> This marker has also a wrong name. It should have a DXYF number, because
> it is a complex marker that is located on two different chromosomes.
>
> I'm not sure how to classify DYS389I and DYS389II in this nomenclature.
> There exists even a third repeat unit downstream of DYS385II so we could
> even talk about a DYS389III segment. Probably a DYZ-number would be
> apropirate.
>
> So, you see that consistency is really not very much followed. When a
> researcher submits a new DNA segment that contains a STR to GDB
> (www.gdb.org) he can choose by himself, if he considers the segment as
> complex and if the complexity is extended to more than one chromosome.
> The GDB submission is very complicated and not very well documented.
> There is only a brief description that the scientist can follow:
> http://www.gdb.org/gdb/SubmissionDirections.html
>
> Even good scientists have problems with this, which seems to result in
> inconsistent marker names. I think the best that we can do is simply
> taking the names as is and not bothering with the misleading nomenclature.
>
> Thomas
>

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