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Archiver > GENEALOGY-DNA > 2005-10 > 1129395819


From: Thomas Krahn <>
Subject: Re: [DNA] DYF markers
Date: Sat, 15 Oct 2005 19:03:39 +0200
References: <434F3DDA.9000108@kerchner.com> <434FDD2D.4050104@kerchner.com> <op.syn17imfpqnhvj@localhost> <010901c5d19e$71f189e0$8998893e@Masterbedroom>
In-Reply-To: <010901c5d19e$71f189e0$8998893e@Masterbedroom>


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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wrote:

>David & List
>
>all the multicopy markers discovered in the Kayser paper
>http://www.journals.uchicago.edu/AJHG/journal/issues/v74n6/41028/brief/41028
>.abstract.html
>were given DYF numbers. I read somewhere (sorry, can't remember where) that
>the F stood for Family and that the D#F format was standard for naming
>multicopy loci in the autosomal chromosomes (where # is the number of the
>chromosome). The S1 on the end allows for numbering individual copies if
>they can be separately identified (using S1, S2, S3 etc). Clearly this has
>not be done consistently for the Y chromosome as we have multicopy markers
>in the DYS format as well. It is a pity that the numbers were not kept
>unique i.e. so you had DYS385 or DYF385S1 but not both. Looking at the
>DNA-FP list of autosomal markers, some of them are up to four digits.
>
>Gareth
>
>
>
>----- Original Message -----
>From: "David F Reynolds" <>
>To: <>
>Sent: Saturday, October 15, 2005 3:51 AM
>Subject: [DNA] DYF markers
>
>
>
>
>>On Fri, 14 Oct 2005 09:30:37 -0700, charles <> wrote:
>>
>>
>>
>>>DYF385S1 and DYF399S1. Don't ask me why they named these markers with
>>>
>>>
>the prefix DYF instead of DYS. The scientists on
>
>
>>>the list can talk to that part.
>>>
>>>
>>Actually, I have wondered about that for a while. Can someone explain the
>>
>>
>DYF###S1 nomenclature?
>
>
>>--david
>>
>>
>
>
>
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