GENEALOGY-DNA-L Archives

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Subject: Full text Sorenson Genomics press release [WATCH QUOTING!!!] 
Date: Tue, 8 Jun 2004 12:21:05 EDT

Lars Mouritsen, the Laboratory Manager at Sorenson, was kind enough to send a
copy of the press release to the G-DNA mailing list yesterday. However, his
e-mail address wasn't subscribed, so it didn't get through. I am posting it on
his behalf, so it will be stored in the archives and people can quote relevant
sections.

Please note that you should LIMIT your quoting to just the section you are
commenting on. This is always good practice, but it is essential in this case,
as the post is very long, and any additions will make your post go over the
size limit.

Ann Turner - GENEALOGY-DNA List Administrator
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Subj: {not a subscriber} Sorenson Genomics public statement about Y
chromosome testing and nomenclature. 06/07/04 
Date: 06/07/04 3:12:44 PM Pacific Daylight Time
From:
To:
Sent from the Internet (Details)

Sorenson Genomics public statement about Y chromosome testing and
nomenclature.  06/07/04

Sorenson Genomics has recently developed a Human Y chromosome test which
may be used for forensic or genealogical purposes.  There has been a
great deal of discussion about the nomenclature used for describing
several short tandem repeat (STR) loci that have been identified
throughout the Y chromosome and particularly those found in the
non-recombining portion.  With the introduction of this new test panel,
the Sorenson Genomics Laboratory will be using 37 different PCR primer
sets.  In more common terms, this translates into 37 different loci with
up to 43 allele values excluding rare alleles that may be observed at
DYS19/DYS394, DYS464 or possibly even other loci.

The Sorenson Genomics Laboratory received ISO17025 accreditation through
the National Forensic Science Technology Center (NFSTC) in March of
2004.  One of the requirements of this accreditation is to comply with
any national or international standards that may be available for a
particular test or testing method.  The National Institute for Standards
and Technology (NIST) has developed and validated such a panel.  NIST is
a United States government agency that is responsible for verifying and
setting traceable standards that allow commercial entities to
effectively report results in the same terms and in the same language.
As a result NIST has made available a commercial standard reference
material known as SRM2395.  The SRM2395 product includes 5 male
specimens and one female specimen.  NIST has either consulted with other
entities, such as Sorenson Genomics, or has themselves taken the time to
perform DNA sequence analysis of many of the STR loci that are commonly
used in the forensic and genealogical communities.  Because sequence
analysis has been performed at each locus, the scientists at NIST have
been able to verify the actual number of repeat values, also known as
allele values, for each locus and for each member of the SRM2395 panel.
The results of this testing have been provided in a well documented set
of instructions that come with the purchase of the SRM 2395.  Some of
this information is also provided on the NIST website
(http://ts.nist.gov/ts/htdocs/230/232/232.htm).

Because Sorenson Genomics is ISO17025 accredited and because NIST now
has a standard reference material available, it has been decided that
all Y chromosome STR results will be compliant with this standard.  It
is expected that eventually all laboratories providing Y chromosome
analysis will conform to this standard since it will allow greater
portability of test results from one database to another without the
need for individual locus conversion, ultimately making things a little
easier for the end users.  The widespread use of this standard will also
help to develop a consensus about the name(s) of each particular locus.

There may be certain instances when our laboratory as well as other
laboratories may not agree on the NIST interpretation of a particular
allele value.  It is hoped, however, that the NIST SRM nomenclature will
be adopted and the allele values will be reported according to that
standard regardless of whether or not the individual organization agrees
with the values that are assigned by NIST to a particular locus.  This
situation certainly exists at the Y-GATA H4 locus as well as the DYS461
locus.

Previously the Y-GATA H4 locus was reported according to White et al.
but upon closer evaluation, the team at NIST has actually determined
that this locus should be reported using the TAGA repeat motif.  If the
GATA motif is used then the reported allele value will be one less than
the NIST SRM value.  Sorenson Genomics is currently compliant with the
NIST SRM nomenclature at this locus.

DYS461 has previously been reported by some laboratories, including
Sorenson Genomics, using only the TAGA repeat motif.  In a recent
peer-reviewed publication by Bosch et al. a CAGA repeat has been
included in the TAGA repeat structure with the understanding that the
inclusion of the single CAGA may be variable in some humans.  Because
NIST has chosen to include the CAGA repeat, laboratory results that have
been previously reported by the Sorenson Genomics Laboratory are
decreased by a single repeat. As a result, the Sorenson Genomics
laboratory will be increasing all prior results as well as all future
results by one value in order to be compliant with the NIST SRM.  These
changes will be reflected on any results that are available through the
Relative Genetics website at www.relativegenetics.com
<http://www.relativegenetics.com/>; .

Other loci that have presented some confusion for the genealogical
community are DYS19/DYS394 and DYS448.  The issue with these loci is
that they have not been called consistently between different
laboratories and databases.  While the different groups reporting such
values may be correct in their nomenclature, we have determined that the
best approach is to comply with the NIST SRM so that the values are
consistent and portable between different databases.

Sorenson Genomics has chosen to include several multi-copy loci in this
new test panel.  These loci are DYS385, YCAII, DYS459 and DYS464.  These
loci are reported as genotypes with comma's separating the allele values
i.e. DYS385 would be reported as 11,14 rather than DYS385a = 11 and
DYS385b = 14.  Matching at the multi-copy loci requires the two
individuals being matched to be the same at both positions in order to
be counted as a full match.  Therefore, if individual A has a value of
11,14 and individual B has a value of 11,15 the two individuals would be
mismatched at that locus.  Likewise, an individual who has a single
value at DYS385 is only reported as having a single value i.e. 11 and
not 11,11 or DYS385a = 11 and DYS385b =11.  We feel that reporting the
multi-copy loci in this way is a more accurate reflection of what is
recommended by the international forensic community.

Within the Sorenson Genomics Y chromosome panel, there are several loci
that have mutation rates that are higher than the general mutation rate
of 0.003, including DYS464.  There are also several loci that have
mutation rates that are much lower than the general mutation rate such
as DYS454.  It is understood by our laboratory that several markers are
highly informative while others are much less informative based on the
mutation rates.  At the present time, we have tried to provide as many
STR markers as is currently reasonable so that the end users will have
as much information as possible to perform their studies.  We realize
that there may come a time in the future when it is decided that one or
more loci have very little value for a particular application and we
reserve the right to add or remove loci in order to provide the consumer
with the most useful information.

Lastly, a recent publication by Kayser et al. has indicated that locus
Y-GATA C4 is now referred to as DYS635.  For the near future, Sorenson
Genomics will report this locus as DYS635 with a comment on the report
indicating that DYS635 is the same as Y-GATA C4.  For the long term,
this locus will be referred to as DYS635 as this is what is recommended
by NIST.

The goal for Sorenson Genomics is to help build consistency within this
relatively new and complex field.  Our intention is to provide a tool to
the world community that may be useful in establishing human
relationships, while allowing portability of data between the various
laboratories performing Y chromosome testing.

More information about the loci we utilize and nomenclature can be found
on our website at www.relativegenetics.com
<http://www.relativegenetics.com/>; .

Thank you,

Lars Mouritsen

Laboratory Manager

Sorenson Genomics Laboratory

2495 S. West Temple

Salt Lake City, Utah 84115

Phone: 801-461-9779

Fax: 801-461-9761

E-mail:  <mailto:>

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