Re: nomenclature for changes from the reference sequence

That link wasn't friendly so I thought I'd attach the pdf. Hopefully the
mailer daemon forwards it properly.

Cheers,
Paul

--
Paul Rigor
http://www.ics.uci.edu/~prigor



On Thu, Jun 30, 2011 at 11:34 AM, Michael Miller <mmiller@systemsbiology.org
> wrote:

> hi all,
>
> in a previous bioRDF call, lena (i think) brought up the question of how
> to encode how a given sequence varies from the reference sequence.  in
> 'Clinical Laboratory Reports in Molecular Pathology', pgs 7 and onward
> there's a nice detailed requirement for this (based on human but can
> probably be extended):
>
> http://www.archivesofpathology.org/doi/pdf/10.1043/1543-2165%282007%29131%
> 5B852%3ACLRIMP%5D2.0.CO%3B2
>
> this came from the HL7 Clinical Genomics mailing list.
>
> cheers,
> michael
>
>
> Michael Miller
> Software Engineer
> Institute for Systems Biology
>
> ----- Original Message -----
> From: "Amnon Shabo" <SHABO@il.ibm.com>
> To: <clingenomics@lists.hl7.org>
> Sent: Monday, June 27, 2011 9:25 AM
> Subject: Harmonizing GTR with proposals from the literature
>
>
> >
> > Dear CGers,
> > Thanks to Mollie who referred us to publications describing molecular
> > testing reports, we can refine our GTR specification if needed.
> > For example, one of the publications I glanced through is a paper titled
> > "Clinical Laboratory Reports in Molecular Pathology" (see
> >
> http://www.archivesofpathology.org/doi/pdf/10.1043/1543-2165%282007%29131%
> 5B852%3ACLRIMP%5D2.0.CO%3B2)
> >
> > In this paper there are sample reports, for example, I extracted the
> > following report on Fragile X Genotyping results, for your convenience:
> >
> > (Embedded image moved to file: pic31376.gif)
> >
> > Looking at the headings, it's similar in essence to the basic outline of
> > the GTR as represented through the "Test Details Section" with different
> > names perhaps, e.g, we use findings rather than results, or methodology
> > rather than procedure. As for the "Comment" heading, we use
> > Recommendations
> > which is more informative to the content of this piece I believe but
> we'd
> > be glad to hear your thoughts. Interpretations are separated to clinical
> > and analytic interpretations which is actually a good idea as I can see
> > research reports using merely the analytic interpretations, but I wonder
>
> > if
> > this specialization of Interpretation should not be optional.
> >
> > Note that the GTR "Test Details Sections" is the parent template of
> > specialized sections by testing type, e.g., Genetic Variations,
> > Cytogenetics, etc. In this way, we can further refine those sections and
> > bind their attributes to corresponding value sets (such as the LOINC
> value
> > sets) and still be consistent with the same outline as described by this
> > abstract section template  "Test Details Section".
> >
> > Let's review this paper and others (e.g., "Clinician Perspectives about
> > Molecular Genetic Testing for Heritable Conditions and Development of a
> > Clinician-Friendly Laboratory Report" at
> > http://moldiag.highwire.org/cgi/reprint/11/2/162) and compare its
> guidance
> > to the GTR and if you think we should make changes to the GTR outline or
> > any other component of the GTR, please post your proposals to our
> mailing
> > list and we could also discuss it in our weekly conf. calls.
> > Thanks,
> > Amnon.
> >
> > ************************************************
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>
>