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#316 Appropriateness of adding phenotypes associated with muscle biopsy results
Hi All,
We have had requests to describe some of the phenotypes associated with the outcome of muscle biopsies. Many of the terms are already present, but some are not. Would it be appropriate to describe these in the HPO? For example, decreased/absent dystrophin in muscle by IHC? What are your thoughts? I will send a number of requests if felt to be appropriate.
Thanks,
Heather Trang
Hi Heather,
bascially, anything that is the outcome of a test done on a patient is appropriate for the HPO. So I think these terms are probably OK, please send them to the tracker.
-Peter
Dr. med. Peter N. Robinson, MSc.
Professor of Medical Genomics
Professor in the Bioinformatics Division of the Department of Mathematics and Computer Science of the Freie Universität Berlin
Institut für Medizinische Genetik und Humangenetik
Charité - Universitätsmedizin Berlin
Augustenburger Platz 1
13353 Berlin
Germany
+4930 450566006
Mobile: 0160 93769872
peter.robinson@charite.de
http://compbio.charite.de
http://www.human-phenotype-ontology.org
Introduction to Bio-Ontologies: http://www.crcpress.com/product/isbn/9781439836651
I have learned from my mistakes, and I am sure I can repeat them exactly
ORCID ID:http://orcid.org/0000-0002-0736-9199
Scopus Author ID 7403719646
Appointment request: http://doodle.com/pnrobinson
Von: Heather Trang [heathertrang@users.sf.net]
Gesendet: Freitag, 13. Juni 2014 23:42
An: Ticket 316
Betreff: [obo:human-phenotype-requests] #316 Appropriateness of adding phenotypes associated with muscle biopsy results
[human-phenotype-requests:#316]http://sourceforge.net/p/obo/human-phenotype-requests/316/ Appropriateness of adding phenotypes associated with muscle biopsy results
Status: unread
Group: musculoskeletal
Created: Fri Jun 13, 2014 09:42 PM UTC by Heather Trang
Last Updated: Fri Jun 13, 2014 09:42 PM UTC
Owner: nobody
Hi All,
We have had requests to describe some of the phenotypes associated with the outcome of muscle biopsies. Many of the terms are already present, but some are not. Would it be appropriate to describe these in the HPO? For example, decreased/absent dystrophin in muscle by IHC? What are your thoughts? I will send a number of requests if felt to be appropriate.
Thanks,
Heather Trang
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#316Hi Peter,
The following are terms that have been requested for description of findings on muscle biopsies. I'm not sure how best to categorize these findings within the ontology. For example, a separate supraterm for "abnormal muscle biopsy" with these as subterms could be considered, but any terms under abnormal muscle morphology that can be observed on muscle biopsy should then be mapped to both locations. I will let you consider. There is a long list of potential phenotypes observed by staining. This is likely simply a starting point. I tried to provide consistent and appropriate definitions.
Sincerely,
Heather
Inflammatory infiltrates present: Staining and immunohistochemistry reveals inflammatory infiltrates in the muscle biopsy tissue
Protein aggregates present: Staining and immunohistochemistry reveals protein aggregates in the muscle biopsy tissue
Absent Merosin Staining, definition: Immunohistochemistry reveals absent merosin protein in the muscle biopsy. Synonym: Absent Laminin alpha 2
Reduced Merosin Staining, definition: Immunohistochemistry reveals reduced merosin protein in the muscle biopsy. Synonym: Reduced Laminin alpha 2
Reduced Laminin Beta 1 Staining, definition: Immunohistochemistry reveals reduced laminin Beta 1 protein in the muscle biopsy.
Reduced Collagen VI Staining, definition: Immunohistochemistry reveals reduced collagen VI protein in the muscle biopsy. Synonym: Reduced collagen 6, reduced collagen six
Absent Dystrophin Staining, definition: Immunohistochemistry reveals absent dystrophin protein in the muscle biopsy.
Reduced Dystrophin Staining, definition: Immunohistochemistry reveals reduced dystrophin protein in the muscle biopsy.
Reduced alpha dystroglycan Staining, definition: Immunohistochemistry reveals reduced alpha dystroglycan protein in the muscle biopsy.
Absent alpha sarcoglycan Staining, definition: Immunohistochemistry reveals absent alpha sarcoglycan protein in the muscle biopsy.
Reduced alpha sarcoglycan Staining, definition: Immunohistochemistry reveals reduced alpha sarcoglycan protein in the muscle biopsy.
Absent beta sarcoglycan Staining, definition: Immunohistochemistry reveals absent beta sarcoglycan protein in the muscle biopsy.
Reduced beta sarcoglycan Staining, definition: Immunohistochemistry reveals reduced beta sarcoglycan protein in the muscle biopsy.
Absent gamma sarcoglycan Staining, definition: Immunohistochemistry reveals absent gamma sarcoglycan protein in the muscle biopsy.
Reduced gamma sarcoglycan Staining, definition: Immunohistochemistry reveals reduced gamma sarcoglyan protein in the muscle biopsy.
Absent delta sarcoglycan Staining, definition: Immunohistochemistry reveals absent delta sarcoglycan protein in the muscle biopsy.
Reduced delta sarcoglycan Staining, definition: Immunohistochemistry reveals reduced delta sarcoglycan protein in the muscle biopsy.
Absent Dysferlin Staining, definition: Immunohistochemistry reveals absent dysferlin protein in the muscle biopsy.
Reduced Dysferlin Staining, definition: Immunohistochemistry reveals reduced dysferlin protein in the muscle biopsy.
Absent Emerin Staining, definition: Immunohistochemistry reveals absent emerin protein in the muscle biopsy.
Reduced Emerin Staining, definition: Immunohistochemistry reveals reduced emerin protein in the muscle biopsy.
Absent Calpain-3 Blotting, definition: Western blot reveals absent calpain-3 protein in the muscle biopsy tissue.
Reduced Calpain-3 Blotting, definition: Western blot reveals reduced calpain-3 protein in the muscle biopsy tissue.
Reduced perlecan Staining, definition: Immunohistochemistry reveals reduced perlecan protein in the muscle biopsy.
Reduced Lamin A/C Staining, definition: Immunohistochemistry reveals reduced lamin A/C protein in the muscle biopsy.
Reduced Lamin A/C Blotting, definition: Western blot reveals reduced lamin A/C protein in the muscle biopsy tissue.
I have added these terms. Note however, that I only made one term for the following:
Reduced Lamin A/C Staining
Reduced Lamin A/C Blotting
This is because the HPO is not modeling lab investigations, and the phenotype is assumed to be the same for both investigations.