Pathology observables

Question on a new concept which seems like a '\Presence property but the finding of post-obstructive pneumonitis (clinical finding) is not allowed in Component:

"Status of tumor associated postobstructive pneumonitis in excised lung specimen (observable entity)"

ISA Observable entity

COMPONENT (Post-obstructive pneumonia, a finding, is not allowed by MRCM)

INHERES IN Specimen from lung obtained by lobectomy

PROPERTY TYPE Presence

TECHNIQUE Anatomic pathology technique

SCALE TYPE Ordinal

Please provide guidance on the modeling

Jim

Revisiting some earlier work, I note a discrepancy between LOINC assignment and our definition.  I think that Swapna appropriately deined this as an area fraction which we do not have in Measurement properties, but I also ask if this would be the correct model for observing the fraction of the cancer that was mucinous adenocarcinoma vs (not mucinous) Adenocarcinoma?

Mucinous histologic fraction of excised colon neoplasm  85282-2

ISA Histologic feature of tumor

COMPONENT Mucinous adenocarcinoma

Direct site Formalin fixed paraffin embedded tissue specimen

INHERENT LOCATION Colon structure

INHERES IN Malignant neoplasm

PROPERTY (Area fraction) has this been added to international?

RELATIVE TO Adenocarcinoma

TECHNIQUE Light microscopy

SCALE TYPE Quantitative

Based on our last call and my analysis of the CAP Lung Biomarker worksheet with input from our FISH expert, I note the following observations and suggestions as related to FISH observables.
 

1. Two specific aspects of FISH are noted in the CAP protocols
   
   1. Copy number for a gene locus
   2. Structural changes of the chromosome related to a gene locus
   3. Each measure a different property: count (number) and structural change
      
      
2. Copy count which includes polyploidy, diploidy, monoploidy or complete deletion are represented by a count/number property.  Therefore, I suggest the observable be modeled as copy count or number of gene X loci observed.  The answer will be an integer.  
   
   
3. Gene amplification, as reported by FISH, is a copy count in excess of some threshold which can vary.  However, gene amplification is not solicited as part of the CAP protocol.  Its representation does not appear to be necessary.
   
   
4. Structural changes (or rearrangements) measure a different property,  Morphologic abnormality of a chromosome.  The specific changes can be translocations, fusions, inversions, etc.  However, they are all morphologic abnormalities of the chromosome.  The CAP protocols solicit the specific changes, and the answer sets as listed indicate, by nomenclature, what type of change was noted.  The ALK gene is an example.  Other gene loci simply solicit if a rearrangement is present or not.  Example the ROS1 gene.
   
   
5. I propose 2-3 types of observable entities
   1. Copy count
   2. Status of rearrangement
   3. Type of rearrangement
      
      
6. SNOMED CT cell structure defines chromosomal pairs.  Concepts for chromosome by number may be indicated for better modeling

Hi Scott,

Copy number for a gene locus, is that the number of genes (as in gene amplification) or number of chromosome copies (as in polysomy/polyploidy)?

While  working on the Inception/Elaboration document for this project, I stumbled across a probable error in my work.  I modeled:

"Status of BRAF V600E sequence variant detection in excised malignant neoplasm of lung (observable entity)"

IS_A  Tumor biomarker

DIRECT_SITE Tissue specimen from lung

INHERENT LOCATION Malignant neoplasm

INHERES_IN BRAF gene locus

PROPERTY TYPE Seqeunce variant property

SCALE TYPE Ordinal value

TECHNIQUE Nucleotide sequencing technique

TIME ASPECT Single point in time

But I think in reality it should probably be:

"Status of BRAF V600E sequence variant detection in excised malignant neoplasm of lung (observable entity)"

IS_A  Tumor biomarker

DIRECT_SITE Tissue specimen from lung

INHERENT LOCATION Malignant neoplasm

INHERES_IN BRAF gene locus

COMPONENT BRAF V600E sequence variant(cell structure)

PROPERTY TYPE Presence

SCALE TYPE Ordinal value

TECHNIQUE Nucleotide sequencing technique

TIME ASPECT Single point in time

Please chime in to guide me here!

Jim

Yes, as I have been preparing and expanding the inception/elaboration document for Cancer patholo0gy, I have noticed that I am inconsistent between 'status of' and 'presence of' and need to correct that for consistency in our content and the documentation.  I plan to post updates to the document this weekend for discvussion next Tuesday.  

Where is the powerpoint from David?

Jim

Daniel

Can we conclude on the modeling of the above concept today?  It is part of the templates documentation that I am adding to the Inception/elaboration document for Pathology observables

Jim