Genomic precision medicine is the use of specific human genetic variant data in order to drive patient-centered research, treatment, and wellness.  It is one of the newest fields of medicine, and significant knowledge disparities exist between scientific researchers who conduct genomic research and clinicians who treat patients.  These disparities are typically borne out in the lack of terminology that intersects genomics with the clinic (although that situation is improving).

Introduction to the code sets

• SNOMED CT is a clinical coding system used for research (and in some areas) billing
• ICD-10-CM is a clinical coding system used chiefly for epidemiology and billing
• NCBI MedGen (short for “Medical Genetics”) is a precision medicine-oriented phenotypic meta-terminology that connects to ClinVar (see below)
• NCBI ClinVar (ClinVar – Variant – MPM Full Subset in Symedical®) is a biological terminology that contains over 1 million genetic variants.  Based on assessment of disease correlation, variants are often assigned associated MedGen terms.

Steps

Part A: Clinical Term Search

1. Navigate to Viewpoint: https://edu.symedical.com/SymedicalIUSOICViewpoint
2. Search for “Non-small cell lung cancer” using the code set SNOMED CT US Edition
3. Click the top search result and note the relationships (Relationships pane) and term mappings (Mappings pane – Make sure to view both Inbound and Outbound tabs)
4. Make a screenshot of the relationship/mapping results and paste it in to your answer document (5 points)
5. Create a new browser window, navigate to Viewpoint, and search for “Non-small cell lung cancer” using the code set NCBI – MedGen
6. Click one of the search results and note the relationships (Relationships pane)
7. If you see no relationships, go back and select another MedGen term from the search results, and repeat steps A5-A6.

Part B: Genetic Term Search

1. Create a second new browser window, navigate to Viewpoint, and search for the word “mutation” using the code set SNOMED CT US Edition
2. Click any term that lists the name of a gene (capital letters + sometimes numbers) followed by “mutation”
3. Note the relationships (Relationships pane)
4. Make a screenshot of the relationship results and paste it in to your answer document (5 points)
5. Create a third new browser window, Search the code set ClinVar for a precise variant related to the gene involved in B2 (these always start with “nm”).  For example, if your term for B2 was “FGFBR2 Mutation Negative”, search ClinVar for “nm fgfbr2”.
6. Select a term that appears in the search results
7. Note the relationships (Relationships pane)

Part C: Analysis

1. First, include screenshots from A4 and B4 above (5 + 5 = 10 points)
2. Compare the relationships and mappings in A3 to the relationships found in A6.  Answer the following:
   1. Compare and contrast the types of terms seen in the relations from A3 vs. those from A6. (10 points)
   2. What does the degree of overlap (or lack thereof) mean for a patient with the disorder that you searched for? (10 points)
3. List the code and term (term description) for the SNOMED term you chose in B2
4. Compare the relationships in B3 to the relationships in B6.  Answer the following:
   1. Compare and contrast the types of terms seen in the relations from B3 vs. those from B6. (10 points)
   2. What do the relationships in B6 mean for a person with the involved ClinVar variant?  On the other hand, if there are no relationships noted, comment on what the consequences might be.  (There are multiple appropriate answers for this.) (10 points)
5. For C2A, C2B, C4A, and C4B, feel free to bring in additional references, which must be cited appropriately

B581/481 Rubric