Discussion on overall clarification on GeneticReference

Return to BRIDG

CLOSED - Need overall clarification on GeneticReference (rows 49 & 50)

Original Definition

DEFINITION: An assembly of nucleotides used to identify genetic variations.

EXAMPLE(S): "A" might be the reference if the test is Nucleotide. "Trp" might be the reference if the test is Amino Acid.

OTHER NAME(S): Reference Sequence

NOTE(S):

Ballot Comment

The sequence is often made up of multiple residues. Proposed wording: ‘"A" might be an element of the reference if the test is Nucleotide. "Trp" might be an element of the reference if the test is Amino Acid.’

Proposed Definition

DEFINITION: An assembly of nucleotides used to identify genetic variations.

EXAMPLE(S): "A" might be an element of the reference if the test is Nucleotide. "Trp" might be an element of the reference if the test is Amino Acid.

OTHER NAME(S): Reference Sequence ID for a sequence in a database

NOTE(S):

Proposed Disposition

Persuasive

Proposed Disposition Comment

Review proposed change with PGx SMEs to ensure change is consistent with their original use case for the concept.

Initial Discussion

Need SME team to refine wording, need to remodel connection between tests and MolBio area of the model, “reference” is an overused word – need clarification

MolSeq to ExpActItem to Activity – leverage this association – find out how test results would be modeled – are they also activity items?

Outstanding Questions

• Are the only kinds of sequences that can be referenced nucleotides (examples reference both nucleotide and amino acid)? Does the definition need to be refined?
• Is the range of possible genetic references the same as the identifier classes in the Molecular Biology sub-domain? (e.g. GeneticVariationIdentifier, ProteinIdentifier, GeneIdentifier, MessengerRNAIdentifier, PathwayIdentifier)
• CDISC PGx SMEs: Are the proposed changes will supportive of your use case?

Responses

Lauren Becnel: The proposed definition is much improved, but its accompanying example should be discarded. Examples: Different versions of genomic references exist for many species. For example, Homo sapiens reference genome utilized by the UCSC Genome Browser hg38 was released in 2013 and hg19 in 2009. Older versions of the assembled reference include hg18.

Q from WENDY (TYPE: EX): Mollie wanted us to provide an actual value of a sequence of nucleotides, not just reference. I found the UCSC Genome Browser http://www.ncbi.nlm.nih.gov/genome/51 but didn't recognize what I thought might be a sequence of nucleotides, but I'm not an expert and was only looking for something like "AMDYSLAAAL..."

DISCUSSION 20160223: update example to the following: "Homo sapiens reference genome utilized by the UCSC Genome Browser hg38 was released in 2013 and hg19 in 2009. Older versions of the assembled reference include hg18."

UPDATE DONE IN MODEL

Return to BRIDG