tbd/ LOINC codes

	A	B	C	D	E	F	G	H
1	current system	Action Item	current code	current display	current definition	definition source	used in the IG	comment
2	http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs	Should be "merged" with therapeutic-implication. Use therapeutic-implication for Obs.code and Obs.component.code	predicted-therapeutic-implication	Predicted Therapeutic Implication	A predicted ramification based on the presence of associated molecular finding(s). Ramifications may include alterations in drug metabolism (or pharmacokinetics) that determine the concentration of the drug, prodrug, and/or break-down products over time; alterations in drug efficacy (or pharmacodynamics) that determine how effective a drug is at a given concentration; alterations that alter the risk of adverse drug events, or other types of implications that indicate altered responsiveness to other types of therapies.		http://build.fhir.org/ig/HL7/genomics-reporting/StructureDefinition-therapeutic-implication.htmlcomponent:predicted-therapeutic-implication
3	http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs	remove prognostic implication from: http://build.fhir.org/ig/HL7/genomics-reporting/StructureDefinition-implication.html	prognostic-implication	Prognostic Implication	Finding of whether a particular somatic genotype/haplotype/variation or combination-thereof predicts a particular outcome for the specified cancer - either on its own or in conjunction with one or more interventions.
4	http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs	(Merge: component:therapy-assessed and therapy-assesed extension,) ask LOINC for a code use-case: component.value can't be a reference	associated-therapy	Associated Therapy	The non-medication therapy (procedure) associated with this implication.
5	http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs	ask for use-cases, need examples, if still needed, do we need this & allelic read depth(LOINC code needs better definition) -> request LOINC Code	region-coverage	Region Coverage	Given as a number between 0 and 100. Mean mapped read depth. Obtained by counting total number of mapped reads and divided by the number of bases in the region sequence. Definition in IG: When sequencing, what % of the region was covered.	allelic read depth defintion in LRI: Specifies the number of reads that identified the allele in question whether it consists of one or a small sequence of contiguous nucleotides. Different methods and purposes require different numbers of reads to be acceptable. Often >400, sometimes as few as 2-4
6	http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs	request LOINC code	molecular-consequence	Molecular Consequence	Annotated changes to sequence features caused by this variant. Terms are from the sequence ontology under SO:0001537. The calculated or observed effect of a variant on its downstream transcript and, if applicable, ensuing protein sequence.
7	http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs	request LOINC code, Discussion: add Definition from LRI to: 82120-7	variant-inheritance	Variant Inheritance	A quality inhering in a variant by virtue of its origin. The terms are in the sequence ontology under SO:0001762.
8	http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs	request LOINC code	diagnostic-implication	Diagnostic Implication	An observation linking a genomic finding with a knowledge base, providing context that may aid in diagnosing a patient with a particular phenotype or condition.
9	http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs	request LOINC code	therapeutic-implication	Therapeutic Implication	An observation linking a genomic finding with a knowledge base, providing potential evidence of an interaction with a specified medication or non-medicinal therapy.
10	http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs	request LOINC code ("opposite" of 51959-5)	uncallable-regions	Uncallable Regions	Contiguous regions where a call was not made. Must be inside the range given by 'ranges examined' in the given reference sequence and coordinate system.
11	http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs	request Loinc code (inlclude reference to SO:0001536)	functional-effect	Functional Effect	The effect of a variant on downstream biological products or pathways (from Sequence Ontology).
12	http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs	request LOINC code	conclusion-string	Conclusion Text	Clinical conclusion (interpretation) of the observation.
13	http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs	request LOINC code, also mention https://loinc.org/79742-3/	condition-inheritance	Condition Inheritance	The transmission pattern of the condition/phenotype in a pedigree.
14	http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs	request LOINC code	variant-confidence-status	Variant Confidence Status	The confidence of a true positive variant call.
15	http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs	request LOINC code	protein-ref-seq	Protein Reference Sequence	A comprehensive, integrated, non-redundant, well-annotated set of reference sequences for proteins.		http://build.fhir.org/ig/HL7/genomics-reporting/StructureDefinition-variant.html
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