Molecular Biology Sub-Domain::PerformedGeneticObservationResult

: Public Class

Created:	3/4/2015 12:20:27 AM
Modified:	7/3/2019 8:13:28 PM

Project:
Author:	wverhoef
Version:	1.0
Phase:	1.0
Status:
Complexity:	Easy
Difficulty:
Priority:
Multiplicity:
Advanced:
UUID:	{C24940C0-063C-4cdd-90B9-B1AE7EB67D98}
Appears In:	UML-Based Comprehensive BRIDG Model Diagram, DEPRECATED Old View MB: Molecular Biology, View MB: Molecular Biology, SDTM IG v3.1.3, SDTM IG v3.2

DEFINITION: The result of assessing a genetic characteristic of a biologic specimen. EXAMPLE(S): For an Amino Acid test the result might be "Arg". OTHER NAME(S): NOTE(S):

Attributes
Associations To
Tagged Values
Other Links

Attribute

Public SC
geneticRegionOfInterest

Details:

Alias:
Initial:
Stereotype:
Ordered:
Range:	Range:0 to 1
Transient:	False
Derived:	False
IsID:	False

Map:PGx v1.0=PG.PGGENRI

Notes:

DEFINITION: The portion of the genome serving as a locus for the test result, often a gene. EXAMPLE(S): EGFR, KRAS, CYP2D6, MYC, MFNG OTHER NAME(S): NOTE(S): These are typically obtained from the gene symbol list maintained by the Human Genome Variation Society (HGVS) =#gt; HUGO Genome Nomenclature Consortium (HGNC), a committee of the Human Genome Organization (HUGO). This can be a gene, a protein, or a sector as described by geneticRegionTypeCode.

Public CD
geneticRegionTypeCode

Details:

Alias:
Initial:
Stereotype:
Ordered:
Range:	Range:0 to 1
Transient:	False
Derived:	False
IsID:	False

Map:PGx v1.0=PG.PGGENTYP

Notes:

DEFINITION: A coded value specifying the kind of portion of the genome serving as a locus for the test result. EXAMPLE(S): GENE, SECTOR, DOMAIN, PROTEIN OTHER NAME(S): NOTE(S):

Public ST
geneticSubregion

Details:

Alias:
Initial:
Stereotype:
Ordered:
Range:	Range:0 to 1
Transient:	False
Derived:	False
IsID:	False

Map:PGx v1.0=PF.PFGENSR

Notes:

DEFINITION: The portion of the genetic region of interest in which the variation was found when the genetic region of interest is a gene. EXAMPLE(S): Exon 15, Intron 1 OTHER NAME(S): NOTE(S): This attribute is only used if geneticRegionTypeCode = "GENE".

Public IVL<INT>
geneticLocation

Details:

Alias:
Initial:
Stereotype:
Ordered:
Range:	Range:0 to 1
Transient:	False
Derived:	False
IsID:	False

Map:PGx v1.0=PF.PFGENLOC

Notes:

DEFINITION: The portion of the sequence that is described by this test result. EXAMPLE(S): 65 213-215 71 213 152 454 -614 -2055 OTHER NAME(S): NOTE(S):

Public ST
geneticTarget

Details:

Alias:
Initial:
Stereotype:
Ordered:
Range:
Transient:	False
Derived:	False
IsID:	False

Map:PGx v1.0=PF.PFGENTRG

Notes:

DEFINITION: The nucleotide or amino acid within the genetic location of interest that is to be compared to the subject's test result. EXAMPLE(S): In CDISC's PGx domains, a PFGENTRG of "A" indicates that you are checking to see if the biospecimen tested has an A in the location specified by the geneticLocationOfInterest, or a value of "del" in PFGENTRG means you are looking for a deletion in that location of interest. OTHER NAME(S): NOTE(S):

Public CD
alleleIndicatorCode

Details:

Alias:
Initial:
Stereotype:
Ordered:
Range:	Range:0 to 1
Transient:	False
Derived:	False
IsID:	False

Map:PGx v1.0=PF.PFALLELC

Notes:

DEFINITION: A coded value specifying one copy of a gene used to differentiate between copies of a gene on a homologous chromosome pair. EXAMPLE(S): 1, 2, A, B OTHER NAME(S): NOTE(S): The convention used to label the copy is often 1 or 2, A or B, because whether a given copy is maternal or paternal is not usually known. The code system used for this concept is expected to be local since there is currently no industry standard.

Public CD
mutationTypeCode

Details:

Alias:
Initial:
Stereotype:
Ordered:
Range:	Range:0 to 1
Transient:	False
Derived:	False
IsID:	False

Map:PGx v1.0=PF.PFMUTYP

Notes:

DEFINITION: Coded value defining the genomic source of the variant, which can indicate the variant context including inherited germline mutations, acquired tumor specific mutations, mutations within a fetus, or unknown origin. EXAMPLE(S): Germline Somatic Prenatal Likely Germline Likely Somatic Likely Prenatal Unknown Genomic Origin OTHER NAME(S): NOTE(S):

Element	Source Role	Target Role
GeneticReference Class	Name: referencingPerformedGeneticObservationResult	Name: referencedGeneticReference
Details: DESCRIPTION:<br/>Each PerformedGeneticObservationResult might reference one GeneticReference. Each GeneticReference always is referenced by one or more PerformedGeneticObservationResult.<br/><br/>DEFINITION:<br/><br/>EXAMPLE(S):<br/>"A" might be the reference if the test result is a Nucleotide.<br/>"Trp" might be the reference if the test result is an Amino Acid.<br/><br/>OTHER NAME(S):<br/><br/>NOTE(S):<br/>
SingleNucleotidePolymorphism Class	Name: referencingPerformedGeneticObservationResult	Name: referencedSingleNucleotidePolymorphism
Details: DESCRIPTION:<br/>Each PerformedGeneticObservationResult might reference one SingleNucleotidePolymorphism. Each SingleNucleotidePolymorphism might be referenced by one or more PerformedGeneticObservationResult.<br/><br/>DEFINITION:<br/>The link between the observed variation in test result and the documented variation in the dbSNP database as identified by an rs number.<br/><br/>EXAMPLE(S):<br/>A given subject, Joe, may have a genetic variation detected by a test result which is a match to a dbSNP variation identified with the rs number "rs1570360". The dbSNP variation ("NM_001025367.2:c.-614A#gt;G") tells us that NM_001025367.2 is the most current reference sequence (".2" means it's version 2). The "c.-614A#gt;G" tells us a nucleotide changed in position "-614" from A to G. <br/><br/>OTHER NAME(S):<br/><br/>NOTE(S):<br/>

Tag	Value
Map:PGx v1.0	PF.PFGENTRG
Details:

Object	Type	Connection	Direction	Notes
PerformedObservationResult	Class	Generalization	To	DESCRIPTION: Each PerformedGeneticObservationResult always specializes one PerformedObservationResult. Each PerformedObservationResult might be specialized by one PerformedGeneticObservationResult. DEFINITION: EXAMPLE(S): OTHER NAME(S): NOTE(S):