: Public Class
Created: 3/4/2015 12:20:27 AM
Modified: 12/8/2017 2:05:25 PM
Project:
Advanced:
DEFINITION:<br/>The result of assessing a genetic characteristic of a biologic specimen.<br/><br/>EXAMPLE(S):<br/>For an Amino Acid test the result might be "Arg".<br/><br/>OTHER NAME(S):<br/><br/>NOTE(S):<br/>
Attribute
Public SC
  geneticRegionOfInterest
Details:
Map:PGx v1.0=PG.PGGENRI
Notes: DEFINITION:<br/>The portion of the genome serving as a locus for the test result, often a gene.  <br/><br/>EXAMPLE(S):<br/>EGFR, KRAS, CYP2D6, MYC, MFNG<br/><br/>OTHER NAME(S):<br/><br/>NOTE(S):<br/>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.<br/>
Public CD
  geneticRegionTypeCode
Details:
Map:PGx v1.0=PG.PGGENTYP
Notes: DEFINITION:<br/>A coded value specifying the kind of portion of the genome serving as a locus for the test result.  <br/><br/>EXAMPLE(S):<br/>GENE, SECTOR, DOMAIN, PROTEIN  <br/><br/>OTHER NAME(S):<br/><br/>NOTE(S):<br/>
Public ST
  geneticSubregion
Details:
Map:PGx v1.0=PF.PFGENSR
Notes: DEFINITION:<br/>The portion of the genetic region of interest in which the variation was found when the genetic region of interest is a gene.  <br/><br/>EXAMPLE(S):<br/>Exon 15, Intron 1<br/><br/>OTHER NAME(S):<br/><br/>NOTE(S):<br/>This attribute is only used if geneticRegionTypeCode = "GENE".<br/>
Public IVL<INT>
  geneticLocation
Details:
Map:PGx v1.0=PF.PFGENLOC
Notes: DEFINITION:<br/>The portion of the sequence that is described by this test result.<br/><br/>EXAMPLE(S):<br/>65<br/>213-215<br/>71<br/>213<br/>152<br/>454<br/>-614<br/>-2055<br/><br/>OTHER NAME(S):<br/><br/>NOTE(S):<br/>
Public ST
  geneticTarget
Details:
Map:PGx v1.0=PF.PFGENTRG
Notes: DEFINITION:<br/>The nucleotide or amino acid within the genetic location of interest that is to be compared to the subject's test result.<br/><br/>EXAMPLE(S):<br/>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.<br/><br/>OTHER NAME(S):<br/><br/>NOTE(S):<br/>
Public CD
  alleleIndicatorCode
Details:
Map:PGx v1.0=PF.PFALLELC
Notes: DEFINITION:<br/>A coded value specifying one copy of a gene used to differentiate between copies of a gene on a homologous chromosome pair.<br/><br/>EXAMPLE(S):<br/>1, 2, A, B<br/><br/>OTHER NAME(S):<br/><br/>NOTE(S):<br/>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.<br/><br/>
Public CD
  mutationTypeCode
Details:
Map:PGx v1.0=PF.PFMUTYP
Notes: DEFINITION:<br/>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.<br/><br/>EXAMPLE(S):<br/>Germline <br/>Somatic <br/>Prenatal <br/>Likely Germline <br/>Likely Somatic <br/>Likely Prenatal <br/>Unknown Genomic Origin <br/><br/>OTHER NAME(S):<br/><br/>NOTE(S):<br/>
Public BL
  derivedIndicator
Details:
Map:PGx v1.0=PF.PFDRVFL
Notes: DEFINITION:<br/>Specifies whether a result represents a calculation performed on other results.<br/><br/>EXAMPLE(S):<br/>For CDISC PGx domains, a lab may report a codon (consists of 3 nucleotides) as a result, e.g. TTT, and the sponsor can derive the fact that this codon codes for an amino acid, Phenylalanine in this case;  the sponsor is using the codon to derive the amino acid. Therefore for the record reporting the amino acid, the derivedIndicator = "true".<br/><br/>OTHER NAME(S):<br/>Derived Flag<br/><br/>NOTE(S):<br/>
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):