: Public Class
Created: 3/4/2015 12:20:27 AM
Modified: 3/25/2015 4:09:54 PM
Project:
Advanced:
DEFINITION:<br /></p><p>The result of assessing a genetic characteristic of a biologic specimen.<br /></p><p><br /></p><p>EXAMPLE(S):<br /></p><p>For an Amino Acid test the result might be "Arg".<br /></p><p><br /></p><p>OTHER NAME(S):<br /></p><p><br /></p><p>NOTE(S):<br /></p>
Attribute
Public SC
  geneticRegionOfInterest
Details:
Map:PGx v1.0=PG.PGGENRI
Notes: DEFINITION:#lt;br /#gt;#lt;/p#gt;#lt;p#gt;The portion of the genome serving as a locus for the test result, often a gene.  #lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;EXAMPLE(S):#lt;br /#gt;#lt;/p#gt;#lt;p#gt;EGFR, KRAS, CYP2D6, MYC, MFNG#lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;OTHER NAME(S):#lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;NOTE(S):#lt;br /#gt;#lt;/p#gt;#lt;p#gt;These are typically obtained from the gene symbol list maintained by the Human Genome Variation Society (HGVS).#lt;br /#gt;#lt;/p#gt;
Public CD
  geneticRegionTypeCode
Details:
Map:PGx v1.0=PG.PGGENTYP
Notes: DEFINITION:#lt;br /#gt;#lt;/p#gt;#lt;p#gt;A coded value specifying the kind of portion of the genome serving as a locus for the test result.  #lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;EXAMPLE(S):#lt;br /#gt;#lt;/p#gt;#lt;p#gt;GENE, SECTOR, DOMAIN, PROTEIN  #lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;OTHER NAME(S):#lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;NOTE(S):#lt;br /#gt;#lt;/p#gt;
Public ST
  geneticSubregion
Details:
Map:PGx v1.0=PF.PFGENSR
Notes: DEFINITION:#lt;br /#gt;#lt;/p#gt;#lt;p#gt;The portion of the genetic region of interest in which the variation was found when the genetic region of interest is a gene.  #lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;EXAMPLE(S):#lt;br /#gt;#lt;/p#gt;#lt;p#gt;Exon 15, Intron 1#lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;OTHER NAME(S):#lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;NOTE(S):#lt;br /#gt;#lt;/p#gt;#lt;p#gt;This attribute is only used if geneticRegionTypeCode = "GENE".#lt;br /#gt;#lt;/p#gt;
Public IVL<INT>
  geneticLocation
Details:
Map:PGx v1.0=PF.PFGENLOC
Notes: DEFINITION:#lt;br /#gt;#lt;/p#gt;#lt;p#gt;The portion of the sequence that is described by this test result.#lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;EXAMPLE(S):#lt;br /#gt;#lt;/p#gt;#lt;p#gt;65#lt;br /#gt;#lt;/p#gt;#lt;p#gt;213-215#lt;br /#gt;#lt;/p#gt;#lt;p#gt;71#lt;br /#gt;#lt;/p#gt;#lt;p#gt;213#lt;br /#gt;#lt;/p#gt;#lt;p#gt;152#lt;br /#gt;#lt;/p#gt;#lt;p#gt;454#lt;br /#gt;#lt;/p#gt;#lt;p#gt;-614#lt;br /#gt;#lt;/p#gt;#lt;p#gt;-2055#lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;OTHER NAME(S):#lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;NOTE(S):#lt;br /#gt;#lt;/p#gt;
Public ST
  geneticTarget
Details:
Map:PGx v1.0=PF.PFGENTRG
Notes: DEFINITION:#lt;br /#gt;#lt;/p#gt;#lt;p#gt;The nucleotide or amino acid within the genetic location of interest that is to be compared to the subject's test result.#lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;EXAMPLE(S):#lt;br /#gt;#lt;/p#gt;#lt;p#gt;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.#lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;OTHER NAME(S):#lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;NOTE(S):#lt;br /#gt;#lt;/p#gt;
Public CD
  alleleIndicatorCode
Details:
Map:PGx v1.0=PF.PFALLELC
Notes: DEFINITION:#lt;br /#gt;#lt;/p#gt;#lt;p#gt;A coded value specifying one copy of a gene used to differentiate between copies of a gene on a homologous chromosome pair.#lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;EXAMPLE(S):#lt;br /#gt;#lt;/p#gt;#lt;p#gt;1, 2, A, B#lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;OTHER NAME(S):#lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;NOTE(S):#lt;br /#gt;#lt;/p#gt;#lt;p#gt;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.#lt;br /#gt;#lt;/p#gt;
Public CD
  mutationTypeCode
Details:
Map:PGx v1.0=PF.PFMUTYP
Notes: DEFINITION:#lt;br /#gt;#lt;/p#gt;#lt;p#gt;A coded value specifying whether a genetic variation is inheritable.#lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;EXAMPLE(S):#lt;br /#gt;#lt;/p#gt;#lt;p#gt;GERMLINE, SOMATIC #lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;OTHER NAME(S):#lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;NOTE(S):#lt;br /#gt;#lt;/p#gt;
Public BL
  derivedIndicator
Details:
Map:PGx v1.0=PF.PFDRVFL
Notes: DEFINITION:#lt;br /#gt;#lt;/p#gt;#lt;p#gt;Specifies whether a result represents a calculation performed on other results.#lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;EXAMPLE(S):#lt;br /#gt;#lt;/p#gt;#lt;p#gt;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".#lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;OTHER NAME(S):#lt;br /#gt;#lt;/p#gt;#lt;p#gt;Derived Flag#lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;NOTE(S):#lt;br /#gt;#lt;/p#gt;
Element Source Role Target Role
SingleNucleotidePolymorphism
Class   		Name: referencingPerformedGeneticObservationResult
  		Name: referencedSingleNucleotidePolymorphism
 
Details:
DESCRIPTION:<br /></p><p>Each PerformedGeneticObservationResult might reference one SingleNucleotidePolymorphism.  Each SingleNucleotidePolymorphism might be referenced by one or more PerformedGeneticObservationResult.<br /></p><p><br /></p><p>DEFINITION:<br /></p><p>The link between the observed variation in test result and the documented variation in the dbSNP database as identified by an rs number.<br /></p><p><br /></p><p>EXAMPLE(S):<br /></p><p>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 /></p><p><br /></p><p>OTHER NAME(S):<br /></p><p><br /></p><p>NOTE(S):<br /></p>
GeneticReference
Class   		Name: referencingPerformedGeneticObservationResult
  		Name: referencedGeneticReference
 
Details:
DESCRIPTION:<br /></p><p>Each PerformedGeneticObservationResult might reference one GeneticReference.  Each GeneticReference always is referenced by one or more PerformedGeneticObservationResult.<br /></p><p><br /></p><p>DEFINITION:<br /></p><p><br /></p><p>EXAMPLE(S):<br /></p><p>"A" might be the reference if the test result is a Nucleotide.<br /></p><p>"Trp" might be the reference if the test result is an Amino Acid.<br /></p><p><br /></p><p>OTHER NAME(S):<br /></p><p><br /></p><p>NOTE(S):<br /></p>
Tag Value
Map:PGx v1.0 PF.PFGENTRG
Details:
 
Object Type Connection Direction Notes
«Comment_Requested» 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):