<?xml version="1.0" encoding="UTF-8"?>
<!-- edited with XMLSpy v2005 rel. 3 U (http://www.altova.com) by Amnon Shabo (HL7) -->
<!-- A GeneticVariation sample to demonstrate the results of a genetic testing for Warfarin Metabolism Panel (CYP2C9 and VKORC1).
-->
<GeneticLoci xsi:schemaLocation="urn:hl7-org:v3 ../../OutputFiles/Schemas/ClinicalGenomicsElements.xsd" xmlns="urn:hl7-org:v3" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" moodCode="EVN">
	<id extension="3991201"/>
	<code displayName="Warfarin Metabolism Panel"/>
	<text>
            *2/*3, CYP2C9
            Heterozygous, -1639G>A, VKORC1
            </text>
	<effectiveTime value="20051025"/>
	<reasonCode code="anticoagulation management"/>
	<!-- The N level of confidentiality means normal confidentiality and the R level means restricted access.-->
	<confidentialityCode code="N" codeSystem="2.16.840.1.113883.5.25"/>
	<!-- Overall result-->
	<interpretationCode code="Low-Metabolizer"/>
	<!-- The documentation association below illustrates the way to point to a human-readable report, for example, in the form of a HL7 CDA document. 
    Alternatively, it is possible to embed the report in the text attribute of the geneticDocument element.-->
	<documentation>
		<geneticDocument>
			<id root="2.16.840.1.113883.19.3.2409" extension="report123456"/>
			<!-- Amnon: the CDA spec lists the LOINC codes for document types but there is none for genetic reports. We need to submit a proposal 
                to add codes to LOINC and update the CDA spec respectively-->
			<code codeSystem="2.16.840.1.113883.6.1" codeSystemName="LOINC" displayName="Molecular Diagnostics Report"/>
			<title>Molecular Diagnostics Report - Warfarin Metabolism Panel (CYP2C9 and VKORC1)</title>
			<effectiveTime value="20060212"/>
		</geneticDocument>
	</documentation>
	<component1>
		<!-- first locus in the test results-->
		<geneticLocus moodCode="EVN">
			<effectiveTime value="20050901"/>
			<value code="CYP2C9" displayName="Cytochrome P450 2C9" codeSystemName="HUGO"/>
			<!-- first allele in locus-->
			<component1>
				<individualAllele moodCode="EVN">
					<value code="CYP2C9*2"/>
					<component3>
						<sequenceVariation moodCode="EVN">
							<!--  THE ACTUAL VARIANT VALUE -->
							<value xsi:type="ST">430C>T</value>
							<derivedFrom>
								<associatedProperty>
									<code code="47999-8" displayName="GENE_REGION" codeSystemName="LOINC"/>
									<value xsi:type="ST">10q24</value>
								</associatedProperty>
							</derivedFrom>
							<derivedFrom>
								<associatedProperty>
									<code displayName="VARIATION_LEVEL"/>
									<value xsi:type="CE" code="Intragenic"/>
								</associatedProperty>
							</derivedFrom>
							<derivedFrom>
								<associatedProperty>
									<code code="VARIANT_TYPE"/>
									<value xsi:type="CE" code="Substitution"/>
								</associatedProperty>
							</derivedFrom>
							<derivedFrom>
								<associatedProperty>
									<code code="48006-1" displayName="AMINO_ACID_CHANGE_TYPE" codeSystemName="LOINC"/>
									<value xsi:type="CE" code="Missense"/>
								</associatedProperty>
							</derivedFrom>
							<derivedFrom>
								<associatedProperty>
									<code code="AMINO_ACID_CHANGE"/>
									<value xsi:type="ST">R144C</value>
								</associatedProperty>
							</derivedFrom>
							<derivedFrom>
								<associatedProperty>
									<code code="VARIANT_REFERENCE"/>
									<value xsi:type="II" root="2.16.840.1.113883.19.3.2409" extension="34447"/>
								</associatedProperty>
							</derivedFrom>
							<!-- associated observation-->
							<derivedFrom>
								<associatedProperty>
									<code code="VARIANT_SOURCE"/>
									<value xsi:type="CE" code="Germline"/>
								</associatedProperty>
							</derivedFrom>
							<derivedFrom>
								<associatedProperty>
									<code code="SIGNIFICANCE"/>
									<value xsi:type="CE" code="Non-incidental"/>
								</associatedProperty>
							</derivedFrom>
						</sequenceVariation>
					</component3>
				</individualAllele>
			</component1>
		</geneticLocus>
	</component1>
	<component1>
		<geneticLocus moodCode="EVN">
			<effectiveTime value="20050901"/>
			<value code="CYP2C9" displayName="Cytochrome P450 2C9 " codeSystemName="HUGO"/>
			<!-- second allele in locus -->
			<component1>
				<individualAllele moodCode="EVN">
					<value code="CYP2C9*3"/>
					<component3>
						<sequenceVariation moodCode="EVN">
							<code code="DNA_CHANGE"/>
							<!--  THE  VARIANT VALUE -->
							<value xsi:type="ST">1075A>C</value>
							<derivedFrom>
								<associatedProperty>
									<code code="GENE.REGION"/>
									<value xsi:type="ST">10q24</value>
								</associatedProperty>
							</derivedFrom>
							<derivedFrom>
								<associatedProperty>
									<code code="VARIATION_LEVEL"/>
									<value xsi:type="CE" code="Intragenic"/>
								</associatedProperty>
							</derivedFrom>
							<derivedFrom>
								<associatedProperty>
									<code code="VARIANT_TYPE"/>
									<value xsi:type="CE" code="Substitution"/>
								</associatedProperty>
							</derivedFrom>
							<derivedFrom>
								<associatedProperty>
									<code code="AMINO_ACID_CHANGE_TYPE"/>
									<value xsi:type="CE" code="Missense"/>
								</associatedProperty>
							</derivedFrom>
							<derivedFrom>
								<associatedProperty>
									<code code="AMINO_ACID_CHANGE"/>
									<value xsi:type="ST">R1036C</value>
								</associatedProperty>
							</derivedFrom>
							<derivedFrom>
								<associatedProperty>
									<code code="VARIANT_REFERENCE"/>
									<value xsi:type="II" root="2.16.840.1.113883.19.3.2409" extension="6186423"/>
								</associatedProperty>
							</derivedFrom>
							<derivedFrom>
								<associatedProperty>
									<code code="VARIANT_SOURCE"/>
									<value xsi:type="CE" code="Germline"/>
								</associatedProperty>
							</derivedFrom>
							<derivedFrom>
								<associatedProperty>
									<code code="SIGNIFICANCE"/>
									<value xsi:type="CE" code="Non-incidental"/>
								</associatedProperty>
							</derivedFrom>
						</sequenceVariation>
					</component3>
				</individualAllele>
			</component1>
		</geneticLocus>
	</component1>
	<!-- the following allele has NOT been found. This is indicated by setting the negationInd to "true"
		Note that this allele can appear in a genetic test order with RQO mood (request) and the negationInd is defaulted to false-->
	<component1>
		<geneticLocus moodCode="EVN">
			<effectiveTime value="20050901"/>
			<value code="CYP2C9" displayName="Cytochrome P450 2C9" codeSystemName="HUGO"/>
			<component1>
				<individualAllele moodCode="EVN" negationInd="true">
					<value code="CYP2C9*4"/>
				</individualAllele>
			</component1>
		</geneticLocus>
	</component1>
	<component1>
		<!-- second locus in the test results-->
		<geneticLocus moodCode="EVN">
			<effectiveTime value="20050901"/>
			<value code="VKORC1" displayName="VITAMIN K EPOXIDE REDUCTASE COMPLEX, SUBUNIT 1" codeSystemName="HUGO"/>
			<component3>
				<sequenceVariation moodCode="EVN">
					<code code="DNA_CHANGE"/>
					<!--  THE  VARIANT VALUE -->
					<value xsi:type="ST">1639G>A</value>
					<derivedFrom>
						<associatedProperty>
							<code code="VARIATION_LEVEL"/>
							<value xsi:type="CE" code="Intron"/>
						</associatedProperty>
					</derivedFrom>
					<derivedFrom>
						<associatedProperty>
							<code code="VARIANT_TYPE"/>
							<value xsi:type="CE" code="Substitution"/>
						</associatedProperty>
					</derivedFrom>
					<derivedFrom>
						<associatedProperty>
							<code code="VARIANT_REFERENCE"/>
							<value xsi:type="II" root="2.16.840.1.113883.19.3.2409" extension="34447"/>
						</associatedProperty>
					</derivedFrom>
					<derivedFrom>
						<associatedProperty>
							<code code="VARIANT_SOURCE"/>
							<value xsi:type="CE" code="Germline"/>
						</associatedProperty>
					</derivedFrom>
					<component>
						<associatedObservation moodCode="EVN">
							<code code="ALLELE_STATE"/>
							<value xsi:type="CE" code="Heterozygous"/>
						</associatedObservation>
					</component>
					<component>
						<associatedObservation moodCode="EVN">
							<code code="SIGNIFICANCE"/>
							<value xsi:type="CE" code="Non-incidental"/>
						</associatedObservation>
					</component>
				</sequenceVariation>
			</component3>
		</geneticLocus>
	</component1>
	<!--  observations asscoaitedwith the GeneticLoci as a whole-->
	<component2>
		<associatedProperty moodCode="DEF">
			<code code="test context"/>
			<value xsi:type="CE" code="Diagnostic"/>
		</associatedProperty>
	</component2>
	<component2>
		<associatedProperty moodCode="DEF">
			<code code="test context"/>
			<value xsi:type="CE" code="germline"/>
		</associatedProperty>
	</component2>
</GeneticLoci>

