Generated Narrative: Organization Inline-Instance-for-oncology-report-example-1 identifier: http://example.org/genomics/NamingSystem/organization/CEGAT name: CEGAT
Generated Narrative: Patient Inline-Instance-for-oncology-report-example-2 Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111)
Generated Narrative: Specimen Inline-Instance-for-oncology-report-example-3 identifier: http://example.org/genomics/NamingSystem/cegat/tissueID/UNKNOWN type: Tumor subject: Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111) Collections - Method BodySite * Biopsy Malignant neoplasm of cardia
Generated Narrative: Observation Inline-Instance-for-oncology-report-example-4 Profile: Variant status: Final category: Laboratory, Genetics code: Genetic variant assessment subject: Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111) effective: 2023-03-05 performer: Organization CEGAT value: Present method: Sequencing specimen: Identifier: http://example.org/genomics/NamingSystem/cegat/tissueID/UNKNOWN component code: Genomic source class value: Somatic component code: Gene studied [ID] value: PIK3CA component code: Human reference sequence assembly version value: GRCh37 component code: DNA change (c.HGVS) value: G}">NM_006218.4:c.3140A>G component code: DNA change type value: substitution component code: Amino acid change (pHGVS) value: NP_006209.2:p.His1047Arg component code: Transcript reference sequence [ID] value: NM_006218.4 component code: Genomic ref allele [ID] value: A component code: Sample VAF value: 0.2188 relative frequency of a particular allele in the specimen (Details: UCUM code1 = '1') component code: Allelic read depth value: 64 reads per base pair (Details: UCUM code1 = '1')
Human reference sequence assembly version
relative frequency of a particular allele in the specimen
Generated Narrative: Observation Inline-Instance-for-oncology-report-example-5 Profile: Variant status: Final category: Laboratory, Genetics code: Genetic variant assessment subject: Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111) effective: 2023-03-05 performer: Organization CEGAT value: Present method: Sequencing specimen: Identifier: http://example.org/genomics/NamingSystem/cegat/tissueID/UNKNOWN component code: Genomic source class value: Somatic component code: Gene studied [ID] value: NRAS component code: Human reference sequence assembly version value: GRCh37 component code: DNA change (c.HGVS) value: T}">NM_002524.4:c.34G>T component code: DNA change type value: substitution component code: Transcript reference sequence [ID] value: NM_002524.4 component code: Genomic ref allele [ID] value: C component code: Sample VAF value: 0.1793 relative frequency of a particular allele in the specimen (Details: UCUM code1 = '1') component code: Allelic read depth value: 145 reads per base pair (Details: UCUM code1 = '1')
Generated Narrative: Observation Inline-Instance-for-oncology-report-example-6 Profile: Variant status: Final category: Laboratory, Genetics code: Genetic variant assessment subject: Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111) effective: 2023-03-05 performer: Organization CEGAT value: Present method: Sequencing specimen: Identifier: http://example.org/genomics/NamingSystem/cegat/tissueID/UNKNOWN component code: Genomic source class value: Somatic component code: Gene studied [ID] value: FBXW7 component code: Human reference sequence assembly version value: GRCh37 component code: DNA change (c.HGVS) value: A}">NM_001349798.2:c.1394G>A component code: DNA change type value: substitution component code: Amino acid change (pHGVS) value: NP_001336727.1:p.Arg465His component code: Transcript reference sequence [ID] value: NM_001349798.2 component code: Genomic ref allele [ID] value: C component code: Sample VAF value: 0.1053 relative frequency of a particular allele in the specimen (Details: UCUM code1 = '1') component code: Allelic read depth value: 57 reads per base pair (Details: UCUM code1 = '1')
Generated Narrative: Observation Inline-Instance-for-oncology-report-example-7 Profile: Variant status: Final category: Laboratory, Genetics code: Genetic variant assessment subject: Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111) effective: 2023-03-05 performer: Organization CEGAT value: Present method: Sequencing specimen: Identifier: http://example.org/genomics/NamingSystem/cegat/tissueID/UNKNOWN component code: Genomic source class value: Somatic component code: Gene studied [ID] value: KMT2D component code: Human reference sequence assembly version value: GRCh37 component code: DNA change (c.HGVS) value: NM_003482.3:c.7900_7901delCA component code: DNA change type value: deletion component code: Transcript reference sequence [ID] value: NM_003482.3 component code: Genomic ref allele [ID] value: CTG component code: Sample VAF value: 0.188 relative frequency of a particular allele in the specimen (Details: UCUM code1 = '1') component code: Allelic read depth value: 117 reads per base pair (Details: UCUM code1 = '1')
Generated Narrative: Observation Inline-Instance-for-oncology-report-example-8 Profile: Variant status: Final category: Laboratory, Genetics code: Genetic variant assessment subject: Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111) effective: 2023-03-05 performer: Organization CEGAT value: Present method: Sequencing specimen: Identifier: http://example.org/genomics/NamingSystem/cegat/tissueID/UNKNOWN component code: Genomic source class value: Somatic component code: Gene studied [ID] value: PIK3CA component code: Human reference sequence assembly version value: GRCh37 component code: DNA change (c.HGVS) value: T}">NM_006218.3:c.333G>T component code: DNA change type value: substitution component code: Transcript reference sequence [ID] value: NM_006218.3 component code: Genomic ref allele [ID] value: G component code: Sample VAF value: 0.1471 relative frequency of a particular allele in the specimen (Details: UCUM code1 = '1') component code: Allelic read depth value: 68 reads per base pair (Details: UCUM code1 = '1')
Generated Narrative: Observation Inline-Instance-for-oncology-report-example-9 Profile: Variant status: Final category: Laboratory, Genetics code: Genetic variant assessment subject: Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111) effective: 2023-03-05 performer: Organization CEGAT value: Present method: Sequencing specimen: Identifier: http://example.org/genomics/NamingSystem/cegat/tissueID/UNKNOWN component code: Genomic source class value: Somatic component code: Gene studied [ID] value: IRS2 component code: Human reference sequence assembly version value: GRCh37 component code: DNA change (c.HGVS) value: T}">NM_003749.2:c.3960C>T component code: DNA change type value: substitution component code: Transcript reference sequence [ID] value: NM_003749.2 component code: Genomic ref allele [ID] value: G component code: Sample VAF value: 0.1343 relative frequency of a particular allele in the specimen (Details: UCUM code1 = '1') component code: Allelic read depth value: 134 reads per base pair (Details: UCUM code1 = '1')
Generated Narrative: Observation Inline-Instance-for-oncology-report-example-10 Profile: Variant status: Final category: Laboratory, Genetics code: Genetic variant assessment subject: Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111) effective: 2023-03-05 performer: Organization CEGAT value: Present method: Sequencing specimen: Identifier: http://example.org/genomics/NamingSystem/cegat/tissueID/UNKNOWN component code: Genomic source class value: Somatic component code: Gene studied [ID] value: CDKN2A component code: Human reference sequence assembly version value: GRCh37 component code: DNA change (c.HGVS) value: NM_000077.4:c.9_32del component code: DNA change type value: deletion component code: Amino acid change (pHGVS) value: NP_000068.1:p.Ala4_Pro11del component code: Transcript reference sequence [ID] value: NM_000077.4 component code: Genomic ref allele [ID] value: AGGCTCCATGCTGCTCCCCGCCGCC component code: Sample VAF value: 0.0536 relative frequency of a particular allele in the specimen (Details: UCUM code1 = '1') component code: Allelic read depth value: 112 reads per base pair (Details: UCUM code1 = '1')
Generated Narrative: Observation Inline-Instance-for-oncology-report-example-11 Profile: Variant status: Final category: Laboratory, Genetics code: Genetic variant assessment subject: Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111) effective: 2023-03-05 performer: Organization CEGAT value: Present method: Sequencing specimen: Identifier: http://example.org/genomics/NamingSystem/cegat/tissueID/UNKNOWN component code: Genomic source class value: Somatic component code: Gene studied [ID] value: RECQL4 component code: Human reference sequence assembly version value: GRCh37 component code: DNA change (c.HGVS) value: T}">NM_004260.4:c.2086C>T component code: DNA change type value: substitution component code: Amino acid change (pHGVS) value: NP_004251.4:p.Arg696Cys component code: Transcript reference sequence [ID] value: NM_004260.4 component code: Genomic ref allele [ID] value: G component code: Sample VAF value: 0.2568 relative frequency of a particular allele in the specimen (Details: UCUM code1 = '1') component code: Allelic read depth value: 148 reads per base pair (Details: UCUM code1 = '1')
Generated Narrative: Observation Inline-Instance-for-oncology-report-example-12 Profile: Variant status: Final category: Laboratory, Genetics code: Genetic variant assessment subject: Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111) effective: 2023-03-05 performer: Organization CEGAT value: Present method: Sequencing specimen: Identifier: http://example.org/genomics/NamingSystem/cegat/tissueID/UNKNOWN component code: Genomic source class value: Somatic component code: Gene studied [ID] value: RYR1 component code: Human reference sequence assembly version value: GRCh37 component code: DNA change (c.HGVS) value: A}">NM_000540.3:c.4964G>A component code: DNA change type value: substitution component code: Amino acid change (pHGVS) value: NP_000531.2:p.Arg1655Leu component code: Transcript reference sequence [ID] value: NM_000540.3 component code: Genomic ref allele [ID] value: G component code: Sample VAF value: 0.2151 relative frequency of a particular allele in the specimen (Details: UCUM code1 = '1') component code: Allelic read depth value: 93 reads per base pair (Details: UCUM code1 = '1')
Generated Narrative: Observation Inline-Instance-for-oncology-report-example-13 Profile: Variant status: Final category: Laboratory, Genetics code: Genetic variant assessment subject: Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111) effective: 2023-03-05 performer: Organization CEGAT value: Present method: Sequencing specimen: Identifier: http://example.org/genomics/NamingSystem/cegat/tissueID/UNKNOWN component code: Genomic source class value: Somatic component code: Gene studied [ID] value: SACS component code: Human reference sequence assembly version value: GRCh37 component code: DNA change (c.HGVS) value: A}">NM_014363.5:c.12118G>A component code: DNA change type value: substitution component code: Transcript reference sequence [ID] value: NM_014363.5 component code: Genomic ref allele [ID] value: C component code: Sample VAF value: 0.3333 relative frequency of a particular allele in the specimen (Details: UCUM code1 = '1') component code: Allelic read depth value: 60 reads per base pair (Details: UCUM code1 = '1')
Generated Narrative: Observation Inline-Instance-for-oncology-report-example-14 Profile: Variant status: Final category: Laboratory, Genetics code: Genetic variant assessment subject: Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111) effective: 2023-03-05 performer: Organization CEGAT value: Present method: Sequencing specimen: Identifier: http://example.org/genomics/NamingSystem/cegat/tissueID/UNKNOWN component code: Genomic source class value: Somatic component code: Gene studied [ID] value: SLIT2 component code: Human reference sequence assembly version value: GRCh37 component code: DNA change (c.HGVS) value: A}">NM_004787.3:c.1290C>A component code: DNA change type value: substitution component code: Transcript reference sequence [ID] value: NM_004787.3 component code: Genomic ref allele [ID] value: C component code: Sample VAF value: 0.2642 relative frequency of a particular allele in the specimen (Details: UCUM code1 = '1') component code: Allelic read depth value: 53 reads per base pair (Details: UCUM code1 = '1')
Generated Narrative: Observation Inline-Instance-for-oncology-report-example-15 Profile: Variant status: Final category: Laboratory, Genetics code: Genetic variant assessment subject: Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111) effective: 2023-03-05 performer: Organization CEGAT value: Present method: Sequencing specimen: Identifier: http://example.org/genomics/NamingSystem/cegat/tissueID/UNKNOWN component code: Genomic source class value: Somatic component code: Gene studied [ID] value: SMARCA4 component code: Human reference sequence assembly version value: GRCh37 component code: DNA change (c.HGVS) value: T}">NM_003072.5:c.2372C>T component code: DNA change type value: substitution component code: Amino acid change (pHGVS) value: NP_003063.2:p.Ala791Val component code: Transcript reference sequence [ID] value: NM_003072.5 component code: Genomic ref allele [ID] value: C component code: Sample VAF value: 0.1938 relative frequency of a particular allele in the specimen (Details: UCUM code1 = '1') component code: Allelic read depth value: 160 reads per base pair (Details: UCUM code1 = '1')
Generated Narrative: DiagnosticReport Inline-Instance-for-oncology-report-example-16 Profile: Genomic Report Genetic analysis report (Genetics) Subject Anonymous Patient (no stated gender), DoB Unknown ( http://example.org/genomics/NamingSystem/cegat/patID#11111) Reported 2019-09-15 11:35:05-0400 Performer Organization CEGAT Identifier http://example.org/genomics/NamingSystem/cegat/reportID/42867 Report Details Code Value Flags When For Genetic variant assessment Present Final 2023-03-05 Genetic variant assessment Present Final 2023-03-05 Genetic variant assessment Present Final 2023-03-05 Genetic variant assessment Present Final 2023-03-05 Genetic variant assessment Present Final 2023-03-05 Genetic variant assessment Present Final 2023-03-05 Genetic variant assessment Present Final 2023-03-05 Genetic variant assessment Present Final 2023-03-05 Genetic variant assessment Present Final 2023-03-05 Genetic variant assessment Present Final 2023-03-05 Genetic variant assessment Present Final 2023-03-05 Genetic variant assessment Present Final 2023-03-05