GenomeX Data Exchange FHIR IG
0.2.0 - draft
GenomeX Data Exchange FHIR IG, published by MITRE. This guide is not an authorized publication; it is the continuous build for version 0.2.0 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/CodeX-HL7-FHIR-Accelerator/GenomeX-DataExchange/ and changes regularly. See the Directory of published versions
{
"resourceType" : "Procedure",
"id" : "HereditaryCancerTestingGenomicStudy",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study"
]
},
"text" : {
"status" : "extensions",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: Procedure HereditaryCancerTestingGenomicStudy</b></p><a name=\"HereditaryCancerTestingGenomicStudy\"> </a><a name=\"hcHereditaryCancerTestingGenomicStudy\"> </a><a name=\"HereditaryCancerTestingGenomicStudy-en-US\"> </a><p><b>Genomic Study Analysis Extension</b>: <a href=\"Procedure-HereditaryCancerTestingGenomicStudyAnalysis.html\">Procedure: extension = ,Sequence analysis of the entire coding region,GRCh38,->Specimen: identifier = http://www.somesystemabc.net/identifiers/specimens#07007253-BLD; status = available; type = Blood specimen (specimen); receivedTime = 2023-07-06 17:06:06+0500,->Jenny M (official) Female, DoB: 1988-02-12 ( Patient ID: 7fb905f171204b94b8ee33d33cb624e6\u00a0(use:\u00a0official,\u00a0)),; status = completed; category = Laboratory; performed[x] = 2023-02-02 01:01:10-0600; note = Genes Analyzed: Sequencing (seq) and large rearrangement analyses were performed for all coding exons in the following genes, unless otherwise indicated: APC, ATM, AXIN2, BAP1, BARD1, BMPR1A, BRCA1, BRCA2, BRIP1, CDH1, CDK4, CDKN2A, CHEK2, CTNNA1, FH, FLCN, HOXB13 (seq only), MEN1, MET, MLH1, MSH2, MSH3 (excluding repetitive portions of exon 1), MSH6, MMAYH, NTHL1, PALB2, PMS2, PTEN, RAD51C, RAD51D, SDHA, SDHB, SDHC, SDHD, SMAD4, STK11, TP53, TSC1, TSC2, VHL. Limited promoter regions may also be analyzed for large rearrangements.,Sequencing (seq) and/or large rearrangement (LR) analyses were performed only for the gene portions indicated in parenthesis for the following genes: EGFR (exons 18-21, seq and LR), EPCAM (exons 8-9, LR only), GREM1 (exon 1 and upstream regulatory regions, LR only), MITF (c.952, seq only), POLE (exonuclease domain, seq only), POLD1 (exonuclease domain, seq only), RET (exons 5, 8, 10, 11, 13-16 seq and LR), TERT (promoter c.DNA -1 to -70, seq only). Other genes not analyzed with this test may also be associated with cancer.,Indication for Testing: It is our understanding that this individual was identified for testing due to a personal or family history suggestive of a hereditary predisposition for cancer.,Associated Cancer Risks and Clinical Management: The "HereditaryCancerTesting Management Tool" associated with this report provides a summary of cancer risk and professional society medical management guidelines that may be useful in developing a plan for this patient based on any clinically significant test results and/or reported personal/family history. In some cases, a HereditaryCancerTesting Management Tool cannot be provided, such as when the result has a special interpretation or includes a mutation with unusual characteristics.,Analysis Description: The Technical Specifications summary (myriad.com/technical-specifications) describes the analysis, method, performance, nomenclature, and interpretive criteria of this test. Current testing technologies are unable to definitively determine whether a variant is germline or somatic in origin, which may significantly impact risk estimates and medical management; therefore, these results should be correlated with this patient's personal and family history. The interpretation of this test may also be impacted if the patient has a hematologic malignancy or an allogeneic bone marrow transplant.</a></p><p><b>status</b>: Completed</p><p><b>category</b>: <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span></p><p><b>code</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-type-cs struc-var}\">HereditaryCancerTesting™ Hereditary Cancer Test</span></p><p><b>subject</b>: <a href=\"Patient-PatientFemale.html\">Jenny M (official) Female, DoB: 1988-02-12 ( Patient ID: 7fb905f171204b94b8ee33d33cb624e6\u00a0(use:\u00a0official,\u00a0))</a></p><p><b>performed</b>: 2023-02-02</p><p><b>reasonCode</b>: <span title=\"Codes:{http://snomed.info/sct 718220008}\">Hereditary breast and ovarian cancer syndrome (disorder)</span></p><p><b>note</b>: Details About Non-Clinically Significant Variants: All individuals carry DNA changes (i.e., variants), and most variants do not increase an individual's risk of cancer or other diseases. When identified, variants of uncertain significance (VUS) are reported. Likely benign variants (Favor Polymorphisms) and benign variants (Polymorphisms) are not reported and available data indicate that these variants most likely do not cause increased cancer risk. Present evidence does not suggest that non-clinically significant variant findings be used to modify patient medical management beyond what is indicated by the personal and family history and any other clinically significant findings., Variant Classification: Organization's myVisionTM Variant Classification Program performs ongoing evaluations of variant classifications. In certain cases, healthcare providers may be contacted for more clinical information or to arrange family testing to aid in variant classification. When new evidence about a variant is identified and determined to result in clinical significance and management change, that information will automatically be made available to the healthcare provider through an amended report.</p></div>"
},
"extension" : [
{
"url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-ext",
"valueReference" : {
🔗 "reference" : "Procedure/HereditaryCancerTestingGenomicStudyAnalysis"
}
}
],
"status" : "completed",
"category" : {
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory",
"display" : "Laboratory"
}
]
},
"code" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-type-cs",
"code" : "struc-var",
"display" : "Structural variation detection"
}
],
"text" : "HereditaryCancerTesting™ Hereditary Cancer Test"
},
"subject" : {
🔗 "reference" : "Patient/PatientFemale"
},
"performedDateTime" : "2023-02-02",
"reasonCode" : [
{
"coding" : [
{
"system" : "http://snomed.info/sct",
"code" : "718220008",
"display" : "Hereditary breast and ovarian cancer syndrome (disorder)"
}
]
}
],
"note" : [
{
"text" : "Details About Non-Clinically Significant Variants: All individuals carry DNA changes (i.e., variants), and most variants do not increase an individual's risk of cancer or other diseases. When identified, variants of uncertain significance (VUS) are reported. Likely benign variants (Favor Polymorphisms) and benign variants (Polymorphisms) are not reported and available data indicate that these variants most likely do not cause increased cancer risk. Present evidence does not suggest that non-clinically significant variant findings be used to modify patient medical management beyond what is indicated by the personal and family history and any other clinically significant findings."
},
{
"text" : "Variant Classification: Organization's myVisionTM Variant Classification Program performs ongoing evaluations of variant classifications. In certain cases, healthcare providers may be contacted for more clinical information or to arrange family testing to aid in variant classification. When new evidence about a variant is identified and determined to result in clinical significance and management change, that information will automatically be made available to the healthcare provider through an amended report."
}
]
}