Genomics Reporting Implementation Guide
1.1.0 - Ballot

This page is part of the Genetic Reporting Implementation Guide (v1.1.0: STU 2 Ballot 1) based on FHIR R4. The current version which supercedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions

: Example - Full Bundle HLA genotyping for HLA-A, HLA-B, and HLA-C, using GLStrings - JSON Representation

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{
  "resourceType" : "Bundle",
  "id" : "CG-IG-HLA-FullBundle-01",
  "type" : "transaction",
  "entry" : [
    {
      "fullUrl" : "urn:uuid:13f34265-335c-4853-bc38-0815315edafa",
      "resource" : {
        "resourceType" : "Patient",
        "text" : {
          "status" : "generated",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">\n            <h4>Donor </h4>\n            <p>name: John Storm</p>\n            <p>gender: male</p>\n            <p>born: 1986-12-31</p>\n          </div>"
        },
        "identifier" : [
          {
            "use" : "usual",
            "type" : {
              "coding" : [
                {
                  "system" : "http://terminology.hl7.org/CodeSystem/v2-0203",
                  "code" : "DR"
                }
              ]
            },
            "system" : "urn:oid:0.0.0.0.0.0.0",
            "value" : "12345",
            "period" : {
              "start" : "2012-11-10"
            },
            "assigner" : {
              "display" : "aDonorRegistry"
            }
          }
        ],
        "name" : [
          {
            "use" : "official",
            "text" : "John Storm",
            "family" : "Storm",
            "given" : [
              "John"
            ]
          },
          {
            "use" : "nickname",
            "text" : "Johnny Storm",
            "family" : "Storm",
            "given" : [
              "Johnny"
            ]
          },
          {
            "use" : "nickname",
            "text" : "The Human Torch"
          }
        ],
        "gender" : "male",
        "birthDate" : "1986-12-31"
      },
      "request" : {
        "method" : "POST",
        "url" : "Patient"
      }
    },
    {
      "fullUrl" : "urn:uuid:e44fbe33-6084-4ae2-a95e-8bc451c63340",
      "resource" : {
        "resourceType" : "Specimen",
        "meta" : {
          "profile" : [
            "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/specimen"
          ]
        },
        "text" : {
          "status" : "generated",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">\n            <pre>a buccal swab</pre>\n          </div>"
        },
        "identifier" : [
          {
            "system" : "http://myorgsurl.com",
            "value" : "123"
          }
        ],
        "accessionIdentifier" : {
          "system" : "http://mylabsurl.com",
          "value" : "456"
        },
        "type" : {
          "coding" : [
            {
              "system" : "http://snomed.info/sct",
              "code" : "122555007",
              "display" : "Venous blood specimen"
            }
          ]
        },
        "subject" : {
          "reference" : "urn:uuid:13f34265-335c-4853-bc38-0815315edafa",
          "type" : "Patient",
          "display" : "John Storm"
        }
      },
      "request" : {
        "method" : "POST",
        "url" : "Specimen"
      }
    },
    {
      "fullUrl" : "urn:uuid:9243cc20-27bd-4f87-ba90-0328ed474950",
      "resource" : {
        "resourceType" : "Organization",
        "text" : {
          "status" : "generated",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">\n            <pre>aTypingLab, Inc</pre>\n          </div>"
        },
        "name" : "aTypingLab Inc",
        "alias" : [
          "aTL"
        ],
        "telecom" : [
          {
            "system" : "phone",
            "value" : "1-800-555-1234",
            "use" : "work",
            "rank" : 1
          }
        ],
        "address" : [
          {
            "use" : "work",
            "type" : "both",
            "text" : "123 Main St, Sometown, ND 99999",
            "line" : [
              "123 Main St"
            ],
            "city" : "Sometown",
            "state" : "ND",
            "postalCode" : "99999",
            "country" : "USA"
          }
        ]
      },
      "request" : {
        "method" : "POST",
        "url" : "Organization"
      }
    },
    {
      "fullUrl" : "urn:uuid:00ef18ad-ed04-4b2c-81ee-b69bb243f0d5",
      "resource" : {
        "resourceType" : "Organization",
        "text" : {
          "status" : "generated",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">\n            <pre>aDonorRegistry</pre>\n          </div>"
        },
        "name" : "aDonorRegistry",
        "alias" : [
          "ADR"
        ],
        "telecom" : [
          {
            "system" : "phone",
            "value" : "1-800-555-6789",
            "use" : "work",
            "rank" : 1
          }
        ],
        "address" : [
          {
            "use" : "work",
            "type" : "both",
            "text" : "456 Main St, Anytown ND, 00000",
            "line" : [
              "456 Main St"
            ],
            "city" : "Anytown",
            "state" : "ND",
            "postalCode" : "00000",
            "country" : "USA"
          }
        ]
      },
      "request" : {
        "method" : "POST",
        "url" : "Organization"
      }
    },
    {
      "fullUrl" : "urn:uuid:99309303-045e-4cf4-90d7-250d7a7476ea",
      "resource" : {
        "resourceType" : "ServiceRequest",
        "meta" : {
          "profile" : [
            "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/servicerequest"
          ]
        },
        "text" : {
          "status" : "generated",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">\n            <pre>HLA typing request for John Storm</pre>\n          </div>"
        },
        "status" : "completed",
        "intent" : "order",
        "code" : {
          "coding" : [
            {
              "system" : "http://loinc.org",
              "code" : "13303-3",
              "display" : "HLA-A+B+C (class I) [Type]"
            }
          ]
        },
        "subject" : {
          "reference" : "urn:uuid:13f34265-335c-4853-bc38-0815315edafa",
          "type" : "Patient",
          "display" : "John Storm"
        },
        "authoredOn" : "2016-11-15",
        "requester" : {
          "reference" : "urn:uuid:00ef18ad-ed04-4b2c-81ee-b69bb243f0d5",
          "type" : "Organization",
          "display" : "aDonorRegistry"
        },
        "performer" : [
          {
            "reference" : "urn:uuid:9243cc20-27bd-4f87-ba90-0328ed474950",
            "type" : "Organization",
            "display" : "aTypingLab, Inc"
          }
        ],
        "reasonCode" : [
          {
            "text" : "tissue typing for donor registry"
          }
        ]
      },
      "request" : {
        "method" : "POST",
        "url" : "ServiceRequest"
      }
    },
    {
      "fullUrl" : "urn:uuid:8200dab6-18a2-4550-b913-a7db480c0804",
      "resource" : {
        "resourceType" : "MolecularSequence",
        "text" : {
          "status" : "generated",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">\n            <pre>&quot;HLA-A*01:01:01:01, exon 2&quot;</pre>\n          </div>"
        },
        "type" : "dna",
        "coordinateSystem" : 0,
        "referenceSeq" : {
          "referenceSeqId" : {
            "coding" : [
              {
                "system" : "http://www.ebi.ac.uk/ipd/imgt/hla",
                "version" : "3.23",
                "code" : "HLA00001"
              }
            ],
            "text" : "HLA-A*01:01:01:01"
          },
          "windowStart" : 503,
          "windowEnd" : 773
        },
        "observedSeq" : "GCTCCCACTCCATGAGGTATTTCTTCACATCCGTGTCCCGGCCCGGCCGCGGGGAGCCCCGCTTCATCGCCGTGGGCTACGTGGACGACACGCAGTTCGTGCGGTTCGACAGCGACGCCGCGAGCCAGAAGATGGAGCCGCGGGCGCCGTGGATAGAGCAGGAGGGGCCGGAGTATTGGGACCAGGAGACACGGAATATGAAGGCCCACTCACAGACTGACCGAGCGAACCTGGGGACCCTGCGCGGCTACTACAACCAGAGCGAGGACG"
      },
      "request" : {
        "method" : "POST",
        "url" : "MolecularSequence"
      }
    },
    {
      "fullUrl" : "urn:uuid:7c393185-f15c-45bc-a714-c0fdbea32675",
      "resource" : {
        "resourceType" : "MolecularSequence",
        "text" : {
          "status" : "generated",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">\n            <pre>&quot;HLA-A*01:01:01:01, exon 3&quot;</pre>\n          </div>"
        },
        "type" : "dna",
        "coordinateSystem" : 0,
        "referenceSeq" : {
          "referenceSeqId" : {
            "coding" : [
              {
                "system" : "http://www.ebi.ac.uk/ipd/imgt/hla",
                "version" : "3.23",
                "code" : "HLA00001"
              }
            ],
            "text" : "HLA-A*01:01:01:01"
          },
          "windowStart" : 1014,
          "windowEnd" : 1290
        },
        "observedSeq" : "GTTCTCACACCATCCAGATAATGTATGGCTGCGACGTGGGGCCGGACGGGCGCTTCCTCCGCGGGTACCGGCAGGACGCCTACGACGGCAAGGATTACATCGCCCTGAACGAGGACCTGCGCTCTTGGACCGCGGCGGACATGGCAGCTCAGATCACCAAGCGCAAGTGGGAGGCGGTCCATGCGGCGGAGCAGCGGAGAGTCTACCTGGAGGGCCGGTGCGTGGACGGGCTCCGCAGATACCTGGAGAACGGGAAGGAGACGCTGCAGCGCACGG"
      },
      "request" : {
        "method" : "POST",
        "url" : "MolecularSequence"
      }
    },
    {
      "fullUrl" : "urn:uuid:65c85f14-c3a0-4b72-818f-820e04fcc621",
      "resource" : {
        "resourceType" : "MolecularSequence",
        "text" : {
          "status" : "generated",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">\n            <pre>&quot;HLA-A*01:02, exon 2&quot;</pre>\n          </div>"
        },
        "type" : "dna",
        "coordinateSystem" : 0,
        "referenceSeq" : {
          "referenceSeqId" : {
            "coding" : [
              {
                "system" : "http://www.ebi.ac.uk/ipd/imgt/hla",
                "version" : "3.23",
                "code" : "HLA00002"
              }
            ],
            "text" : "HLA-A*01:02"
          },
          "windowStart" : 503,
          "windowEnd" : 773
        },
        "observedSeq" : "GCTCCCACTCCATGAGGTATTTCTCCACATCCGTGTCCCGGCCCGGCAGTGGAGAGCCCCGCTTCATCGCAGTGGGCTACGTGGACGACACGCAGTTCGTGCGGTTCGACAGCGACGCCGCGAGCCAGAAGATGGAGCCGCGGGCGCCGTGGATAGAGCAGGAGGGGCCGGAGTATTGGGACCAGGAGACACGGAATATGAAGGCCCACTCACAGACTGACCGAGCGAACCTGGGGACCCTGCGCGGCTACTACAACCAGAGCGAGGACG"
      },
      "request" : {
        "method" : "POST",
        "url" : "MolecularSequence"
      }
    },
    {
      "fullUrl" : "urn:uuid:fbba9fe7-0ece-4ec1-9233-a437a8d242a0",
      "resource" : {
        "resourceType" : "MolecularSequence",
        "text" : {
          "status" : "generated",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">\n            <pre>&quot;HLA-A*01:02, exon 3&quot;</pre>\n          </div>"
        },
        "type" : "dna",
        "coordinateSystem" : 0,
        "referenceSeq" : {
          "referenceSeqId" : {
            "coding" : [
              {
                "system" : "http://www.ebi.ac.uk/ipd/imgt/hla",
                "version" : "3.23",
                "code" : "HLA00002"
              }
            ],
            "text" : "HLA-A*01:02"
          },
          "windowStart" : 1014,
          "windowEnd" : 1290
        },
        "observedSeq" : "GTTCTCACACCATCCAGATAATGTATGGCTGCGACGTGGGGCCGGACGGGCGCTTCCTCCGCGGGTACCGGCAGGACGCCTACGACGGCAAGGATTACATCGCCCTGAACGAGGACCTGCGCTCTTGGACCGCGGCGGACATGGCAGCTCAGATCACCAAGCGCAAGTGGGAGGCGGTCCATGCGGCGGAGCAGCGGAGAGTCTACCTGGAGGGCCGGTGCGTGGACGGGCTCCGCAGATACCTGGAGAACGGGAAGGAGACGCTGCAGCGCACGG"
      },
      "request" : {
        "method" : "POST",
        "url" : "MolecularSequence"
      }
    },
    {
      "fullUrl" : "urn:uuid:b7765bbf-df40-486a-9f2f-404309643de6",
      "resource" : {
        "resourceType" : "Observation",
        "meta" : {
          "profile" : [
            "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype"
          ]
        },
        "text" : {
          "status" : "generated",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">\n            <pre>HLA-A:01:01:01G</pre>\n          </div>"
        },
        "status" : "final",
        "category" : [
          {
            "coding" : [
              {
                "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
                "code" : "laboratory"
              }
            ]
          }
        ],
        "code" : {
          "coding" : [
            {
              "system" : "http://loinc.org",
              "code" : "84414-2",
              "display" : "Haplotype name"
            }
          ]
        },
        "subject" : {
          "reference" : "urn:uuid:13f34265-335c-4853-bc38-0815315edafa",
          "type" : "Patient",
          "display" : "John Storm"
        },
        "effectiveDateTime" : "2016-12-15",
        "valueCodeableConcept" : {
          "coding" : [
            {
              "system" : "http://www.ebi.ac.uk/ipd/imgt/hla",
              "version" : "3.23",
              "code" : "HLA-A*01:01:01G",
              "display" : "HLA-A*01:01:01G"
            }
          ]
        },
        "method" : {
          "coding" : [
            {
              "system" : "http://www.ncbi.nlm.nih.gov/gtr",
              "code" : "GTR000000000.0"
            }
          ],
          "text" : "NGS based Class I HLA-A, -B, -C genotyping"
        },
        "specimen" : {
          "reference" : "urn:uuid:e44fbe33-6084-4ae2-a95e-8bc451c63340",
          "display" : "buccal swab from John Storm"
        },
        "derivedFrom" : [
          {
            "reference" : "urn:uuid:8200dab6-18a2-4550-b913-a7db480c0804",
            "type" : "MolecularSequence",
            "display" : "HLA-A*01:01:01:01, exon 2"
          },
          {
            "reference" : "urn:uuid:7c393185-f15c-45bc-a714-c0fdbea32675",
            "type" : "MolecularSequence",
            "display" : "HLA-A*01:01:01:01, exon 3"
          }
        ],
        "component" : [
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "48018-6",
                  "display" : "Gene studied [ID]"
                }
              ]
            },
            "valueCodeableConcept" : {
              "coding" : [
                {
                  "system" : "http://www.genenames.org/geneId",
                  "code" : "HGNC:4931",
                  "display" : "HLA-A"
                }
              ]
            }
          }
        ]
      },
      "request" : {
        "method" : "POST",
        "url" : "Observation"
      }
    },
    {
      "fullUrl" : "urn:uuid:d98d92a7-0e86-4ae5-b036-b7e1bba6ec32",
      "resource" : {
        "resourceType" : "Observation",
        "meta" : {
          "profile" : [
            "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype"
          ]
        },
        "text" : {
          "status" : "generated",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">\n            <pre>HLA-A*01:02</pre>\n          </div>"
        },
        "status" : "final",
        "category" : [
          {
            "coding" : [
              {
                "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
                "code" : "laboratory"
              }
            ]
          }
        ],
        "code" : {
          "coding" : [
            {
              "system" : "http://loinc.org",
              "code" : "84414-2",
              "display" : "Haplotype name"
            }
          ]
        },
        "subject" : {
          "reference" : "urn:uuid:13f34265-335c-4853-bc38-0815315edafa",
          "type" : "Patient",
          "display" : "John Storm"
        },
        "effectiveDateTime" : "2016-12-15",
        "valueCodeableConcept" : {
          "coding" : [
            {
              "system" : "http://www.ebi.ac.uk/ipd/imgt/hla",
              "version" : "3.23",
              "code" : "HLA-A*01:02",
              "display" : "HLA-A*01:02"
            }
          ]
        },
        "method" : {
          "coding" : [
            {
              "system" : "http://www.ncbi.nlm.nih.gov/gtr",
              "code" : "GTR000000000.0"
            }
          ],
          "text" : "NGS based Class I HLA-A, -B, -C genotyping"
        },
        "specimen" : {
          "reference" : "urn:uuid:e44fbe33-6084-4ae2-a95e-8bc451c63340",
          "display" : "buccal swab from John Storm"
        },
        "derivedFrom" : [
          {
            "reference" : "urn:uuid:65c85f14-c3a0-4b72-818f-820e04fcc621",
            "type" : "MolecularSequence",
            "display" : "HLA-A*01:02, exon 2"
          },
          {
            "reference" : "urn:uuid:fbba9fe7-0ece-4ec1-9233-a437a8d242a0",
            "type" : "MolecularSequence",
            "display" : "HLA-A*01:02, exon 3"
          }
        ],
        "component" : [
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "48018-6",
                  "display" : "Gene studied [ID]"
                }
              ]
            },
            "valueCodeableConcept" : {
              "coding" : [
                {
                  "system" : "http://www.genenames.org/geneId",
                  "code" : "HGNC:4931",
                  "display" : "HLA-A"
                }
              ]
            }
          }
        ]
      },
      "request" : {
        "method" : "POST",
        "url" : "Observation"
      }
    },
    {
      "fullUrl" : "urn:uuid:49a86246-4004-42eb-9bdc-f542f93f9228",
      "resource" : {
        "resourceType" : "Observation",
        "meta" : {
          "profile" : [
            "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype"
          ]
        },
        "text" : {
          "status" : "generated",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">\n            <pre>HLA-A:01:01G+HLA-A*01:02</pre>\n          </div>"
        },
        "basedOn" : [
          {
            "reference" : "urn:uuid:99309303-045e-4cf4-90d7-250d7a7476ea",
            "type" : "ServiceRequest",
            "display" : "Class I HLA genotyping for John Storm"
          }
        ],
        "status" : "final",
        "category" : [
          {
            "coding" : [
              {
                "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
                "code" : "laboratory"
              }
            ]
          }
        ],
        "code" : {
          "coding" : [
            {
              "system" : "http://loinc.org",
              "code" : "84413-4",
              "display" : "Genotype display name"
            }
          ]
        },
        "subject" : {
          "reference" : "urn:uuid:13f34265-335c-4853-bc38-0815315edafa",
          "type" : "Patient",
          "display" : "John Storm"
        },
        "effectiveDateTime" : "2016-12-15",
        "valueCodeableConcept" : {
          "coding" : [
            {
              "system" : "http://glstring.org",
              "version" : "1.0",
              "code" : "hla#3.23.0#HLA-A:01:01G+HLA-A*01:02"
            }
          ]
        },
        "method" : {
          "coding" : [
            {
              "system" : "http://www.ncbi.nlm.nih.gov/gtr",
              "code" : "GTR000000000.0"
            }
          ],
          "text" : "NGS based Class I HLA-A, -B, -C genotyping"
        },
        "specimen" : {
          "reference" : "urn:uuid:e44fbe33-6084-4ae2-a95e-8bc451c63340",
          "display" : "buccal swab from John Storm"
        },
        "derivedFrom" : [
          {
            "reference" : "urn:uuid:b7765bbf-df40-486a-9f2f-404309643de6",
            "type" : "Observation",
            "display" : "HLA-A*01:01:01G, exons 2 and 3"
          },
          {
            "reference" : "urn:uuid:d98d92a7-0e86-4ae5-b036-b7e1bba6ec32",
            "type" : "Observation",
            "display" : "HLA-A*01:02, exons 2 and 3"
          }
        ],
        "component" : [
          {
            "code" : {
              "coding" : [
                {
                  "system" : "http://loinc.org",
                  "code" : "48018-6",
                  "display" : "Gene studied [ID]"
                }
              ]
            },
            "valueCodeableConcept" : {
              "coding" : [
                {
                  "system" : "http://www.genenames.org/geneId",
                  "code" : "HGNC:4931",
                  "display" : "HLA-A"
                }
              ]
            }
          }
        ]
      },
      "request" : {
        "method" : "POST",
        "url" : "Observation"
      }
    },
    {
      "fullUrl" : "urn:uuid:cbabf93e-1b4b-46f2-ba1e-d84862670670",
      "resource" : {
        "resourceType" : "MolecularSequence",
        "text" : {
          "status" : "generated",
          "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">\n            <pre>&quot;HLA-B*15:01:01:01, exon 2&quot;</pre>\n          </div>"
        },
        "type" : "dna",
        "coordinateSystem" : 0,
        "referenceSeq" : {
          "referenceSeqId" : {
            "coding" : [
              {
                "system" : "http://www.ebi.ac.uk/ipd/imgt/hla",
                "version" : "3.23",
                "code" : "HLA00162"
              }
            ],
            "text" : "HLA-B*15:01:01:01"
          },
          "windowStart" : 486,
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