Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 4.0.0-cibuild built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions

## Example Bundle: bundle-CG-IG-HLA-FullBundle-01

Bundle bundle-CG-IG-HLA-FullBundle-01 of type transaction

Entry 1 - fullUrl = urn:uuid:13f34265-335c-4853-bc38-0815315edafa

Resource Patient:

> Generated Narrative: Patient CG-IG-HLA-FullBundle-01-1

> John Storm(official) Male, DoB: 1986-12-31 ( Donor Registration Number (use: usual, period: 2012-11-10 --> (ongoing)))

Request:

    POST Patient

Entry 2 - fullUrl = urn:uuid:e44fbe33-6084-4ae2-a95e-8bc451c63340

Resource Specimen:

> Generated Narrative: Specimen CG-IG-HLA-FullBundle-01-2

> identifier: `http://example.org`/123

> accessionIdentifier: `http://example.org`/456

> type: Venous blood specimen

> subject: John Storm

Request:

    POST Specimen

Entry 3 - fullUrl = urn:uuid:9243cc20-27bd-4f87-ba90-0328ed474950

Resource Organization:

> Generated Narrative: Organization CG-IG-HLA-FullBundle-01-3

> name: aTypingLab Inc

> alias: aTL

> telecom: ph: 1-800-555-1234(Work)

> address: 123 Main St, Sometown, ND 99999(work)

Request:

    POST Organization

Entry 4 - fullUrl = urn:uuid:00ef18ad-ed04-4b2c-81ee-b69bb243f0d5

Resource Organization:

> Generated Narrative: Organization CG-IG-HLA-FullBundle-01-4

> name: aDonorRegistry

> alias: ADR

> telecom: ph: 1-800-555-6789(Work)

> address: 456 Main St, Anytown ND, 00000(work)

Request:

    POST Organization

Entry 5 - fullUrl = urn:uuid:99309303-045e-4cf4-90d7-250d7a7476ea

Resource ServiceRequest:

> Generated Narrative: ServiceRequest CG-IG-HLA-FullBundle-01-5

> status: Completed

> intent: Order

> code: HLA-A+B+C (class I) [Type]

> subject: John Storm

> authoredOn: 2016-11-15

> requester: aDonorRegistry

> performer: aTypingLab, Inc

> reasonCode: tissue typing for donor registry

Request:

    POST ServiceRequest

Entry 6 - fullUrl = urn:uuid:8200dab6-18a2-4550-b913-a7db480c0804

Resource MolecularSequence:

> Generated Narrative: MolecularSequence CG-IG-HLA-FullBundle-01-6

> type: DNA Sequence

> coordinateSystem: 0

> ### ReferenceSeqs

> - | ReferenceSeqId | WindowStart | WindowEnd
> * | HLA-A*01:01:01:01 | 503 | 773

> observedSeq: GCTCCCACTCCATGAGGTATTTCTTCACATCCGTGTCCCGGCCCGGCCGCGGGGAGCCCCGCTTCATCGCCGTGGGCTACGTGGACGACACGCAGTTCGTGCGGTTCGACAGCGACGCCGCGAGCCAGAAGATGGAGCCGCGGGCGCCGTGGATAGAGCAGGAGGGGCCGGAGTATTGGGACCAGGAGACACGGAATATGAAGGCCCACTCACAGACTGACCGAGCGAACCTGGGGACCCTGCGCGGCTACTACAACCAGAGCGAGGACG

Request:

    POST MolecularSequence

Entry 7 - fullUrl = urn:uuid:7c393185-f15c-45bc-a714-c0fdbea32675

Resource MolecularSequence:

> Generated Narrative: MolecularSequence CG-IG-HLA-FullBundle-01-7

> type: DNA Sequence

> coordinateSystem: 0

> ### ReferenceSeqs

> - | ReferenceSeqId | WindowStart | WindowEnd
> * | HLA-A*01:01:01:01 | 1014 | 1290

> observedSeq: GTTCTCACACCATCCAGATAATGTATGGCTGCGACGTGGGGCCGGACGGGCGCTTCCTCCGCGGGTACCGGCAGGACGCCTACGACGGCAAGGATTACATCGCCCTGAACGAGGACCTGCGCTCTTGGACCGCGGCGGACATGGCAGCTCAGATCACCAAGCGCAAGTGGGAGGCGGTCCATGCGGCGGAGCAGCGGAGAGTCTACCTGGAGGGCCGGTGCGTGGACGGGCTCCGCAGATACCTGGAGAACGGGAAGGAGACGCTGCAGCGCACGG

Request:

    POST MolecularSequence

Entry 8 - fullUrl = urn:uuid:65c85f14-c3a0-4b72-818f-820e04fcc621

Resource MolecularSequence:

> Generated Narrative: MolecularSequence CG-IG-HLA-FullBundle-01-8

> type: DNA Sequence

> coordinateSystem: 0

> ### ReferenceSeqs

> - | ReferenceSeqId | WindowStart | WindowEnd
> * | HLA-A*01:02 | 503 | 773

> observedSeq: GCTCCCACTCCATGAGGTATTTCTCCACATCCGTGTCCCGGCCCGGCAGTGGAGAGCCCCGCTTCATCGCAGTGGGCTACGTGGACGACACGCAGTTCGTGCGGTTCGACAGCGACGCCGCGAGCCAGAAGATGGAGCCGCGGGCGCCGTGGATAGAGCAGGAGGGGCCGGAGTATTGGGACCAGGAGACACGGAATATGAAGGCCCACTCACAGACTGACCGAGCGAACCTGGGGACCCTGCGCGGCTACTACAACCAGAGCGAGGACG

Request:

    POST MolecularSequence

Entry 9 - fullUrl = urn:uuid:fbba9fe7-0ece-4ec1-9233-a437a8d242a0

Resource MolecularSequence:

> Generated Narrative: MolecularSequence CG-IG-HLA-FullBundle-01-9

> type: DNA Sequence

> coordinateSystem: 0

> ### ReferenceSeqs

> - | ReferenceSeqId | WindowStart | WindowEnd
> * | HLA-A*01:02 | 1014 | 1290

> observedSeq: GTTCTCACACCATCCAGATAATGTATGGCTGCGACGTGGGGCCGGACGGGCGCTTCCTCCGCGGGTACCGGCAGGACGCCTACGACGGCAAGGATTACATCGCCCTGAACGAGGACCTGCGCTCTTGGACCGCGGCGGACATGGCAGCTCAGATCACCAAGCGCAAGTGGGAGGCGGTCCATGCGGCGGAGCAGCGGAGAGTCTACCTGGAGGGCCGGTGCGTGGACGGGCTCCGCAGATACCTGGAGAACGGGAAGGAGACGCTGCAGCGCACGG

Request:

    POST MolecularSequence

Entry 10 - fullUrl = urn:uuid:b7765bbf-df40-486a-9f2f-404309643de6

Resource Observation:

> Generated Narrative: Observation CG-IG-HLA-FullBundle-01-10

> Profile: Haplotype

> status: Final

> category: Laboratory, Genetics

> code: Haplotype name

> subject: John Storm

> effective: 2016-12-15

> performer: aTypingLab, Inc

> value: HLA-A*01:01:01G

> method: NGS based Class I HLA-A, -B, -C genotyping

> specimen: buccal swab from John Storm

> derivedFrom:

> - HLA-A*01:01:01:01, exon 2
> - HLA-A*01:01:01:01, exon 3

> ### Components

> - | Code | Value[x]
> * | Gene studied [ID] | HLA-A

Request:

    POST Observation

Entry 11 - fullUrl = urn:uuid:d98d92a7-0e86-4ae5-b036-b7e1bba6ec32

Resource Observation:

> Generated Narrative: Observation CG-IG-HLA-FullBundle-01-11

> Profile: Haplotype

> status: Final

> category: Laboratory, Genetics

> code: Haplotype name

> subject: John Storm

> effective: 2016-12-15

> performer: aTypingLab, Inc

> value: HLA-A*01:02

> method: NGS based Class I HLA-A, -B, -C genotyping

> specimen: buccal swab from John Storm

> derivedFrom:

> - HLA-A*01:02, exon 2
> - HLA-A*01:02, exon 3

> ### Components

> - | Code | Value[x]
> * | Gene studied [ID] | HLA-A

Request:

    POST Observation

Entry 12 - fullUrl = urn:uuid:49a86246-4004-42eb-9bdc-f542f93f9228

Resource Observation:

> Generated Narrative: Observation CG-IG-HLA-FullBundle-01-12

> Profile: Genotype

> basedOn: Class I HLA genotyping for John Storm

> status: Final

> category: Laboratory, Genetics

> code: Genotype display name

> subject: John Storm

> effective: 2016-12-15

> performer: aTypingLab, Inc

> value: hla#3.23.0#HLA-A:01:01G+HLA-A*01:02

> method: NGS based Class I HLA-A, -B, -C genotyping

> specimen: buccal swab from John Storm

> derivedFrom:

> - HLA-A*01:01:01G, exons 2 and 3
> - HLA-A*01:02, exons 2 and 3

> ### Components

> - | Code | Value[x]
> * | Gene studied [ID] | HLA-A

Request:

    POST Observation

Entry 13 - fullUrl = urn:uuid:cbabf93e-1b4b-46f2-ba1e-d84862670670

Resource MolecularSequence:

> Generated Narrative: MolecularSequence CG-IG-HLA-FullBundle-01-13

> type: DNA Sequence

> coordinateSystem: 0

> ### ReferenceSeqs

> - | ReferenceSeqId | WindowStart | WindowEnd
> * | HLA-B*15:01:01:01 | 486 | 756

> observedSeq: GCTCCCACTCCATGAGGTATTTCTACACCGCCATGTCCCGGCCCGGCCGCGGGGAGCCCCGCTTCATCGCAGTGGGCTACGTGGACGACACCCAGTTCGTGAGGTTCGACAGCGACGCCGCGAGTCCGAGGATGGCGCCCCGGGCGCCATGGATAGAGCAGGAGGGGCCGGAGTATTGGGACCGGGAGACACAGATCTCCAAGACCAACACACAGACTTACCGAGAGAGCCTGCGGAACCTGCGCGGCTACTACAACCAGAGCGAGGCCG

Request:

    POST MolecularSequence

Entry 14 - fullUrl = urn:uuid:c233ad3d-1572-48d6-93da-0a583535e138

Resource MolecularSequence:

> Generated Narrative: MolecularSequence CG-IG-HLA-FullBundle-01-14

> type: DNA Sequence

> coordinateSystem: 0

> ### ReferenceSeqs

> - | ReferenceSeqId | WindowStart | WindowEnd
> * | HLA-B*15:01:01:01 | 1001 | 1277

> observedSeq: GGTCTCACACCCTCCAGAGGATGTACGGCTGCGACGTGGGGCCGGACGGGCGCCTCCTCCGCGGGCATGACCAGTCCGCCTACGACGGCAAGGATTACATCGCCCTGAACGAGGACCTGAGCTCCTGGACCGCGGCGGACACGGCGGCTCAGATCACCCAGCGCAAGTGGGAGGCGGCCCGTGAGGCGGAGCAGTGGAGAGCCTACCTGGAGGGCCTGTGCGTGGAGTGGCTCCGCAGATACCTGGAGAACGGGAAGGAGACGCTGCAGCGCGCGG

Request:

    POST MolecularSequence

Entry 15 - fullUrl = urn:uuid:05fa52d7-5c67-460a-8722-d3460b24d6fe

Resource MolecularSequence:

> Generated Narrative: MolecularSequence CG-IG-HLA-FullBundle-01-15

> type: DNA Sequence

> coordinateSystem: 0

> ### ReferenceSeqs

> - | ReferenceSeqId | WindowStart | WindowEnd
> * | HLA-B*57:01:01 | 485 | 755

> observedSeq: GCTCCCACTCCATGAGGTATTTCTACACCGCCATGTCCCGGCCCGGCCGCGGGGAGCCCCGCTTCATCGCAGTGGGCTACGTGGACGACACCCAGTTCGTGAGGTTCGACAGCGACGCCGCGAGTCCGAGGATGGCGCCCCGGGCGCCATGGATAGAGCAGGAGGGGCCGGAGTATTGGGACGGGGAGACACGGAACATGAAGGCCTCCGCGCAGACTTACCGAGAGAACCTGCGGATCGCGCTCCGCTACTACAACCAGAGCGAGGCCG

Request:

    POST MolecularSequence

Entry 16 - fullUrl = urn:uuid:db69e549-6267-4777-b4b9-8813f3329309

Resource MolecularSequence:

> Generated Narrative: MolecularSequence CG-IG-HLA-FullBundle-01-16

> type: DNA Sequence

> coordinateSystem: 0

> ### ReferenceSeqs

> - | ReferenceSeqId | WindowStart | WindowEnd
> * | HLA-B*57:01:01 | 1001 | 1277

> observedSeq: GGTCTCACATCATCCAGGTGATGTATGGCTGCGACGTGGGGCCGGACGGGCGCCTCCTCCGCGGGCATGACCAGTCCGCCTACGACGGCAAGGATTACATCGCCCTGAACGAGGACCTGAGCTCCTGGACCGCGGCGGACACGGCGGCTCAGATCACCCAGCGCAAGTGGGAGGCGGCCCGTGTGGCGGAGCAGCTGAGAGCCTACCTGGAGGGCCTGTGCGTGGAGTGGCTCCGCAGATACCTGGAGAACGGGAAGGAGACGCTGCAGCGCGCGG

Request:

    POST MolecularSequence

Entry 17 - fullUrl = urn:uuid:e2092243-2970-49d2-a90f-b90d1d49715a

Resource Observation:

> Generated Narrative: Observation CG-IG-HLA-FullBundle-01-17

> Profile: Haplotype

> status: Final

> category: Laboratory, Genetics

> code: Haplotype name

> subject: John Storm

> effective: 2016-12-15

> performer: aTypingLab, Inc

> value: HLA-B*15:01:01G

> method: NGS based Class I HLA-A, -B, -C genotyping

> specimen: buccal swab from John Storm

> derivedFrom:

> - HLA-B*15:01:01:01, exon 2
> - HLA-B*15:01:01:01, exon 3

> ### Components

> - | Code | Value[x]
> * | Gene studied [ID] | HLA-B

Request:

    POST Observation

Entry 18 - fullUrl = urn:uuid:792be53e-d4fb-4887-a367-815ef6c706e5

Resource Observation:

> Generated Narrative: Observation CG-IG-HLA-FullBundle-01-18

> Profile: Haplotype

> status: Final

> category: Laboratory, Genetics

> code: Haplotype name

> subject: John Storm

> effective: 2016-12-15

> performer: aTypingLab, Inc

> value: HLA-B*57:01:01G

> method: NGS based Class I HLA-A, -B, -C genotyping

> specimen: buccal swab from John Storm

> derivedFrom:

> - HLA-B*57:01:01, exon 2
> - HLA-B*57:01:01, exon 3

> ### Components

> - | Code | Value[x]
> * | Gene studied [ID] | HLA-B

Request:

    POST Observation

Entry 19 - fullUrl = urn:uuid:60613a43-c4cb-4502-b3e2-cf9215feaa70

Resource Observation:

> Generated Narrative: Observation CG-IG-HLA-FullBundle-01-19

> Profile: Genotype

> basedOn: Class I HLA genotyping for John Storm

> status: Final

> category: Laboratory, Genetics

> code: Genotype display name

> subject: John Storm

> effective: 2016-12-15

> performer: aTypingLab, Inc

> value: hla#3.23.0#HLA-B*15:01:01G+HLA-B*57:01:01G

> method: NGS based Class I HLA-A, -B, -C genotyping

> specimen: buccal swab from John Storm

> derivedFrom:

> - HLA-B*15:01:01G, exons 2 and 3
> - HLA-B*57:01:01G, exons 2 and 3

> ### Components

> - | Code | Value[x]
> * | Gene studied [ID] | HLA-B

Request:

    POST Observation

Entry 20 - fullUrl = urn:uuid:bb55c2bc-5ad2-4bc1-8ff3-c407d06b12d0

Resource MolecularSequence:

> Generated Narrative: MolecularSequence CG-IG-HLA-FullBundle-01-20

> type: DNA Sequence

> coordinateSystem: 0

> ### ReferenceSeqs

> - | ReferenceSeqId | WindowStart | WindowEnd
> * | HLA-C*01:02:01 | 486 | 756

> observedSeq: GCTCCCACTCCATGAAGTATTTCTTCACATCCGTGTCCCGGCCTGGCCGCGGAGAGCCCCGCTTCATCTCAGTGGGCTACGTGGACGACACGCAGTTCGTGCGGTTCGACAGCGACGCCGCGAGTCCGAGAGGGGAGCCGCGGGCGCCGTGGGTGGAGCAGGAGGGGCCGGAGTATTGGGACCGGGAGACACAGAAGTACAAGCGCCAGGCACAGACTGACCGAGTGAGCCTGCGGAACCTGCGCGGCTACTACAACCAGAGCGAGGCCG

Request:

    POST MolecularSequence

Entry 21 - fullUrl = urn:uuid:46938bb2-0486-4e87-bfd3-89aab2d5e22f

Resource MolecularSequence:

> Generated Narrative: MolecularSequence CG-IG-HLA-FullBundle-01-21

> type: DNA Sequence

> coordinateSystem: 0

> ### ReferenceSeqs

> - | ReferenceSeqId | WindowStart | WindowEnd
> * | HLA-C*01:02:01 | 1002 | 1278

> observedSeq: GGTCTCACACCCTCCAGTGGATGTGTGGCTGCGACCTGGGGCCCGACGGGCGCCTCCTCCGCGGGTATGACCAGTACGCCTACGACGGCAAGGATTACATCGCCCTGAACGAGGACCTGCGCTCCTGGACCGCCGCGGACACCGCGGCTCAGATCACCCAGCGCAAGTGGGAGGCGGCCCGTGAGGCGGAGCAGCGGAGAGCCTACCTGGAGGGCACGTGCGTGGAGTGGCTCCGCAGATACCTGGAGAACGGGAAGGAGACGCTGCAGCGCGCGG

Request:

    POST MolecularSequence

Entry 22 - fullUrl = urn:uuid:2ae2ff34-279e-43c2-9018-b054fd3fc1ce

Resource MolecularSequence:

> Generated Narrative: MolecularSequence CG-IG-HLA-FullBundle-01-22

> type: DNA Sequence

> coordinateSystem: 0

> ### ReferenceSeqs

> - | ReferenceSeqId | WindowStart | WindowEnd
> * | HLA-C*03:04:01:01 | 486 | 756

> observedSeq: GCTCCCACTCCATGAGGTATTTCTACACCGCTGTGTCCCGGCCCGGCCGCGGGGAGCCCCACTTCATCGCAGTGGGCTACGTGGACGACACGCAGTTCGTGCGGTTCGACAGCGACGCCGCGAGTCCGAGAGGGGAGCCGCGGGCGCCGTGGGTGGAGCAGGAGGGGCCGGAGTATTGGGACCGGGAGACACAGAAGTACAAGCGCCAGGCACAGACTGACCGAGTGAGCCTGCGGAACCTGCGCGGCTACTACAACCAGAGCGAGGCCG

Request:

    POST MolecularSequence

Entry 23 - fullUrl = urn:uuid:19153ef1-68c6-47a2-9676-c4eefbd39af9

Resource MolecularSequence:

> Generated Narrative: MolecularSequence CG-IG-HLA-FullBundle-01-23

> type: DNA Sequence

> coordinateSystem: 0

> ### ReferenceSeqs

> - | ReferenceSeqId | WindowStart | WindowEnd
> * | HLA-C*03:04:01:01 | 1001 | 1277

> observedSeq: GGTCTCACATCATCCAGAGGATGTATGGCTGCGACGTGGGGCCCGACGGGCGCCTCCTCCGCGGGTATGACCAGTACGCCTACGACGGCAAGGATTACATCGCCCTGAACGAGGATCTGCGCTCCTGGACCGCCGCGGACACGGCGGCTCAGATCACCCAGCGCAAGTGGGAGGCGGCCCGTGAGGCGGAGCAGCTGAGAGCCTACCTGGAGGGCCTGTGCGTGGAGTGGCTCCGCAGATACCTGAAGAATGGGAAGGAGACGCTGCAGCGCGCGG

Request:

    POST MolecularSequence

Entry 24 - fullUrl = urn:uuid:709c5315-9403-4867-9d82-0b953836665f

Resource Observation:

> Generated Narrative: Observation CG-IG-HLA-FullBundle-01-24

> Profile: Haplotype

> status: Final

> category: Laboratory, Genetics

> code: Haplotype name

> subject: John Storm

> effective: 2016-12-15

> performer: aTypingLab, Inc

> value: HLA-C*01:02:01G

> method: NGS based Class I HLA-A, -B, -C genotyping

> specimen: buccal swab from John Storm

> derivedFrom:

> - HLA-C*01:02:01, exon 2
> - HLA-C*01:02:01, exon 3

> ### Components

> - | Code | Value[x]
> * | Gene studied [ID] | HLA-C

Request:

    POST Observation

Entry 25 - fullUrl = urn:uuid:8b2aa21c-1426-4717-8ab0-a84d83df7d47

Resource Observation:

> Generated Narrative: Observation CG-IG-HLA-FullBundle-01-25

> Profile: Haplotype

> status: Final

> category: Laboratory, Genetics

> code: Haplotype name

> subject: John Storm

> effective: 2016-12-15

> performer: aTypingLab, Inc

> value: HLA-C*01:02:01G

> method: NGS based Class I HLA-A, -B, -C genotyping

> specimen: buccal swab from John Storm

> derivedFrom:

> - HLA-C*03:04:01:01, exon 2
> - HLA-C*03:04:01:01, exon 3

> ### Components

> - | Code | Value[x]
> * | Gene studied [ID] | HLA-C

Request:

    POST Observation

Entry 26 - fullUrl = urn:uuid:0e0a780e-4486-4cd0-bfae-7243c579f208

Resource Observation:

> Generated Narrative: Observation CG-IG-HLA-FullBundle-01-26

> Profile: Genotype

> basedOn: Class I HLA genotyping for John Storm

> status: Final

> category: Laboratory, Genetics

> code: Genotype display name

> subject: John Storm

> effective: 2016-12-15

> performer: aTypingLab, Inc

> value: hla#3.23.0#HLA-C*01:02:01G+HLA-C*03:04:01G

> method: NGS based Class I HLA-A, -B, -C genotyping

> specimen: buccal swab from John Storm

> derivedFrom:

> - HLA-C*03:04:01G, exons 2 and 3
> - HLA-C*01:02:01G, exons 2 and 3

> ### Components

> - | Code | Value[x]
> * | Gene studied [ID] | HLA-C

Request:

    POST Observation

Entry 27 - fullUrl = urn:uuid:b0a4b18e-94e7-4b1b-8031-c7ae4bdd8db9

Resource DiagnosticReport:

> Generated Narrative: DiagnosticReport CG-IG-HLA-FullBundle-01-27

> Profile: Genomic Report

> ## Genetic analysis report (Genetics)

> Subject | John Storm(official) Male, DoB: 1986-12-31 ( Donor Registration Number (use: usual, period: 2012-11-10 --> (ongoing)))
> When For | 2016-12-15
> Reported | 2016-12-15 14:15:30-0600
> Performer | aTypingLab Inc

> Report Details

> Code | Value | Flags
> Genotype display name | hla#3.23.0#HLA-A:01:01G+HLA-A*01:02 | Final
> Genotype display name | hla#3.23.0#HLA-B*15:01:01G+HLA-B*57:01:01G | Final
> Genotype display name | hla#3.23.0#HLA-C*01:02:01G+HLA-C*03:04:01G | Final

Request:

    POST DiagnosticReport