bundle-CG-IG-HLA-FullBundle-01 - Genomics Reporting Implementation Guide v3.0.1-SNAPSHOT

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.1-SNAPSHOT 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

Generated Narrative: 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://myorgsurl.com/123
accessionIdentifier: http://mylabsurl.com/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

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

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

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

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

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

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

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

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

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

Genetic analysis report (Genetics)
Subject Not done yet
When For 2016-12-15
Reported 2016-12-15 14:15:30-0600
Performer aTypingLab Inc
Report Details
Code Value

Request:

POST DiagnosticReport