FHIRGenomicsOperations.postman_collection.json

{
	"info": {
		"_postman_id": "e28d19b3-f53d-413c-8692-69f658646741",
		"name": "FHIRGenomicsOperations",
		"schema": "https://schema.getpostman.com/json/collection/v2.1.0/collection.json",
		"_exporter_id": "8256147",
		"_collection_link": "https://crimson-crater-424865.postman.co/workspace/My-Workspace~f83b8d59-4041-4daf-8360-4f753d67bb63/collection/8256147-e28d19b3-f53d-413c-8692-69f658646741?action=share&source=collection_link&creator=8256147"
	},
	"item": [
		{
			"name": "find-subject-variants",
			"item": [
				{
					"name": "find-subject-variants",
					"request": {
						"method": "GET",
						"header": [],
						"url": {
							"raw": "https://fhir-gen-ops.herokuapp.com/subject-operations/genotype-operations/$find-subject-variants?subject=NB6TK329&testIdentifiers=TL000016660-ASM&includeVariants=true&ranges=NC_000002.12:178525988-178807423,NC_000002.12:178525988-178807423",
							"protocol": "https",
							"host": [
								"fhir-gen-ops",
								"herokuapp",
								"com"
							],
							"path": [
								"subject-operations",
								"genotype-operations",
								"$find-subject-variants"
							],
							"query": [
								{
									"key": "subject",
									"value": "NB6TK329"
								},
								{
									"key": "testIdentifiers",
									"value": "TL000016660-ASM"
								},
								{
									"key": "specimenIdentifiers",
									"value": "GS000016660-ASM",
									"disabled": true
								},
								{
									"key": "genomicSourceClass",
									"value": "germline",
									"disabled": true
								},
								{
									"key": "testDateRange",
									"value": "ge2014-01-01",
									"disabled": true
								},
								{
									"key": "includeVariants",
									"value": "true"
								},
								{
									"key": "testDateRange",
									"value": "le2014-05-01",
									"disabled": true
								},
								{
									"key": "includePhasing",
									"value": "true",
									"disabled": true
								},
								{
									"key": "ranges",
									"value": "NC_000002.12:178525988-178807423,NC_000002.12:178525988-178807423"
								}
							]
						}
					},
					"response": []
				},
				{
					"name": "LDLR query using build37 range",
					"request": {
						"method": "GET",
						"header": [],
						"url": {
							"raw": "https://fhir-gen-ops.herokuapp.com/subject-operations/genotype-operations/$find-subject-variants?subject=HG00403&ranges=NC_000019.9:11200138-11244496&includeVariants=true&includePhasing=true",
							"protocol": "https",
							"host": [
								"fhir-gen-ops",
								"herokuapp",
								"com"
							],
							"path": [
								"subject-operations",
								"genotype-operations",
								"$find-subject-variants"
							],
							"query": [
								{
									"key": "subject",
									"value": "HG00403"
								},
								{
									"key": "testIdentifiers",
									"value": "TL000016660-ASM",
									"disabled": true
								},
								{
									"key": "specimenIdentifiers",
									"value": "GS000016660-ASM",
									"disabled": true
								},
								{
									"key": "genomicSourceClass",
									"value": "germline",
									"disabled": true
								},
								{
									"key": "testDateRange",
									"value": "ge2014-01-01",
									"disabled": true
								},
								{
									"key": "testDateRange",
									"value": "le2014-05-01",
									"disabled": true
								},
								{
									"key": "ranges",
									"value": "NC_000019.9:11200138-11244496"
								},
								{
									"key": "includeVariants",
									"value": "true"
								},
								{
									"key": "includePhasing",
									"value": "true"
								}
							]
						}
					},
					"response": []
				},
				{
					"name": "LDLR query using build38 range",
					"request": {
						"method": "GET",
						"header": [],
						"url": {
							"raw": "https://fhir-gen-ops.herokuapp.com/subject-operations/genotype-operations/$find-subject-variants?subject=HG00403&includeVariants=true&ranges=NC_000019.10:11089431-11133820",
							"protocol": "https",
							"host": [
								"fhir-gen-ops",
								"herokuapp",
								"com"
							],
							"path": [
								"subject-operations",
								"genotype-operations",
								"$find-subject-variants"
							],
							"query": [
								{
									"key": "subject",
									"value": "HG00403"
								},
								{
									"key": "testIdentifiers",
									"value": "TL000016660-ASM",
									"disabled": true
								},
								{
									"key": "specimenIdentifiers",
									"value": "GS000016660-ASM",
									"disabled": true
								},
								{
									"key": "genomicSourceClass",
									"value": "germline",
									"disabled": true
								},
								{
									"key": "testDateRange",
									"value": "ge2014-01-01",
									"disabled": true
								},
								{
									"key": "testDateRange",
									"value": "le2014-05-01",
									"disabled": true
								},
								{
									"key": "includeVariants",
									"value": "true"
								},
								{
									"key": "ranges",
									"value": "NC_000019.10:11089431-11133820"
								}
							]
						}
					},
					"response": []
				},
				{
					"name": "LDLR exon 7 query",
					"request": {
						"method": "GET",
						"header": [],
						"url": {
							"raw": "https://fhir-gen-ops.herokuapp.com/subject-operations/genotype-operations/$find-subject-variants?subject=HG00403&ranges=NC_000019.9:11221327-11221447&includeVariants=true",
							"protocol": "https",
							"host": [
								"fhir-gen-ops",
								"herokuapp",
								"com"
							],
							"path": [
								"subject-operations",
								"genotype-operations",
								"$find-subject-variants"
							],
							"query": [
								{
									"key": "subject",
									"value": "HG00403"
								},
								{
									"key": "testIdentifiers",
									"value": "TL000016660-ASM",
									"disabled": true
								},
								{
									"key": "specimenIdentifiers",
									"value": "GS000016660-ASM",
									"disabled": true
								},
								{
									"key": "genomicSourceClass",
									"value": "germline",
									"disabled": true
								},
								{
									"key": "testDateRange",
									"value": "ge2014-01-01",
									"disabled": true
								},
								{
									"key": "testDateRange",
									"value": "le2014-05-01",
									"disabled": true
								},
								{
									"key": "ranges",
									"value": "NC_000019.9:11221327-11221447"
								},
								{
									"key": "includeVariants",
									"value": "true"
								}
							]
						}
					},
					"response": []
				}
			]
		},
		{
			"name": "find-subject-specific-variants",
			"item": [
				{
					"name": "find-subject-specific-variants",
					"request": {
						"method": "GET",
						"header": [],
						"url": {
							"raw": "https://fhir-gen-ops.herokuapp.com/subject-operations/genotype-operations/$find-subject-specific-variants?subject=m123&variants=NC_000005.9:g.112102032A>T",
							"protocol": "https",
							"host": [
								"fhir-gen-ops",
								"herokuapp",
								"com"
							],
							"path": [
								"subject-operations",
								"genotype-operations",
								"$find-subject-specific-variants"
							],
							"query": [
								{
									"key": "testIdentifiers",
									"value": "TL000016660-ASM",
									"disabled": true
								},
								{
									"key": "specimenIdentifiers",
									"value": "GS000016660-ASM",
									"disabled": true
								},
								{
									"key": "genomicSourceClass",
									"value": "germline",
									"disabled": true
								},
								{
									"key": "testDateRange",
									"value": "ge2014-01-01",
									"disabled": true
								},
								{
									"key": "subject",
									"value": "m123"
								},
								{
									"key": "variants",
									"value": "NC_000005.9:g.112102032A>T"
								}
							]
						}
					},
					"response": []
				},
				{
					"name": "ClinVar 819274, DOES normalize",
					"request": {
						"method": "GET",
						"header": [],
						"url": {
							"raw": "https://fhir-gen-ops.herokuapp.com/subject-operations/genotype-operations/$find-subject-specific-variants?subject=m123&variants=NM_001127510.3:c.145A>T",
							"protocol": "https",
							"host": [
								"fhir-gen-ops",
								"herokuapp",
								"com"
							],
							"path": [
								"subject-operations",
								"genotype-operations",
								"$find-subject-specific-variants"
							],
							"query": [
								{
									"key": "testIdentifiers",
									"value": "TL000016660-ASM",
									"disabled": true
								},
								{
									"key": "specimenIdentifiers",
									"value": "GS000016660-ASM",
									"disabled": true
								},
								{
									"key": "genomicSourceClass",
									"value": "germline",
									"disabled": true
								},
								{
									"key": "testDateRange",
									"value": "ge2014-01-01",
									"disabled": true
								},
								{
									"key": "subject",
									"value": "m123"
								},
								{
									"key": "variants",
									"value": "NM_001127510.3:c.145A>T"
								}
							]
						}
					},
					"response": []
				},
				{
					"name": "ClinVar 1097908, DOES NOT normalize",
					"request": {
						"method": "GET",
						"header": [],
						"url": {
							"raw": "https://fhir-gen-ops.herokuapp.com/subject-operations/genotype-operations/$find-subject-specific-variants?subject=m123&variants=NM_001385641.1:c.804C>T",
							"protocol": "https",
							"host": [
								"fhir-gen-ops",
								"herokuapp",
								"com"
							],
							"path": [
								"subject-operations",
								"genotype-operations",
								"$find-subject-specific-variants"
							],
							"query": [
								{
									"key": "testIdentifiers",
									"value": "TL000016660-ASM",
									"disabled": true
								},
								{
									"key": "specimenIdentifiers",
									"value": "GS000016660-ASM",
									"disabled": true
								},
								{
									"key": "genomicSourceClass",
									"value": "germline",
									"disabled": true
								},
								{
									"key": "testDateRange",
									"value": "ge2014-01-01",
									"disabled": true
								},
								{
									"key": "subject",
									"value": "m123"
								},
								{
									"key": "variants",
									"value": "NM_001385641.1:c.804C>T"
								}
							]
						}
					},
					"response": []
				},
				{
					"name": "Polygenic risk score",
					"request": {
						"method": "GET",
						"header": [],
						"url": {
							"raw": "https://fhir-gen-ops.herokuapp.com/subject-operations/genotype-operations/$find-subject-specific-variants?subject=HG00404&variants=NC_000005.9:112154946:CC:C,NC_000005.9:112157612:C:T,NC_000017.10:41246373:G:,NC_000017.10:41243854:AAA:AAAA,NC_000013.10:32900284:C:A,NC_000019.9:11216262:C:A,NC_000014.8:23894101:A:T",
							"protocol": "https",
							"host": [
								"fhir-gen-ops",
								"herokuapp",
								"com"
							],
							"path": [
								"subject-operations",
								"genotype-operations",
								"$find-subject-specific-variants"
							],
							"query": [
								{
									"key": "testIdentifiers",
									"value": "TL000016660-ASM",
									"disabled": true
								},
								{
									"key": "specimenIdentifiers",
									"value": "GS000016660-ASM",
									"disabled": true
								},
								{
									"key": "genomicSourceClass",
									"value": "germline",
									"disabled": true
								},
								{
									"key": "testDateRange",
									"value": "ge2014-01-01",
									"disabled": true
								},
								{
									"key": "subject",
									"value": "HG00404"
								},
								{
									"key": "variants",
									"value": "NC_000005.9:112154946:CC:C,NC_000005.9:112157612:C:T,NC_000017.10:41246373:G:,NC_000017.10:41243854:AAA:AAAA,NC_000013.10:32900284:C:A,NC_000019.9:11216262:C:A,NC_000014.8:23894101:A:T"
								}
							]
						}
					},
					"response": []
				}
			]
		},
		{
			"name": "find-subject-structural-intersecting-variants",
			"item": [
				{
					"name": "find-subject-structural-intersecting-variants",
					"request": {
						"method": "GET",
						"header": [],
						"url": {
							"raw": "https://fhir-gen-ops.herokuapp.com/subject-operations/genotype-operations/$find-subject-structural-intersecting-variants?subject=HCC1143&ranges=NC_000007.14:116672195-116798386&specimenIdentifiers=HCC1143-Sp1",
							"protocol": "https",
							"host": [
								"fhir-gen-ops",
								"herokuapp",
								"com"
							],
							"path": [
								"subject-operations",
								"genotype-operations",
								"$find-subject-structural-intersecting-variants"
							],
							"query": [
								{
									"key": "subject",
									"value": "HCC1143"
								},
								{
									"key": "ranges",
									"value": "NC_000007.14:116672195-116798386"
								},
								{
									"key": "includeVariants",
									"value": "true",
									"disabled": true
								},
								{
									"key": "specimenIdentifiers",
									"value": "HCC1143-Sp1"
								}
							]
						}
					},
					"response": []
				},
				{
					"name": "SVs intersecting EGFR or KIT exon 11",
					"request": {
						"method": "GET",
						"header": [],
						"url": {
							"raw": "https://fhir-gen-ops.herokuapp.com/subject-operations/genotype-operations/$find-subject-structural-intersecting-variants?subject=HCC1143&ranges=NC_000007.14:55019016-55211628,NC_000004.12:54727415-54727542&specimenIdentifiers=HCC1143-Sp1",
							"protocol": "https",
							"host": [
								"fhir-gen-ops",
								"herokuapp",
								"com"
							],
							"path": [
								"subject-operations",
								"genotype-operations",
								"$find-subject-structural-intersecting-variants"
							],
							"query": [
								{
									"key": "subject",
									"value": "HCC1143"
								},
								{
									"key": "ranges",
									"value": "NC_000007.14:55019016-55211628,NC_000004.12:54727415-54727542"
								},
								{
									"key": "includeVariants",
									"value": "true",
									"disabled": true
								},
								{
									"key": "specimenIdentifiers",
									"value": "HCC1143-Sp1"
								}
							]
						}
					},
					"response": []
				},
				{
					"name": "SVs intersecting the A-band of TTN",
					"request": {
						"method": "GET",
						"header": [],
						"url": {
							"raw": "https://fhir-gen-ops.herokuapp.com/subject-operations/genotype-operations/$find-subject-structural-intersecting-variants?subject=ABC789&ranges=NC_000002.12:179400709-179483218&includeVariants=true",
							"protocol": "https",
							"host": [
								"fhir-gen-ops",
								"herokuapp",
								"com"
							],
							"path": [
								"subject-operations",
								"genotype-operations",
								"$find-subject-structural-intersecting-variants"
							],
							"query": [
								{
									"key": "subject",
									"value": "ABC789"
								},
								{
									"key": "ranges",
									"value": "NC_000002.12:179400709-179483218"
								},
								{
									"key": "includeVariants",
									"value": "true"
								}
							]
						}
					},
					"response": []
				},
				{
					"name": "SVs intersecting BRCA1 or BRCA2",
					"request": {
						"method": "GET",
						"header": [],
						"url": {
							"raw": "https://fhir-gen-ops.herokuapp.com/subject-operations/genotype-operations/$find-subject-structural-intersecting-variants?subject=HCC1143&ranges=NC_000017.11:43044294-43125364,NC_000013.11:32315507-32400268&includeVariants=true",
							"protocol": "https",
							"host": [
								"fhir-gen-ops",
								"herokuapp",
								"com"
							],
							"path": [
								"subject-operations",
								"genotype-operations",
								"$find-subject-structural-intersecting-variants"
							],
							"query": [
								{
									"key": "subject",
									"value": "HCC1143"
								},
								{
									"key": "ranges",
									"value": "NC_000017.11:43044294-43125364,NC_000013.11:32315507-32400268"
								},
								{
									"key": "includeVariants",
									"value": "true"
								}
							]
						}
					},
					"response": []
				}
			]
		},
		{
			"name": "find-subject-structural-subsuming-variants",
			"item": [
				{
					"name": "find-subject-structural-subsuming-variants",
					"request": {
						"method": "GET",
						"header": [],
						"url": {
							"raw": "https://fhir-gen-ops.herokuapp.com/subject-operations/genotype-operations/$find-subject-structural-subsuming-variants?subject=FLATIRON2&ranges=NC_000007.14:116672195-116798386&includeVariants=true",
							"protocol": "https",
							"host": [
								"fhir-gen-ops",
								"herokuapp",
								"com"
							],
							"path": [
								"subject-operations",
								"genotype-operations",
								"$find-subject-structural-subsuming-variants"
							],
							"query": [
								{
									"key": "subject",
									"value": "FLATIRON2"
								},
								{
									"key": "ranges",
									"value": "NC_000007.14:116672195-116798386"
								},
								{
									"key": "genomicSourceClass",
									"value": "germline",
									"disabled": true
								},
								{
									"key": "testDateRange",
									"value": "ge2014-01-01",
									"disabled": true
								},
								{
									"key": "specimenIdentifiers",
									"value": "HCC1143-Sp1",
									"disabled": true
								},
								{
									"key": "includeVariants",
									"value": "true"
								}
							]
						}
					},
					"response": []
				},
				{
					"name": "SVs subsuming MET",
					"request": {
						"method": "GET",
						"header": [],
						"url": {
							"raw": "https://fhir-gen-ops.herokuapp.com/subject-operations/genotype-operations/$find-subject-structural-subsuming-variants?subject=HCC1143&ranges=NC_000007.14:116672195-116798386&specimenIdentifiers=HCC1143-Sp1&includeVariants=true",
							"protocol": "https",
							"host": [
								"fhir-gen-ops",
								"herokuapp",
								"com"
							],
							"path": [
								"subject-operations",
								"genotype-operations",
								"$find-subject-structural-subsuming-variants"
							],
							"query": [
								{
									"key": "subject",
									"value": "HCC1143"
								},
								{
									"key": "ranges",
									"value": "NC_000007.14:116672195-116798386"
								},
								{
									"key": "specimenIdentifiers",
									"value": "HCC1143-Sp1"
								},
								{
									"key": "genomicSourceClass",
									"value": "germline",
									"disabled": true
								},
								{
									"key": "testDateRange",
									"value": "ge2014-01-01",
									"disabled": true
								},
								{
									"key": "includeVariants",
									"value": "true"
								}
							]
						}
					},
					"response": []
				},
				{
					"name": "SVs subsuming CYP2D6",
					"request": {
						"method": "GET",
						"header": [],
						"url": {
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								{
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				{
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								{
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					"response": []
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				{
					"name": "Hereditary Paraganglioma-Pheochromocytoma Syndrome",
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						"header": [],
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								{
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				{
					"name": "HBOC, LS, FH",
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						"header": [],
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								{
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								{
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				{
					"name": "Hemachromatosis",
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							"protocol": "https",
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								{
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								{
									"key": "subject",
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								{
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							"protocol": "https",
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								{
									"key": "featureConsequences",
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								{
									"key": "variants",
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				{
					"name": "ALK, BRAF, EGFR consequences",
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									"key": "featureConsequences",
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								{
									"key": "variants",
									"value": "NM_178349.2:c.118G>T",
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				{
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								{
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					"response": []
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				{
					"name": "Molecular consequences of NC_000001.10:86852620:A:G",
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								{
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								{
									"key": "testIdentifiers",
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									"key": "specimenIdentifiers",
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								{
									"key": "genomicSourceClass",
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								}
							]
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					},
					"response": []
				},
				{
					"name": "AND example",
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							"query": [
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								{
									"key": "variants",
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								{
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								{
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					},
					"response": []
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				{
					"name": "OR example",
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						"header": [],
						"url": {
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								{
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				{
					"name": "BRAF V600E",
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							"path": [
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							"query": [
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								{
									"key": "testIdentifiers",
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								{
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								{
									"key": "genomicSourceClass",
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								{
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							"protocol": "https",
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							"path": [
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							"query": [
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								{
									"key": "includePatientList",
									"value": "true"
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							]
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					},
					"response": []
				},
				{
					"name": "BRCA1,  BRCA2 SVs in population",
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						"header": [],
						"url": {
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							"protocol": "https",
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							"path": [
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								{
									"key": "includePatientList",
									"value": "true"
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							]
						}
					},
					"response": []
				},
				{
					"name": "CYP2D6 SVs in population",
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						"header": [],
						"url": {
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							"protocol": "https",
							"host": [
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							],
							"path": [
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							"query": [
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									"key": "ranges",
									"value": "NC_000022.10:42522500-42526812"
								},
								{
									"key": "includePatientList",
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							]
						}
					},
					"response": []
				}
			]
		},
		{
			"name": "find-population-structural-subsuming-variants",
			"item": [
				{
					"name": "find-population-structural-subsuming-variants",
					"request": {
						"method": "GET",
						"header": [],
						"url": {
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							"protocol": "https",
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							],
							"path": [
								"subject-operations",
								"metadata-operations",
								"$find-study-metadata"
							],
							"query": [
								{
									"key": "subject",
									"value": "HCC1143"
								},
								{
									"key": "ranges",
									"value": "NC_000007.14:55019016-55211628"
								},
								{
									"key": "genomicSourceClass",
									"value": "germline",
									"disabled": true
								},
								{
									"key": "testDateRange",
									"value": "ge2014-02-02",
									"disabled": true
								}
							]
						}
					},
					"response": []
				}
			]
		},
		{
			"name": "UTILITY find-the-gene",
			"item": [
				{
					"name": "find-the-gene",
					"request": {
						"method": "GET",
						"header": [],
						"url": {
							"raw": "https://fhir-gen-ops.herokuapp.com/utilities/find-the-gene?range=NC_000014.9:23429328-23429328",
							"protocol": "https",
							"host": [
								"fhir-gen-ops",
								"herokuapp",
								"com"
							],
							"path": [
								"utilities",
								"find-the-gene"
							],
							"query": [
								{
									"key": "genomicSourceClass",
									"value": "germline",
									"disabled": true
								},
								{
									"key": "testDateRange",
									"value": "ge2014-02-02",
									"disabled": true
								},
								{
									"key": "range",
									"value": "NC_000014.9:23429328-23429328"
								}
							]
						}
					},
					"response": []
				}
			]
		},
		{
			"name": "UTILITY get-feature-coordinates",
			"item": [
				{
					"name": "get-feature-coordinates",
					"request": {
						"method": "GET",
						"header": [],
						"url": {
							"raw": "https://fhir-gen-ops.herokuapp.com/utilities/get-feature-coordinates?gene=BRCA1",
							"protocol": "https",
							"host": [
								"fhir-gen-ops",
								"herokuapp",
								"com"
							],
							"path": [
								"utilities",
								"get-feature-coordinates"
							],
							"query": [
								{
									"key": "genomicSourceClass",
									"value": "germline",
									"disabled": true
								},
								{
									"key": "testDateRange",
									"value": "ge2014-02-02",
									"disabled": true
								},
								{
									"key": "gene",
									"value": "BRCA1"
								}
							]
						}
					},
					"response": []
				}
			]
		}
	]
}