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IGO Request Schema
ao508 edited this page Jul 26, 2024
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4 revisions
Page contents:
| field | description | type | required |
|---|---|---|---|
| requestId | identifier, assigned by IGO, and a subset of projectId
|
string | y |
| projectId | identifier, assigned by IGO, prefix of requestId
|
string | y |
| samples | array of samples (see table below for JSON property details) | array[samples] | y |
| bicAnalysis | indicates if request is for BIC | boolean | y |
| isCmoRequest | indicates if request is for CMO | boolean | y |
| recipe | baitset, gene panel used for request | string | y |
| pooledNormals | list of fastQ paths | array[string] | y* (optionally if normal samples not included in request samples list) |
| field | description | type | required |
|---|---|---|---|
| igoId | identifier, assigned by IGO | string | y |
| cmoPatientId | identifier, part of the sample submission process via CRBD | string | y |
| cmoSampleClass | used as part of the CMO label generation (see note) | string | y* (optionally, in combination with or in place of other properties required for CMO labels) |
| investigatorSampleId | identifier, used by default in certain cell line sample cases | string | y |
| specimenType | used as part of the CMO label generation (see note) | string | y* (optionally, in combination with or in place of other properties required for CMO labels) |
| sampleOrigin | used as part of the CMO label generation (see note) | string | y* (optionally, in combination with or in place of other properties required for CMO labels) |
| baitSet | used as part of the CMO label generation (see note) | string | y* (optionally, in combination with or in place of other properties required for CMO labels) |
| igoComplete | indicator if analysis is complete for sample (i.e., fastqs available) | boolean | y |
| cmoSampleIdFields | extra information for CMO label generation (see note) | map{string, string} | y* (optionally, in combination with or in place of other properties required for CMO labels) |
CMO label generation:
Link to documentation: CMO Label Generation rules
Sample Origin accepted values:
- Block
- Bone Marrow Aspirate
- Buccal Swab
- Buffy Coat
- Cell Pellet
- Cells
- Cerebrospinal Fluid
- Core Biopsy
- Curls
- Cytospin
- Fine Needle Aspirate
- Fingernails
- Organoid
- Other
- Plasma
- Punch
- Rapid Autopsy Tissue
- Saliva
- Slides
- Sorted Cells
- Tissue
- Urine
- Viably Frozen Cells
- Whole Blood
Specimen Type accepted values:
- Biopsy
- Resection
- Blood
- CellLine
- cfDNA
- Exosome
- PDX
- Xenograft
- XenograftDerivedCellLine
- RapidAutopsy
- Fingernails
- Organoid
- Saliva
- other
CMO Sample Class accepted values:
- Adjacent Normal
- Adjacent Tissue
- Cell free
- Local Recurrence
- Metastasis
- Normal
- Other
- Primary
- Recurrence
- Tumor
- Unknown Tumor
CMO Sample ID Fields: These are additional properties provided by IGO that are optionally used in combination with or in place of other properties used in the CMO sample label generation process.
| field | description | type |
|---|---|---|
| naToExtract | optionally used for resolving the nucleic acid abbreviation | string |
| normalizedPatientId | optionally used in case of non-standard CMO patient IDs for cell line samples | string |
| sampleType | optionally used for resolving the sample type abbreviation | string |
| recipe | optionally used for resolving the nucleic acid abbreviation | string |
{
"properties": {
"requestId": {
"type": "string"
},
"recipe": {
"type": "string"
},
"projectManagerName": {
"type": "string"
},
"piEmail": {
"type": "string"
},
"labHeadName": {
"type": "string"
},
"labHeadEmail": {
"type": "string"
},
"investigatorName": {
"type": "string"
},
"investigatorEmail": {
"type": "string"
},
"dataAnalystName": {
"type": "string"
},
"dataAnalystEmail": {
"type": "string"
},
"otherContactEmails": {
"type": "string"
},
"dataAccessEmails": {
"type": "string"
},
"qcAccessEmails": {
"type": "string"
},
"isCmoRequest": {
"type": "boolean"
},
"bicAnalysis": {
"type": "boolean"
},
"samples": {
"type": "array",
"items": {
"type": "object",
"properties": {
"cmoSampleName": {
"type": "string"
},
"sampleName": {
"type": "string"
},
"cmoSampleClass": {
"type": "string"
},
"oncoTreeCode": {
"type": "string"
},
"collectionYear": {
"type": "string"
},
"tubeId": {
"type": "string"
},
"qcReports": {
"type": "array",
"items": {
"type": "object",
"properties": {
"qcReportType": {
"type": "string"
},
"comments": {
"type": "string"
},
"investigatorDecision": {
"type": "string"
}
},
"required": []
}
},
"libraries": {
"type": "array",
"items": {
"type": "object",
"properties": {
"barcodeId": {
"type": "string"
},
"barcodeIndex": {
"type": "string"
},
"libraryIgoId": {
"type": "string"
},
"libraryVolume": {
"type": "number"
},
"libraryConcentrationNgul": {
"type": "number"
},
"captureConcentrationNm": {
"type": "string"
},
"captureInputNg": {
"type": "string"
},
"captureName": {
"type": "string"
},
"runs": {
"type": "array",
"items": {
"type": "object",
"properties": {
"runMode": {
"type": "string"
},
"runId": {
"type": "string"
},
"flowCellId": {
"type": "string"
},
"readLength": {
"type": "string"
},
"runDate": {
"type": "string"
},
"flowCellLanes": {
"type": "array",
"items": {
"type": "number"
}
},
"fastqs": {
"type": "array",
"items": {
"type": "string"
}
}
},
"required": []
}
}
},
"required": []
}
},
"cmoPatientId": {
"type": "string"
},
"igoId": {
"type": "string"
},
"investigatorSampleId": {
"type": "string"
},
"species": {
"type": "string"
},
"sex": {
"type": "string"
},
"tumorOrNormal": {
"type": "string"
},
"preservation": {
"type": "string"
},
"specimenType": {
"type": "string"
},
"sampleOrigin": {
"type": "string"
},
"tissueLocation": {
"type": "string"
},
"baitSet": {
"type": "string"
},
"igoComplete": {
"type": "boolean"
},
"cmoSampleIdFields": {
"type": "object",
"properties": {
"naToExtract": {
"type": "string"
},
"sampleType": {
"type": "string"
},
"normalizedPatientId": {
"type": "string"
},
"recipe": {
"type": "string"
}
},
"required": [
"sampleType",
"recipe"
]
},
"status": {
"type": "object",
"properties": {
"validationStatus": {
"type": "boolean"
},
"validationReport": {
"type": "string"
}
},
"required": [
"validationStatus",
"validationReport"
]
}
},
"required": [
"cmoSampleClass",
"cmoPatientId",
"igoId",
"investigatorSampleId",
"specimenType",
"sampleOrigin",
"baitSet",
"igoComplete",
"cmoSampleIdFields"
]
}
},
"pooledNormals": {
"type": "array",
"items": {
"type": "string"
}
},
"projectId": {
"type": "string"
}
},
"required": [
"requestId",
"recipe",
"isCmoRequest",
"bicAnalysis",
"samples",
"pooledNormals",
"projectId"
]
}
{
"requestId": "MOCKREQUEST1_B",
"recipe": "GENESET101_BAITS",
"projectManagerName": "Bar, Foo",
"piEmail": "[email protected]",
"labHeadName": "Foo Bar",
"labHeadEmail": "[email protected]",
"investigatorName": "John Smith",
"investigatorEmail": "[email protected]",
"dataAnalystName": "Poin Dexter",
"dataAnalystEmail": "[email protected]",
"otherContactEmails": "[email protected]",
"dataAccessEmails": "",
"qcAccessEmails": "",
"isCmoRequest": true,
"bicAnalysis": false,
"samples": [
{
"cmoSampleName": "C-MP789JR-X001-d",
"sampleName": "XXX002_P3_12345_L1",
"cmoSampleClass": "Primary",
"oncoTreeCode": "CLL",
"collectionYear": "",
"tubeId": "",
"qcReports": [
{
"qcReportType": "LIBRARY",
"comments": "",
"investigatorDecision": "Continue processing"
}
],
"libraries": [
{
"barcodeId": "IDT29",
"barcodeIndex": "ATTGAGGA",
"libraryIgoId": "MOCKREQUEST1_B_1_1_1_1",
"libraryVolume": 35.0,
"libraryConcentrationNgul": 34.8,
"captureConcentrationNm": "11.49425287356322",
"captureInputNg": "400.0",
"captureName": "Pool-MOCKREQUEST1_B-Tube7_1",
"runs": [
{
"runMode": "HiSeq High Output",
"runId": "RUNID_0123",
"flowCellId": "X5KL2KKAY",
"readLength": "",
"runDate": "2018-06-05",
"flowCellLanes": [
5
],
"fastqs": [
"/FASTQ/Project_MOCKREQUEST1_B/Sample_XXX002_P3_12345_L1_IGO_MOCKREQUEST1_B_1/XXX002_P3_12345_L1_IGO_MOCKREQUEST1_B_1_S82_R1_001.fastq.gz",
"/FASTQ/Project_MOCKREQUEST1_B/Sample_XXX002_P3_12345_L1_IGO_MOCKREQUEST1_B_1/XXX002_P3_12345_L1_IGO_MOCKREQUEST1_B_1_S82_R2_001.fastq.gz"
]
}
]
}
],
"cmoPatientId": "C-MP789JR",
"igoId": "MOCKREQUEST1_B_1",
"investigatorSampleId": "XXX002_P3_12345_L1",
"species": "Human",
"sex": "F",
"tumorOrNormal": "Tumor",
"preservation": "Frozen",
"specimenType": "PDX",
"sampleOrigin": "Tissue",
"tissueLocation": "",
"baitSet": "GENESET101_BAITS",
"igoComplete": true,
"cmoSampleIdFields": {
"naToExtract": "",
"sampleType": "Tissue",
"normalizedPatientId": "MRN_REDACTED",
"recipe": "GENESET101_BAITS"
},
"status": {
"validationStatus": true,
"validationReport": "{}"
}
},
{
"cmoSampleName": "C-MP789JR-N001-d",
"sampleName": "01-0012345a",
"cmoSampleClass": "Normal",
"oncoTreeCode": "CLL",
"collectionYear": "",
"tubeId": "",
"qcReports": [
{
"qcReportType": "LIBRARY",
"comments": "",
"investigatorDecision": "Continue processing"
}
],
"libraries": [
{
"barcodeId": "TNG41",
"barcodeIndex": "CGACTGGA",
"libraryIgoId": "MOCKREQUEST1_B_2_1_1_1",
"libraryVolume": 35.0,
"libraryConcentrationNgul": 33.5,
"captureConcentrationNm": "5.074626865671642",
"captureInputNg": "170.0",
"captureName": "Pool-MOCKREQUEST1_B-Tube7_1",
"runs": [
{
"runMode": "HiSeq High Output",
"runId": "RUNID_0123",
"flowCellId": "X5KL2KKAY",
"readLength": "",
"runDate": "2018-06-05",
"flowCellLanes": [
5
],
"fastqs": [
"/FASTQ/Project_MOCKREQUEST1_B/Sample_01-0012345a_IGO_MOCKREQUEST1_B_2/01-0012345a_IGO_MOCKREQUEST1_B_2_S83_R2_001.fastq.gz",
"/FASTQ/Project_MOCKREQUEST1_B/Sample_01-0012345a_IGO_MOCKREQUEST1_B_2/01-0012345a_IGO_MOCKREQUEST1_B_2_S83_R1_001.fastq.gz"
]
}
]
}
],
"cmoPatientId": "C-MP789JR",
"igoId": "MOCKREQUEST1_B_2",
"investigatorSampleId": "01-0012345a",
"species": "Human",
"sex": "F",
"tumorOrNormal": "Normal",
"preservation": "Frozen",
"specimenType": "Blood",
"sampleOrigin": "Whole Blood",
"tissueLocation": "",
"baitSet": "GENESET101_BAITS",
"igoComplete": true,
"cmoSampleIdFields": {
"naToExtract": "",
"sampleType": "Whole Blood",
"normalizedPatientId": "MRN_REDACTED",
"recipe": "GENESET101_BAITS"
},
"status": {
"validationStatus": true,
"validationReport": "{}"
}
},
{
"cmoSampleName": "C-8DH24X-X001-d",
"sampleName": "XXX002_P1_12348a_R_43",
"cmoSampleClass": "Primary",
"oncoTreeCode": "COAD",
"collectionYear": "",
"tubeId": "",
"qcReports": [
{
"qcReportType": "LIBRARY",
"comments": "",
"investigatorDecision": "Continue processing"
}
],
"libraries": [
{
"barcodeId": "TNG53",
"barcodeIndex": "GCTCGGTA",
"libraryIgoId": "MOCKREQUEST1_B_3_1_1_1",
"libraryVolume": 35.0,
"libraryConcentrationNgul": 35.2,
"captureConcentrationNm": "11.363636363636363",
"captureInputNg": "400.0",
"captureName": "Pool-MOCKREQUEST1_B-Tube7_1",
"runs": [
{
"runMode": "HiSeq High Output",
"runId": "RUNID_0123",
"flowCellId": "X5KL2KKAY",
"readLength": "",
"runDate": "2018-06-05",
"flowCellLanes": [
5
],
"fastqs": [
"/FASTQ/Project_MOCKREQUEST1_B/Sample_XXX002_P1_12348a_R_43_IGO_MOCKREQUEST1_B_3/XXX002_P1_12348a_R_43_IGO_MOCKREQUEST1_B_3_S84_R1_001.fastq.gz",
"/FASTQ/Project_MOCKREQUEST1_B/Sample_XXX002_P1_12348a_R_43_IGO_MOCKREQUEST1_B_3/XXX002_P1_12348a_R_43_IGO_MOCKREQUEST1_B_3_S84_R2_001.fastq.gz"
]
}
]
}
],
"cmoPatientId": "C-8DH24X",
"igoId": "MOCKREQUEST1_B_3",
"investigatorSampleId": "XXX002_P1_12348a_R_43",
"species": "Human",
"sex": "M",
"tumorOrNormal": "Tumor",
"preservation": "Frozen",
"specimenType": "PDX",
"sampleOrigin": "Tissue",
"tissueLocation": "",
"baitSet": "GENESET101_BAITS",
"igoComplete": true,
"cmoSampleIdFields": {
"naToExtract": "",
"sampleType": "Tissue",
"normalizedPatientId": "MRN_REDACTED",
"recipe": "GENESET101_BAITS"
},
"status": {
"validationStatus": true,
"validationReport": "{}"
}
},
{
"cmoSampleName": "C-8DH24X-N001-d",
"sampleName": "01-XXXXXXXa",
"cmoSampleClass": "Normal",
"oncoTreeCode": "COAD",
"collectionYear": "",
"tubeId": "",
"qcReports": [
{
"qcReportType": "LIBRARY",
"comments": "",
"investigatorDecision": "Continue processing"
}
],
"libraries": [
{
"barcodeId": "TNG65",
"barcodeIndex": "TGGAACAA",
"libraryIgoId": "MOCKREQUEST1_B_4_1_1_1",
"libraryVolume": 35.0,
"libraryConcentrationNgul": 34.1,
"captureConcentrationNm": "4.9853372434017595",
"captureInputNg": "170.0",
"captureName": "Pool-MOCKREQUEST1_B-Tube7_1",
"runs": [
{
"runMode": "HiSeq High Output",
"runId": "RUNID_0123",
"flowCellId": "X5KL2KKAY",
"readLength": "",
"runDate": "2018-06-05",
"flowCellLanes": [
5
],
"fastqs": [
"/FASTQ/Project_MOCKREQUEST1_B/Sample_01-XXXXXXXa_IGO_MOCKREQUEST1_B_4/01-XXXXXXXa_IGO_MOCKREQUEST1_B_4_S85_R1_001.fastq.gz",
"/FASTQ/Project_MOCKREQUEST1_B/Sample_01-XXXXXXXa_IGO_MOCKREQUEST1_B_4/01-XXXXXXXa_IGO_MOCKREQUEST1_B_4_S85_R2_001.fastq.gz"
]
}
]
}
],
"cmoPatientId": "C-8DH24X",
"igoId": "MOCKREQUEST1_B_4",
"investigatorSampleId": "01-XXXXXXXa",
"species": "Human",
"sex": "M",
"tumorOrNormal": "Normal",
"preservation": "Frozen",
"specimenType": "Blood",
"sampleOrigin": "Whole Blood",
"tissueLocation": "",
"baitSet": "GENESET101_BAITS",
"igoComplete": true,
"cmoSampleIdFields": {
"naToExtract": "",
"sampleType": "Whole Blood",
"normalizedPatientId": "MRN_REDACTED",
"recipe": "GENESET101_BAITS"
},
"status": {
"validationStatus": true,
"validationReport": "{}"
}
}
],
"pooledNormals": [
"/FASTQ/Project_POOLEDNORMALS/Sample_FFPEPOOLEDNORMAL_IGO_GENESET101_TAGCTTGA/FFPEPOOLEDNORMAL_IGO_GENESET101_TAGCTTGA_S23_R1_001.fastq.gz",
"/FASTQ/Project_POOLEDNORMALS/Sample_FFPEPOOLEDNORMAL_IGO_GENESET101_TAGCTTGA/FFPEPOOLEDNORMAL_IGO_GENESET101_TAGCTTGA_S23_R2_001.fastq.gz",
"/FASTQ/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_AMBIGUOUS_TTAGGCTG/FROZENPOOLEDNORMAL_IGO_AMBIGUOUS_TTAGGCTG_S86_R1_001.fastq.gz",
"/FASTQ/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_AMBIGUOUS_TTAGGCTG/FROZENPOOLEDNORMAL_IGO_AMBIGUOUS_TTAGGCTG_S86_R2_001.fastq.gz",
"/FASTQ/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_HEMESET_v1_TTAGGCTG/FROZENPOOLEDNORMAL_IGO_HEMESET_v1_TTAGGCTG_S147_R1_001.fastq.gz",
"/FASTQ/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_HEMESET_v1_TTAGGCTG/FROZENPOOLEDNORMAL_IGO_HEMESET_v1_TTAGGCTG_S147_R2_001.fastq.gz",
"/FASTQ/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_GENESET101_TTAGGCTG/FROZENPOOLEDNORMAL_IGO_GENESET101_TTAGGCTG_S196_R1_001.fastq.gz",
"/FASTQ/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_GENESET101_TTAGGCTG/FROZENPOOLEDNORMAL_IGO_GENESET101_TTAGGCTG_S196_R2_001.fastq.gz",
"/FASTQ/Project_POOLEDNORMALS/Sample_MOUSEPOOLEDNORMAL_IGO_AMBIGUOUS_GGCGTCAT/MOUSEPOOLEDNORMAL_IGO_AMBIGUOUS_GGCGTCAT_S61_R1_001.fastq.gz",
"/FASTQ/Project_POOLEDNORMALS/Sample_MOUSEPOOLEDNORMAL_IGO_AMBIGUOUS_GGCGTCAT/MOUSEPOOLEDNORMAL_IGO_AMBIGUOUS_GGCGTCAT_S61_R2_001.fastq.gz"
],
"projectId": "MOCKREQUEST1"
}