{ "$schema": "https://json-schema.org/draft/2020-12/schema", "title": "Basic structures", "description": "Non-identifiable structures", "type": "object", "definitions": { "AlignmentMetrics": { "description": "Used by alignment dataset to store AlignmentMetrics\n", "type": "object", "properties": { "sequencing_type": { "$ref": "core.json#/definitions/SequencingType" }, "vendor": { "$ref": "core.json#/definitions/Vendor" }, "mean_depth": { "type": "number" }, "median_insert_size": { "type": "number" } } }, "Billing": { "title": "Billing Information", "description": "Options are currently self-pay, insurance, and institutional billing.", "type": "array", "maxItems": 1, "items": { "oneOf": [ { "$ref": "#/definitions/BillingSelf" }, { "$ref": "#/definitions/BillingInsurance" }, { "$ref": "#/definitions/BillingInstitutional" } ] } }, "BillingInsurance": { "title": "Insurance Billing (Commercial, Medicaid, Medicare)", "additionalProperties": false, "type": "object", "properties": { "billing_type": { "type": "string", "title": "Billing Type", "default": "INSURANCE", "enum": [ "INSURANCE" ] }, "insurance": { "type": "array", "minItems": 1, "maxItems": 2, "items": { "$ref": "#/definitions/Insurance" } } }, "required": [ "billing_type", "insurance" ] }, "BillingSelf": { "title": "Patient Pay", "additionalProperties": false, "type": "object", "properties": { "billing_type": { "type": "string", "title": "Billing Type", "default": "SELF", "enum": [ "SELF" ] }, "stripe_paymentintent_id": { "type": "string" }, "promo_code": { "type": "string" } }, "required": [ "billing_type" ] }, "BillingInstitutional": { "title": "Institutional Billing", "additionalProperties": false, "type": "object", "properties": { "billing_type": { "type": "string", "title": "Billing Type", "default": "INSTITUTIONAL", "enum": [ "INSTITUTIONAL" ] }, "billing_code": { "type": "string", "maxLength": 64, "title": "Billing Code", "description": "Institutional code for billing" } }, "required": [ "billing_type" ] }, "File": { "type": "object", "required": [ "uri", "mimetype" ], "properties": { "uri": { "type": "string" }, "mimetype": { "type": "string" }, "description": { "type": "string" }, "sha512": { "type": "string", "pattern": "^[0-9a-fA-F]{128}$" }, "crc64nvme": { "type": "string", "pattern": "^[A-Za-z0-9+/_-]{11}=$" }, "sha256": { "type": "string", "pattern": "^[0-9a-fA-F]{64}$" } }, "examples": [ { "uri": "s3://somebucket/path/to/report.json", "description": "Report in JSON format", "mimetype": "application/json", "sha512": "1b3c34b32bba4ece72a7b9a1ee53359fe7238be5986984463b5da41baf3b53bce66c87d7f5557021c553a1bbeac175eac2b4923329b993fba11a93502c256912" }, { "uri": "s3://somebucket/path/to/report.pdf", "description": "Report in PDF format", "mimetype": "application/pdf", "sha512": "cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e" }, { "uri": "s3://somebucket/path/to/SM123.R1.fastq.gz", "description": "R1 FastQ file", "mimetype": "application/x.seq-na-fastq;type=paired_end;direction=R1", "sha512": "3ef109fe55e194a0f37b5936405dcf2b96ce7eeb8891d59650c708d26f256d018fd8f98c6efb7da8f85029a3708e34f86a54e700ba3b36fb0967aa869ed37915" } ] }, "Gene": { "type": "object", "additionalProperties": false, "properties": { "ncbi_gene_id": { "title": "NCBI Gene ID", "type": "string" }, "primary_symbol": { "title": "Primary Symbol", "type": "string" }, "alternate_symbols": { "title": "Alternate Symbols", "type": "array", "items": { "type": "string" }, "uniqueItems": true }, "references": { "title": "Gene References", "type": "array", "items": { "$ref": "#/definitions/Reference" } } }, "examples": [ { "ncbi_gene_id": 672, "primary_symbol": "BRCA1", "alternate_symbols": [ "BRCAI", "BRCC1", "FANCS", "IRIS", "PNCA4", "PSCP" ], "references": [ { "type": "pubmed", "value": "123456" } ] } ] }, "Genotype": { "type": "object", "additionalProperties": false, "properties": { "gene_symbol": { "type": "string", "examples": [ "CYP2B6", "CYP2C19", "CYP2D6" ] }, "haplotypes": { "type": "string", "examples": [ "*3/*4", "*5/*17", "*1/*8" ] } } }, "PGxDrugGuidance": { "type": "object", "additionalProperties": false, "properties": { "drug": { "type": "string", "examples": [ "amphetamine", "codeine" ] }, "genes": { "description": "list of dictionaries with gene and phenotype corresponding to a drug impact", "type": "array", "items": { "$ref": "#/definitions/PGxFinding" } }, "therapeutic_area": { "type": "string", "description": "future plans for drug categories to reference an enum (SC-7141)", "examples": [ "BEHAVIORAL_HEALTH", "PAIN_MANAGEMENT", "CARDIOLOGY" ] }, "toplines": { "description": "future plans for finding in toplines to reference an enum (SC-7141)", "type": "object", "allOf": [ { "$ref": "#/definitions/ToplineFinding" }, { "properties": { "finding": { "$ref": "core.json#/definitions/PGxImpactToplineFinding" } } } ], "examples": [ { "finding": "CONTRAINDICATED", "text": "Avoid codeine use because of potential for serous toxicity. If opioid use is warranted, consider a non-tramadol opioid." } ] } } }, "PGxFinding": { "type": "object", "additionalProperties": false, "properties": { "raw_call": { "type": "string", "example": "*4/*6" }, "rsid_based": { "type": "boolean", "example": false }, "activity_score": { "type": "number", "example": 1.0 }, "genotype": { "$ref": "#/definitions/Genotype" }, "gene_phenotype": { "$ref": "core.json#/definitions/PGxGenePhenotype" }, "reference": { "$ref": "#/definitions/Reference" } } }, "Reference": { "description": "Stores a reference or citation to external data\nThe following types of Reference are supported:\n\n * `doi`: stores a refernece to a [Digital Object Identifier](https://www.doi.org/). **NOTE: pubmed should be preferred over doi for scientific publications.**\n * `pubmed`: stores a reference to a [PubMed](https://pubmed.ncbi.nlm.nih.gov/) identifier as the `value`. The PubMed identifier may be replaced with the publication title, authors, etc. during rendering. \n * `url`: stores a reference to a website (typically starting with `https:`).\n\nThe `display` property, if set, contains text that will be used when representing the reference in written docuemnts. ", "type": "object", "additionalProperties": false, "required": [ "type", "value" ], "properties": { "display": { "title": "Display", "description": "Text to display for reference", "type": "string" }, "type": { "title": "Type", "type": "string", "enum": [ "doi", "pubmed", "url" ] }, "value": { "title": "Value", "type": "string" }, "accessed_at": { "title": "Accessed At", "oneOf": [ { "$ref": "core.json#/definitions/Date", "title": "Date" }, { "$ref": "core.json#/definitions/UTCTimestamp", "title": "Datetime" } ] } }, "examples": [ { "type": "doi", "value": "10.1007/10753.1573-2576", "display": "Inflammation" }, { "type": "pubmed", "value": "123456" }, { "type": "url", "value": "https://cpicpgx.org/guidelines/cpic-guideline-for-proton-pump-inhibitors-and-cyp2c19/", "display": "CPIC CYP2C19 Guidelines", "accessed_at": "2018-11-13T20:20:39+00:00" } ] }, "Lab": { "type": "object", "additionalProperties": false, "properties": { "name": { "type": "string" }, "address": { "$ref": "#/definitions/Address" }, "clia_number": { "type": "string" }, "cap_number": { "type": "string" }, "directors": { "type": "array", "items": { "$ref": "#/definitions/LabDirector" } }, "clinical_scientists": { "type": "array", "items": { "type": "object", "properties": { "name": { "$ref": "#/definitions/Name" } } } }, "product_mapping": { "description": "Maps internal sequencing protocols to their corresponding product id at the lab.", "type": "object", "propertyNames": { "$ref": "./core.json#/definitions/SequencingProtocol" }, "additionalProperties": { "type": "string" } }, "test_properties": { "type": "object", "description": "Additional properties to include in the report when this lab is used.", "propertyNames": { "$ref": "./core.json#/definitions/ConfirmationMethod" }, "additionalProperties": { "type": "object", "properties": { "methods": { "type": "array", "items": { "type": "string" } }, "limitations": { "type": "array", "items": { "type": "string" } } }, "additionalProperties": false } } }, "required": [ "name" ], "examples": [ { "name": "MyOme", "address": { "city": "San Carlos", "country": "USA", "postal_code": "94070", "region": "CA", "street_address": "930 Brittan Ave" }, "clia_number": null, "cap_number": null, "directors": [ { "_id": "I/daea778e-11eb-6447", "email": "ford@myclinic.com", "fax": "415-555-1212", "name": { "first": "Ford", "last": "Prefect", "title": "Dr." }, "phone": "+1-415-555-1212" } ], "product_mapping": { "HC_WGS": "C_WGS" } } ] }, "ProductDataCAD": { "type": "object", "title": "Inputs for IPRS CAD", "additionalProperties": false, "required": [ "smoking", "diabetes", "cholesterol", "blood_pressure" ], "properties": { "smoking": { "$ref": "./requisition_observations/smoking.json" }, "diabetes": { "$ref": "./requisition_observations/diabetes.json" }, "cholesterol": { "$ref": "./requisition_observations/cholesterol.json" }, "blood_pressure": { "$ref": "./requisition_observations/blood_pressure.json" } } }, "ProductDataPR41003": { "type": "object", "title": "Inputs for IPRS Breast Cancer", "description": "Additional data needed for iPRS Breast Cancer", "additionalProperties": false, "properties": { "weight": { "$ref": "./requisition_observations/weight.json" }, "height": { "$ref": "./requisition_observations/height.json" }, "ashkenazi_jewish": { "$ref": "./requisition_observations/ashkenazi_jewish.json" }, "tyrer_cuzick_inputs": { "$ref": "./requisition_observations/tyrer_cuzick_inputs.json" } } }, "ProductDataPR41003WithDependencies": { "type": "object", "title": "Inputs for IPRS Breast Cancer", "description": "Additional data needed for iPRS Breast Cancer", "additionalProperties": false, "properties": { "weight": { "$ref": "./requisition_observations/weight.json" }, "height": { "$ref": "./requisition_observations/height.json" }, "ashkenazi_jewish": { "$ref": "./requisition_observations/ashkenazi_jewish.json" }, "tyrer_cuzick_inputs": { "$ref": "./requisition_observations/tyrer_cuzick_inputs_with_dependencies.json" } } }, "ProductDataPR4001Empower": { "type": "object", "description": "Additional data needed for product ID PR4001 with TC outputs and a data sample", "required": [ "tc_data", "data_files", "data_sample_info" ], "properties": { "tc_data": { "type": "object", "description": "Extra data required for computation. The content requirements depend on the selected product ID.", "additionalProperties": false, "required": [ "five_year_risk", "lifetime_risk", "n_first_degree_affected" ], "properties": { "five_year_risk": { "description": "Five year risk score in decimal format.", "type": "number", "minimum": 0, "maximum": 1 }, "lifetime_risk": { "description": "Lifetime year risk score in decimal format.", "type": "number", "minimum": 0, "maximum": 1 }, "n_first_degree_affected": { "description": "Number of first degree", "type": "integer" } } }, "data_files": { "type": "array", "items": { "type": "object", "$ref": "#/definitions/File" } }, "data_sample_info": { "type": "object", "additionalProperties": false, "required": [ "collection_date", "received_date", "sample_type" ], "properties": { "sample_type": { "type": "string", "enum": [ "DATA" ] }, "collection_date": { "type": "string", "pattern": "[12]\\d{3}-[01]\\d-[0123]\\d" }, "received_date": { "type": "string", "pattern": "[12]\\d{3}-[01]\\d-[0123]\\d" } } } }, "example": { "tc_data": { "five_year_risk": 0.012, "lifetime_risk": 0.022, "n_first_degree_affected": 2 }, "data_files": [ { "uri": "s3://bucket/R1.fastq", "sha512": "3b7fc7cc370707c1df045c35342f3d64ea7076", "description": "R1 Fastq sequence", "mimetype": "application/x.seq-na-fastq;type=paired_end;direction=R1" }, { "uri": "s3://bucket/R2.fastq", "sha512": "3b7fc7cc370707c1df045c35342f3d64ea7076", "description": "R2 Fastq sequence", "mimetype": "application/x.seq-na-fastq;type=paired_end;direction=R2" } ], "data_sample_info": { "sample_type": "DATA", "collection_date": "2022-12-21", "received_date": "2022-12-23" } } }, "ProductDataT2D": { "type": "object", "title": "Inputs for IPRS T2D", "additionalProperties": false, "required": [ "smoking", "glucose", "triglyceride", "cholesterol", "blood_pressure", "diabetes_family_history", "body_mass_index", "waist_circumference" ], "properties": { "smoking": { "$ref": "./requisition_observations/smoking.json" }, "cholesterol": { "$ref": "./requisition_observations/cholesterol.json" }, "glucose": { "$ref": "./requisition_observations/glucose.json" }, "triglyceride": { "$ref": "./requisition_observations/triglyceride.json" }, "blood_pressure": { "$ref": "./requisition_observations/blood_pressure.json" }, "diabetes_family_history": { "$ref": "./requisition_observations/diabetes_family_history.json" }, "body_mass_index": { "$ref": "./requisition_observations/body_mass_index.json" }, "waist_circumference": { "$ref": "./requisition_observations/waist_circumference.json" } } }, "ProductDataPRC": { "type": "object", "title": "Inputs for IPRS PRC", "additionalProperties": false, "required": [ "diagnosed_with_prostate_cancer", "prostate_cancer_family_history" ], "properties": { "diagnosed_with_prostate_cancer": { "$ref": "./requisition_observations/diagnosed_with_prostate_cancer.json" }, "prostate_cancer_family_history": { "$ref": "./requisition_observations/prostate_cancer_family_history.json" } } }, "Signature": { "type": "object", "additionalProperties": false, "properties": { "image": { "type": "string", "description": "base64 encoded data url Tip: Generate with `convert signature.png -quality 70 -geometry 400x400 inline:gif:-`", "examples": [ "data:image/gif;base64,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" ] }, "user": { "type": "string", "examples": [ "U/61be-4d38-644f" ] }, "name": { "$ref": "#/definitions/Name", "examples": [ { "first": "Random", "last": "Person" } ] }, "email": { "type": "string", "format": "email", "examples": [ "random.person@somelab.com" ] }, "utc_timestamp": { "$ref": "core.json#/definitions/UTCTimestamp" } } }, "ReportNextSteps": { "title": "Next Steps", "type": "array", "items": { "type": "string" }, "example": [ "Women with an estimated lifetime breast cancer risk of 20% or higher should speak with their healthcare provider about American Cancer Society (ACS) guidelines for increased breast cancer surveillance as outlined below, as well as published recommendations for risk-reducing agents and comprehensive risk assessment.", "Annual mammograms starting at age 40 or 10 years younger than the earliest breast cancer diagnosis in the family (but no earlier than age 30)\\n", "Annual breast MRI starting at age 40 or 10 years younger than the earliest breast cancer diagnosis in the family (but no earlier than age 25)\\n", "These results should be interpreted in the context of the individual's personal medical history and family history. The patient's female relatives may wish to speak with their healthcare provider to undergo a personalized risk assessment." ] }, "PRSNextSteps": { "title": "PRS Next Steps", "type": "object", "description": "Specifies next steps for a given risk level.", "properties": { "general_guidance": { "type": "string", "description": "General guidance for this PRS type, regardless of risk." }, "risk_level_specific": { "type": "string", "description": "Risk-level-specific guidance." } }, "required": [ "general_guidance", "risk_level_specific" ] }, "FamilyVariantVariation": { "type": "object", "additionalProperties": false, "properties": { "event": { "title": "Variant", "type": "string" }, "display": { "title": "Variant Analyzed", "type": "string" }, "summary": { "title": "Variant Summary", "type": "string" }, "size_mb": { "title": "Size in Mb (If applicable)", "type": "number" } }, "required": [ "event", "display" ], "examples": [ { "event": "c.1359+601A>G", "display": "NM_000466.3:c.1359+601A>G", "summary": "PEX1 gene, NM_000466.3:c.1359+601A>G, Uncertain Significance" } ] }, "RareDiseaseVariation": { "type": "object", "additionalProperties": false, "properties": { "hgvs_g_38": { "title": "HGVS (g.) - GRCh38", "type": [ "string", "null" ], "$ref": "core.json#/definitions/HGVSExpressionOrNone" }, "hgvs_g_37": { "title": "HGVS (g.) - GRCh37", "type": [ "string", "null" ], "$ref": "core.json#/definitions/HGVSExpressionOrNone" }, "hgvs_t": { "title": "HGVS (c.)", "type": [ "string", "null" ], "$ref": "core.json#/definitions/HGVSExpressionOrNone" }, "hgvs_p": { "title": "HGVS (p.)", "type": [ "string", "null" ], "$ref": "core.json#/definitions/HGVSExpressionOrNone" }, "display": { "title": "Variant Display", "type": [ "string", "null" ] }, "chromosome_region": { "title": "Chromosome Region", "$ref": "core.json#/definitions/ChromosomeRegion" } }, "required": [ "display" ], "examples": [ { "hgvs_g_38": "NC_000017.11:g.43045685T>C", "hgvs_g_37": "NC_000017.11:g.43045685T>C", "hgvs_t": "NM_007294.4(BRCA1):c.5585A>G", "hgvs_p": "NP_009225.1:p.His1862Arg", "display": "NM_007294.4(BRCA1):c.5585A>G (p.His1862Arg)", "chromosome_region": "chr17:1000-2000" } ] }, "TREVariation": { "type": "object", "additionalProperties": false, "required": [ "display", "alleles" ], "properties": { "hgvs_g_38": { "title": "HGVS (g.) - GRCh38", "type": [ "string", "null" ], "$ref": "core.json#/definitions/HGVSExpressionOrNone" }, "display": { "title": "Display", "type": [ "string", "null" ] }, "chromosome_region": { "title": "Chromosome Region", "$ref": "core.json#/definitions/ChromosomeRegion" }, "alleles": { "title": "Alleles", "type": "object", "additionalProperties": false, "properties": { "allele1": { "$ref": "#/definitions/TREVariationAllele" }, "allele2": { "$ref": "#/definitions/TREVariationAllele" } } } }, "examples": [ { "hgvs_g_38": "NC_000014.9:g.[92071010CAG[100]];[92071010CAG[100]]", "display": "NC_000014.9:g.[92071010CAG[100]];[92071010CAG[100]]", "chromosome_region": "chr17:1000-2000" } ] }, "TREVariationAllele": { "type": "object", "additionalProperties": false, "required": [ "repeat_count", "motif", "repeat_range", "classification_group", "classification" ], "properties": { "hgvs_g_38": { "title": "HGVS (g.) - GRCh38", "type": [ "string", "null" ] }, "repeat_count": { "title": "Repeat Count", "type": "integer" }, "motif": { "title": "Repeat Motif", "type": "string" }, "event": { "title": "Pathogenic event", "type": "string" }, "repeat_range": { "title": "Repeat Range", "type": "array", "minItems": 1, "maxItems": 2, "items": { "type": "integer" } }, "classification_group": { "title": "Classification Group", "type": "string" }, "classification": { "title": "ACMG Classification", "$ref": "core.json#/definitions/ACMGPlusNegativeClassification" }, "number": { "type": "integer" } }, "examples": [ { "hgvs_g_38": "NC_000014.9:g.[92071010CAG[100]]", "repeat_count": 100, "repeat_range": [ 30, 10000 ], "event": "\u226530 CAG repeats", "classification_group": "pathogenic", "classification": "PATHOGENIC" } ] }, "RareDiseaseQCMetrics": { "type": "object", "additionalProperties": false, "properties": { "mean_depth": { "title": "Mean Depth", "type": "number", "examples": [ 35.8 ] }, "qc_10x_cov_perc": { "title": "QC 10x Coverage Percentage", "type": "number", "examples": [ 0.953 ] } } }, "SampleRequest": { "type": "object", "title": "Sample Request", "properties": { "send_kit": { "title": "Send Kit", "type": "boolean" }, "send_kit_address": { "$ref": "#/definitions/Address" }, "type": { "$ref": "core.json#/definitions/SampleType" } }, "required": [ "send_kit", "type" ], "examples": [ { "type": "Saliva", "send_kit": true, "send_kit_address": { "city": "San Carlos", "country": "USA", "postal_code": "94070", "region": "CA", "street_address": "930 Brittan Ave" } } ] }, "Supersedes": { "type": "object", "additionalProperties": false, "properties": { "report_id": { "$ref": "ids.json#/definitions/ReportId" }, "report_date": { "$ref": "core.json#/definitions/Date" }, "supersede_type": { "$ref": "core.json#/definitions/SupersedeType" }, "changes": { "type": "array", "items": { "type": "object", "properties": { "original": { "type": "string" }, "revised": { "type": "string" } } }, "example": [ { "original": "a negative report", "revised": "a pathogenic BRCA2 report" }, { "original": "sample ID SM-12345", "revised": "sample ID SM-67890" } ] } } }, "Variation": { "type": "object", "additionalProperties": false, "properties": { "hgvs_g": { "title": "HGVS (g.) - Legacy. Retained for backwards compatibility", "$ref": "core.json#/definitions/HGVSExpression" }, "hgvs_g_37": { "title": "HGVS (g.) - GRCh37", "$ref": "core.json#/definitions/HGVSExpression" }, "hgvs_g_38": { "title": "HGVS (g.) - GRCh38", "type": [ "string", "null" ], "$ref": "core.json#/definitions/HGVSExpressionOrNone" }, "hgvs_t": { "title": "HGVS (c.)", "$ref": "core.json#/definitions/HGVSExpression" }, "hgvs_p": { "title": "HGVS (p.)", "$ref": "core.json#/definitions/HGVSExpression" }, "display": { "title": "Display", "type": "string" } }, "required": [ "display" ], "examples": [ { "hgvs_g": "NC_000017.11:g.43045685T>C", "hgvs_g_37": "NC_000017.11:g.43045685T>C", "hgvs_g_38": "NC_000017.11:g.43045685T>C", "hgvs_t": "NM_007294.4(BRCA1):c.5585A>G", "hgvs_p": "NP_009225.1:p.His1862Arg", "display": "NM_007294.4(BRCA1):c.5585A>G (p.His1862Arg)" } ] }, "VariationClassification": { "type": "object", "additionalProperties": false, "required": [ "classification" ], "properties": { "variantfinding_id": { "$ref": "ids.json#/definitions/VariantFindingId" }, "finding_type": { "$ref": "core.json#/definitions/FindingType" }, "disease": { "title": "Disease", "type": "string", "examples": [ "PMS2 is associated with..." ] }, "variation": { "title": "Variation", "$ref": "#/definitions/Variation" }, "event": { "title": "Pathogenic event", "type": "string" }, "gene": { "title": "Gene", "$ref": "#/definitions/Gene" }, "classification": { "title": "ACMG Classification", "anyOf": [ { "$ref": "core.json#/definitions/ACMGClassification" }, { "const": "NEGATIVE" } ] }, "mode_of_inheritance": { "$ref": "core.json#/definitions/Inheritance" }, "zygosity": { "$ref": "core.json#/definitions/Zygosity" }, "evidence": { "title": "Evidence", "type": "string", "examples": [ "This variant has been seen in % of the individuals with condition. Has been observed to segreate with disease in at least on ene condition.\nFor these reasons the variant has been classified as pathogenic.\n* This variant has been seen in XXX% of the individuals with condition. Has been observed to segreate with disease in at least on econdition. * For these reasons the variant has been classified as pathogenic." ] }, "references": { "title": "References", "type": "array", "items": { "$ref": "#/definitions/Reference" } } } }, "LabDirector": { "type": "object", "required": [ "name", "npi" ], "properties": { "name": { "$ref": "#/definitions/Name" }, "npi": { "$ref": "core.json#/definitions/NPI" } } }, "Address": { "type": "object", "additionalProperties": false, "properties": { "street_address": { "type": "string", "title": "Street Address", "description": "Number and street" }, "street_address_2": { "type": [ "string", "null" ], "title": "Street Address Line 2" }, "city": { "type": "string", "title": "City" }, "region": { "type": "string", "title": "Region", "description": "State, province, or other country-specific region" }, "postal_code": { "type": "string", "title": "Postal Code", "description": "Country-specific code for geographic districts" }, "country": { "type": [ "string", "null" ], "title": "Country", "description": "Country name or abbreviation" } }, "required": [ "street_address", "city", "region", "postal_code" ], "examples": [ { "street_address": "930 Brittan Ave", "city": "San Carlos", "region": "CA", "postal_code": "94070", "country": "USA" } ] }, "AddressOptional": { "type": "object", "additionalProperties": false, "properties": { "street_address": { "type": "string", "title": "Street Address", "description": "Number and street" }, "street_address_2": { "type": [ "string", "null" ], "title": "Street Address Line 2" }, "city": { "type": "string", "title": "City" }, "region": { "type": "string", "title": "Region", "description": "State, province, or other country-specific region" }, "postal_code": { "type": "string", "title": "Postal Code", "description": "Country-specific code for geographic districts" }, "country": { "type": [ "string", "null" ], "title": "Country", "description": "Country name or abbreviation" } }, "examples": [ { "street_address": "930 Brittan Ave", "city": "San Carlos", "region": "CA", "postal_code": "94070", "country": "USA" } ] }, "ContactInfo": { "type": "object", "additionalProperties": false, "properties": { "address": { "title": "Address", "$ref": "#/definitions/Address" }, "email": { "$ref": "core.json#/definitions/EmailAddress" }, "phone": { "type": "string", "title": "Phone Number" }, "fax": { "type": [ "string", "null" ], "title": "Fax Number" } } }, "ContactInfoOptional": { "type": "object", "additionalProperties": false, "properties": { "address": { "title": "Address", "$ref": "#/definitions/AddressOptional" }, "email": { "$ref": "core.json#/definitions/EmailAddress" }, "phone": { "type": "string", "title": "Phone Number" }, "fax": { "type": "string", "title": "Fax Number" } } }, "ContactInfoForFamilyMember": { "type": "object", "additionalProperties": false, "properties": { "prefill_button": { "type": "string", "title": "Prefill Button" }, "address": { "title": "Address", "$ref": "#/definitions/Address" }, "email": { "$ref": "core.json#/definitions/EmailAddress" }, "phone": { "type": "string", "title": "Phone Number" }, "fax": { "type": "string", "title": "Fax Number" } } }, "Demographics": { "type": "object", "title": "Demographics", "properties": { "dob": { "$ref": "core.json#/definitions/Date", "title": "Date of Birth", "description": "mm/dd/yyyy" }, "sex": { "$ref": "core.json#/definitions/BiologicalSex", "title": "Sex" }, "gender": { "$ref": "core.json#/definitions/Gender" } } }, "Insurance": { "title": "Insurance information", "type": "object", "required": [ "policyholder_name", "company", "member_id", "relationship_to_policyholder" ], "properties": { "policyholder_name": { "title": "Policy Holder Name", "$ref": "#/definitions/Name", "required": [ "first", "last" ] }, "policyholder_dob": { "title": "Policyholder Date of Birth", "$ref": "core.json#/definitions/Date", "description": "mm/dd/yyyy" }, "policyholder_sex": { "title": "Policyholder Sex", "$ref": "core.json#/definitions/BiologicalSex" }, "policyholder_address": { "title": "Policyholder Address", "$ref": "#/definitions/Address" }, "company": { "title": "Name of Insurance Company", "type": "string" }, "phone": { "title": "Insurance Phone Number", "type": "string" }, "member_id": { "title": "Member ID", "type": "string" }, "group_number": { "title": "Group Number", "type": "string" }, "prior_auth_number": { "title": "Prior Authorization Number", "type": "string" }, "relationship_to_policyholder": { "title": "Patient Relationship to Policyholder", "description": "", "$ref": "core.json#/definitions/Relationship" }, "relationship_to_policyholder_other": { "title": "Patient Relationship to Policyholder Other: ", "type": "string" }, "epsdt_coverage": { "title": "EPSDT Coverage", "description": "If the patient is under 21 years old and has a Medicaid plan, please provide the following information for Early and Periodic Screening, Diagnosis, and Treatment (EPSDT) coverage.", "type": "object", "properties": { "medicaid_plan": { "title": "Medicaid Plan", "type": "string" }, "medicaid_number": { "title": "Medicaid Number", "type": "string" }, "attestations": { "title": "I attest that test results will impact medical management, including treatment or care decisions as follows:", "type": "array", "items": { "type": "string", "enum": [ "My patient may be eligible for specific drug therapies or clinical trials", "My patient may be referred for additional medical consultations and/or support services for additional treatments and surveillance", "My patient's medication may change if genetic findings indicate risk for adverse reactions or poor drug metabolism" ] }, "uniqueItems": true } } } } }, "Link": { "type": "object", "properties": { "uri": { "type": "string", "format": "uri" }, "display": { "type": "string" } } }, "Name": { "type": "object", "title": "Name", "additionalProperties": false, "properties": { "first": { "type": "string", "title": "First" }, "middle": { "type": [ "string", "null" ], "title": "Middle" }, "last": { "type": "string", "title": "Last" }, "credentials": { "type": [ "string", "null" ], "title": "Credentials", "description": "e.g. M.D., Ph.D." } }, "examples": [ { "first": "Zaphod", "middle": "Vogon", "last": "Beeblebrox", "credentials": "M.D., Ph.D." } ] }, "ToplineFinding": { "properties": { "finding": { "title": "Finding", "anyOf": [ { "$ref": "core.json#/definitions/MonogenicToplineFinding" }, { "$ref": "core.json#/definitions/PRSToplineFinding" }, { "$ref": "core.json#/definitions/PGxImpactToplineFinding" }, { "$ref": "core.json#/definitions/RareDiseaseToplineFinding" } ], "type": "string" }, "text": { "title": "Text", "type": "string" } }, "required": [ "finding", "text" ] }, "Text": { "description": "NOT IN USE YET", "type": "object", "properties": { "format": { "type": "string", "enum": [ "plain", "markdown" ], "default": "plain" }, "value": { "type": "string" } } }, "LogItem": { "type": "object", "additionalProperties": false, "properties": { "facility": { "type": "string" }, "ts": { "$ref": "core.json#/definitions/UTCTimestamp" }, "level": { "$ref": "core.json#/definitions/LogLevel" }, "text": { "type": "string" } }, "examples": [ { "facility": "pipeline", "level": "WARNING", "ts": "2018-11-13T20:20:39+00:00", "text": "oops!" }, { "facility": "secondary", "level": "INFO", "ts": "2018-11-13T20:20:39+00:00", "text": "Sample is not human!" } ] }, "Consent": { "type": "object", "properties": { "type": { "$ref": "core.json#/definitions/ConsentType" }, "protocol_id": { "type": "string" } } }, "ExternalIdentifiers": { "type": "object", "description": "External identifiers that can be associated with reports", "additionalProperties": false, "properties": { "external_order_id": { "type": "string" }, "external_clinic_id": { "type": "string" }, "external_deidentified_id": { "type": "string" }, "original_external_order_id": { "type": "string" } }, "examples": [ { "external_order_id": "1234567890" }, { "external_clinic_id": "Clinic-0123456" }, { "external_deidentified_id": "1231-2312-3123-1231" }, { "original_external_order_id": "1234567891" } ] } } }