Biomarker¶
Referenced schema · Source · Dereferenced version
A Cat-VRS CategoricalVariant. Root type Biomarker with one subtype per biomarker_type value.
Root type shared by every biomarker. Subtypes below are selected by the biomarker_type field; the top-level schema closes the record.
Fields¶
| Field | Type | Required | Description |
|---|---|---|---|
id |
string matching ^bmkr:\d+$ |
yes | |
type |
always CategoricalVariant |
yes | |
name |
string | yes | |
allele |
string or null matching ^ga4gh:VA.[A-Za-z0-9_-]{32}$ |
yes | Foreign key to alleles.id. |
copyChange |
string or null matching ^copy_change:efo:\d+$ |
yes | Foreign key to copy_changes.id. |
function |
string or null matching ^func:so:\d+$ |
yes | Foreign key to function_consequences.id. |
genes |
array of string matching ^gene:hgnc:\d+$ |
yes | |
location |
array of string matching ^ga4gh:SL.[A-Za-z0-9_-]{32}$ |
yes | |
biomarker_type |
one of Copy number, Copy number (arm level), Gene fusion, Germline variant, Haplotype genotype, Homologous recombination, Microsatellite stability, Mismatch repair, Protein expression, Rearrangement, Somatic variant, Translocation, Tumor mutational burden, Wild type |
yes | |
extensions |
array of Extension | yes |
Subtypes¶
Every record matches exactly one subtype, which adds to the fields above.
| Subtype | Applies when | Description |
|---|---|---|
| Copy Number | biomarker_type is Copy number |
Gene-level copy number change. |
| Copy Number (arm level) | biomarker_type is Copy number (arm level) |
Chromosome arm-level copy number change. |
| Gene fusion | biomarker_type is Gene fusion |
Gene fusion: one or two partner genes joined via an AdjacencyConstraint at dereference time. Shares Rearrangement base's shape. |
| Germline Variant | biomarker_type is Germline variant |
Germline variant in a single gene. |
| Haplotype genotype | biomarker_type is Haplotype genotype |
Haplotype genotype, e.g. HLA-A*02:01. |
| Homologous Recombination | biomarker_type is Homologous recombination |
Homologous recombination status. |
| Microsatellite Stability | biomarker_type is Microsatellite stability |
Microsatellite instability status. |
| Mismatch Repair | biomarker_type is Mismatch repair |
Mismatch repair status. |
| Protein expression | biomarker_type is Protein expression |
Protein expression, e.g. PD-L1 TPS >= 1%. |
| Rearrangement | biomarker_type is Rearrangement |
Chromosomal rearrangement that is neither a gene fusion nor a translocation (see Gene fusion, Translocation). Shares Rearrangement base's shape. |
| Somatic Variant | biomarker_type is Somatic variant |
Somatic variant in a single gene. |
| Translocation | biomarker_type is Translocation |
Chromosomal translocation between one or two partner genes. Shares Rearrangement base's shape. |
| Tumor mutational burden | biomarker_type is Tumor mutational burden |
Tumor mutational burden classification. |
| Wild type | biomarker_type is Wild type |
Absence of variants in a gene. |
Copy Number¶
Gene-level copy number change.
Builds on Biomarker.
| Field | Type | Required | Description |
|---|---|---|---|
biomarker_type |
always Copy number |
||
extensions |
array of extensions: cytoband (string or null, required) |
||
genes |
array (exactly 1 item) | ||
allele |
null | ||
location |
array (at most 0 items) | ||
copyChange |
string | ||
function |
null |
Copy Number (arm level)¶
Chromosome arm-level copy number change.
Builds on Biomarker.
| Field | Type | Required | Description |
|---|---|---|---|
biomarker_type |
always Copy number (arm level) |
||
extensions |
array of extensions: chromosome (string, required), arm (one of p, q, required) |
||
genes |
array (at most 0 items) | ||
allele |
null | ||
location |
array (exactly 1 item) | ||
copyChange |
string | ||
function |
null |
Gene fusion¶
Gene fusion: one or two partner genes joined via an AdjacencyConstraint at dereference time. Shares Rearrangement base's shape.
Builds on Rearrangement base.
| Field | Type | Required | Description |
|---|---|---|---|
biomarker_type |
always Gene fusion |
||
genes |
array (1 to 2 items) | ||
location |
array (at most 0 items) |
Germline Variant¶
Germline variant in a single gene.
Builds on Biomarker.
| Field | Type | Required | Description |
|---|---|---|---|
biomarker_type |
always Germline variant |
||
extensions |
array of extensions: chromosome (string, required), start_position (integer or null, required), end_position (integer or null, required), reference_allele (string or null, required), alternate_allele (string or null, required), cdna_change (string or null, required), protein_change (string or null, required), variant_annotation (string or null, required), exon (integer or string or null, required), rsid (string or null, required), hgvsg (string or null, required), hgvsc (string or null, required), requires_pathogenic (boolean, required) |
||
genes |
array (exactly 1 item) | ||
allele |
null | ||
location |
array (exactly 1 item) | ||
copyChange |
null | ||
function |
null |
Haplotype genotype¶
Haplotype genotype, e.g. HLA-A*02:01.
Builds on Biomarker.
| Field | Type | Required | Description |
|---|---|---|---|
biomarker_type |
always Haplotype genotype |
||
genes |
array (at most 0 items) | ||
allele |
null | ||
location |
array (at most 0 items) | ||
copyChange |
null | ||
function |
null |
Homologous Recombination¶
Homologous recombination status.
Builds on Biomarker.
| Field | Type | Required | Description |
|---|---|---|---|
biomarker_type |
always Homologous recombination |
||
extensions |
array of extensions: status (string, required) |
||
genes |
array (at most 0 items) | ||
allele |
null | ||
location |
array (at most 0 items) | ||
copyChange |
null | ||
function |
null |
Microsatellite Stability¶
Microsatellite instability status.
Builds on Biomarker.
| Field | Type | Required | Description |
|---|---|---|---|
biomarker_type |
always Microsatellite stability |
||
extensions |
array of extensions: status (one of Microsatellite instability-high (MSI-H), Microsatellite instability-low (MSI-L), Microsatellite stable (MSS), required) |
||
genes |
array (at most 0 items) | ||
allele |
null | ||
location |
array (at most 0 items) | ||
copyChange |
null | ||
function |
null |
Mismatch Repair¶
Mismatch repair status.
Builds on Biomarker.
| Field | Type | Required | Description |
|---|---|---|---|
biomarker_type |
always Mismatch repair |
||
extensions |
array of extensions: status (one of Deficient, Proficient, required) |
||
genes |
array (at most 0 items) | ||
allele |
null | ||
location |
array (at most 0 items) | ||
copyChange |
null | ||
function |
null |
Protein expression¶
Protein expression, e.g. PD-L1 TPS >= 1%.
Builds on Biomarker.
| Field | Type | Required | Description |
|---|---|---|---|
biomarker_type |
always Protein expression |
||
extensions |
array of extensions: marker (string, required), unit (string, required), equality (one of =, >=, <=, <, >, required), value (number or string, required) |
||
genes |
array (at most 0 items) | ||
allele |
null | ||
location |
array (at most 0 items) | ||
copyChange |
null | ||
function |
null |
Rearrangement¶
Chromosomal rearrangement that is neither a gene fusion nor a translocation (see Gene fusion, Translocation). Shares Rearrangement base's shape.
Builds on Rearrangement base.
| Field | Type | Required | Description |
|---|---|---|---|
biomarker_type |
always Rearrangement |
||
genes |
array (at most 2 items) | ||
location |
array (at most 0 items) |
Somatic Variant¶
Somatic variant in a single gene.
Builds on Biomarker.
| Field | Type | Required | Description |
|---|---|---|---|
biomarker_type |
always Somatic variant |
||
extensions |
array of extensions: chromosome (string, required), start_position (integer or null, required), end_position (integer or null, required), reference_allele (string or null, required), alternate_allele (string or null, required), cdna_change (string or null, required), protein_change (string or null, required), variant_annotation (string or null, required), exon (integer or string or null, required), hgvsg (string or null, required), hgvsc (string or null, required), rsid (string or null), requires_oncogenic (boolean) |
||
genes |
array (exactly 1 item) | ||
copyChange |
null |
Translocation¶
Chromosomal translocation between one or two partner genes. Shares Rearrangement base's shape.
Builds on Rearrangement base.
| Field | Type | Required | Description |
|---|---|---|---|
biomarker_type |
always Translocation |
||
genes |
array (at most 2 items) | ||
location |
array (at most 2 items) |
Tumor mutational burden¶
Tumor mutational burden classification.
Builds on Biomarker.
| Field | Type | Required | Description |
|---|---|---|---|
biomarker_type |
always Tumor mutational burden |
||
extensions |
array of extensions: classification (string, required), minimum_mutations (number or null, required), minimum_mutations_per_megabase (number or null, required) |
||
genes |
array (at most 0 items) | ||
allele |
null | ||
location |
array (at most 0 items) | ||
copyChange |
null | ||
function |
null |
Wild type¶
Absence of variants in a gene.
Builds on Biomarker.
| Field | Type | Required | Description |
|---|---|---|---|
biomarker_type |
always Wild type |
||
genes |
array (exactly 1 item) | ||
allele |
null | ||
location |
array (exactly 1 item) | ||
copyChange |
null | ||
function |
null |
Definitions¶
Rearrangement base¶
Structural shape shared by Rearrangement, Translocation, and Gene fusion: no allele, copy change, or function consequence, and no extensions besides biomarker_type. Each subtype sets its own location constraint.
Builds on Biomarker.
| Field | Type | Required | Description |
|---|---|---|---|
allele |
null | ||
copyChange |
null | ||
function |
null |
JSON Schema¶
Full JSON Schema
{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"$id": "https://moalmanac.org/schemas/referenced/biomarkers.schema.json",
"title": "Biomarker",
"description": "A Cat-VRS CategoricalVariant. Root type `Biomarker` with one subtype per `biomarker_type` value.",
"$ref": "#/$defs/Biomarker",
"allOf": [
{
"if": {
"required": [
"biomarker_type"
],
"properties": {
"biomarker_type": {
"const": "Copy number"
}
}
},
"then": {
"$ref": "#/$defs/Copy Number"
}
},
{
"if": {
"required": [
"biomarker_type"
],
"properties": {
"biomarker_type": {
"const": "Copy number (arm level)"
}
}
},
"then": {
"$ref": "#/$defs/Copy Number (arm level)"
}
},
{
"if": {
"required": [
"biomarker_type"
],
"properties": {
"biomarker_type": {
"const": "Gene fusion"
}
}
},
"then": {
"$ref": "#/$defs/Gene fusion"
}
},
{
"if": {
"required": [
"biomarker_type"
],
"properties": {
"biomarker_type": {
"const": "Germline variant"
}
}
},
"then": {
"$ref": "#/$defs/Germline Variant"
}
},
{
"if": {
"required": [
"biomarker_type"
],
"properties": {
"biomarker_type": {
"const": "Haplotype genotype"
}
}
},
"then": {
"$ref": "#/$defs/Haplotype genotype"
}
},
{
"if": {
"required": [
"biomarker_type"
],
"properties": {
"biomarker_type": {
"const": "Homologous recombination"
}
}
},
"then": {
"$ref": "#/$defs/Homologous Recombination"
}
},
{
"if": {
"required": [
"biomarker_type"
],
"properties": {
"biomarker_type": {
"const": "Microsatellite stability"
}
}
},
"then": {
"$ref": "#/$defs/Microsatellite Stability"
}
},
{
"if": {
"required": [
"biomarker_type"
],
"properties": {
"biomarker_type": {
"const": "Mismatch repair"
}
}
},
"then": {
"$ref": "#/$defs/Mismatch Repair"
}
},
{
"if": {
"required": [
"biomarker_type"
],
"properties": {
"biomarker_type": {
"const": "Protein expression"
}
}
},
"then": {
"$ref": "#/$defs/Protein expression"
}
},
{
"if": {
"required": [
"biomarker_type"
],
"properties": {
"biomarker_type": {
"const": "Rearrangement"
}
}
},
"then": {
"$ref": "#/$defs/Rearrangement"
}
},
{
"if": {
"required": [
"biomarker_type"
],
"properties": {
"biomarker_type": {
"const": "Somatic variant"
}
}
},
"then": {
"$ref": "#/$defs/Somatic Variant"
}
},
{
"if": {
"required": [
"biomarker_type"
],
"properties": {
"biomarker_type": {
"const": "Translocation"
}
}
},
"then": {
"$ref": "#/$defs/Translocation"
}
},
{
"if": {
"required": [
"biomarker_type"
],
"properties": {
"biomarker_type": {
"const": "Tumor mutational burden"
}
}
},
"then": {
"$ref": "#/$defs/Tumor mutational burden"
}
},
{
"if": {
"required": [
"biomarker_type"
],
"properties": {
"biomarker_type": {
"const": "Wild type"
}
}
},
"then": {
"$ref": "#/$defs/Wild type"
}
}
],
"unevaluatedProperties": false,
"$defs": {
"Biomarker": {
"description": "Root type shared by every biomarker. Subtypes below are selected by the `biomarker_type` field; the top-level schema closes the record.",
"type": "object",
"required": [
"id",
"type",
"name",
"allele",
"copyChange",
"function",
"genes",
"location",
"biomarker_type",
"extensions"
],
"properties": {
"id": {
"type": "string",
"pattern": "^bmkr:\\d+$"
},
"type": {
"const": "CategoricalVariant"
},
"name": {
"type": "string"
},
"allele": {
"type": [
"string",
"null"
],
"pattern": "^ga4gh:VA\\.[A-Za-z0-9_-]{32}$",
"description": "Foreign key to `alleles.id`."
},
"copyChange": {
"type": [
"string",
"null"
],
"pattern": "^copy_change:efo:\\d+$",
"description": "Foreign key to `copy_changes.id`."
},
"function": {
"type": [
"string",
"null"
],
"pattern": "^func:so:\\d+$",
"description": "Foreign key to `function_consequences.id`."
},
"genes": {
"type": "array",
"items": {
"type": "string",
"pattern": "^gene:hgnc:\\d+$",
"description": "Foreign key to `genes.id`."
}
},
"location": {
"type": "array",
"items": {
"type": "string",
"pattern": "^ga4gh:SL\\.[A-Za-z0-9_-]{32}$",
"description": "Foreign key to `sequence_locations.id`."
}
},
"biomarker_type": {
"enum": [
"Copy number",
"Copy number (arm level)",
"Gene fusion",
"Germline variant",
"Haplotype genotype",
"Homologous recombination",
"Microsatellite stability",
"Mismatch repair",
"Protein expression",
"Rearrangement",
"Somatic variant",
"Translocation",
"Tumor mutational burden",
"Wild type"
]
},
"extensions": {
"type": "array",
"items": {
"$ref": "extension.schema.json"
}
}
}
},
"Copy Number": {
"description": "Gene-level copy number change.",
"allOf": [
{
"$ref": "#/$defs/Biomarker"
},
{
"properties": {
"biomarker_type": {
"const": "Copy number"
},
"extensions": {
"type": "array",
"items": {
"anyOf": [
{
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "cytoband"
},
"value": {
"type": [
"string",
"null"
]
}
}
}
]
},
"allOf": [
{
"contains": {
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "cytoband"
},
"value": {
"type": [
"string",
"null"
]
}
}
}
}
]
},
"genes": {
"type": "array",
"minItems": 1,
"maxItems": 1
},
"allele": {
"type": "null"
},
"location": {
"type": "array",
"maxItems": 0
},
"copyChange": {
"type": "string"
},
"function": {
"type": "null"
}
}
}
]
},
"Copy Number (arm level)": {
"description": "Chromosome arm-level copy number change.",
"allOf": [
{
"$ref": "#/$defs/Biomarker"
},
{
"properties": {
"biomarker_type": {
"const": "Copy number (arm level)"
},
"extensions": {
"type": "array",
"items": {
"anyOf": [
{
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "chromosome"
},
"value": {
"type": "string"
}
}
},
{
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "arm"
},
"value": {
"enum": [
"p",
"q"
]
}
}
}
]
},
"allOf": [
{
"contains": {
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "chromosome"
},
"value": {
"type": "string"
}
}
}
},
{
"contains": {
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "arm"
},
"value": {
"enum": [
"p",
"q"
]
}
}
}
}
]
},
"genes": {
"type": "array",
"maxItems": 0
},
"allele": {
"type": "null"
},
"location": {
"type": "array",
"minItems": 1,
"maxItems": 1
},
"copyChange": {
"type": "string"
},
"function": {
"type": "null"
}
}
}
]
},
"Gene fusion": {
"description": "Gene fusion: one or two partner genes joined via an AdjacencyConstraint at dereference time. Shares `Rearrangement base`'s shape.",
"allOf": [
{
"$ref": "#/$defs/Rearrangement base"
},
{
"properties": {
"biomarker_type": {
"const": "Gene fusion"
},
"genes": {
"type": "array",
"minItems": 1,
"maxItems": 2
},
"location": {
"type": "array",
"maxItems": 0
}
}
}
]
},
"Germline Variant": {
"description": "Germline variant in a single gene.",
"allOf": [
{
"$ref": "#/$defs/Biomarker"
},
{
"properties": {
"biomarker_type": {
"const": "Germline variant"
},
"extensions": {
"type": "array",
"items": {
"anyOf": [
{
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "chromosome"
},
"value": {
"type": "string"
}
}
},
{
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "start_position"
},
"value": {
"type": [
"integer",
"null"
]
}
}
},
{
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "end_position"
},
"value": {
"type": [
"integer",
"null"
]
}
}
},
{
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "reference_allele"
},
"value": {
"type": [
"string",
"null"
]
}
}
},
{
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "alternate_allele"
},
"value": {
"type": [
"string",
"null"
]
}
}
},
{
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "cdna_change"
},
"value": {
"type": [
"string",
"null"
]
}
}
},
{
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "protein_change"
},
"value": {
"type": [
"string",
"null"
]
}
}
},
{
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "variant_annotation"
},
"value": {
"type": [
"string",
"null"
]
}
}
},
{
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "exon"
},
"value": {
"type": [
"integer",
"string",
"null"
]
}
}
},
{
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "rsid"
},
"value": {
"type": [
"string",
"null"
]
}
}
},
{
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "hgvsg"
},
"value": {
"type": [
"string",
"null"
]
}
}
},
{
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "hgvsc"
},
"value": {
"type": [
"string",
"null"
]
}
}
},
{
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "requires_pathogenic"
},
"value": {
"type": "boolean"
}
}
}
]
},
"allOf": [
{
"contains": {
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "chromosome"
},
"value": {
"type": "string"
}
}
}
},
{
"contains": {
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "start_position"
},
"value": {
"type": [
"integer",
"null"
]
}
}
}
},
{
"contains": {
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "end_position"
},
"value": {
"type": [
"integer",
"null"
]
}
}
}
},
{
"contains": {
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "reference_allele"
},
"value": {
"type": [
"string",
"null"
]
}
}
}
},
{
"contains": {
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "alternate_allele"
},
"value": {
"type": [
"string",
"null"
]
}
}
}
},
{
"contains": {
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "cdna_change"
},
"value": {
"type": [
"string",
"null"
]
}
}
}
},
{
"contains": {
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "protein_change"
},
"value": {
"type": [
"string",
"null"
]
}
}
}
},
{
"contains": {
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "variant_annotation"
},
"value": {
"type": [
"string",
"null"
]
}
}
}
},
{
"contains": {
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "exon"
},
"value": {
"type": [
"integer",
"string",
"null"
]
}
}
}
},
{
"contains": {
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "rsid"
},
"value": {
"type": [
"string",
"null"
]
}
}
}
},
{
"contains": {
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "hgvsg"
},
"value": {
"type": [
"string",
"null"
]
}
}
}
},
{
"contains": {
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "hgvsc"
},
"value": {
"type": [
"string",
"null"
]
}
}
}
},
{
"contains": {
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "requires_pathogenic"
},
"value": {
"type": "boolean"
}
}
}
}
]
},
"genes": {
"type": "array",
"minItems": 1,
"maxItems": 1
},
"allele": {
"type": "null"
},
"location": {
"type": "array",
"minItems": 1,
"maxItems": 1
},
"copyChange": {
"type": "null"
},
"function": {
"type": "null"
}
}
}
]
},
"Haplotype genotype": {
"description": "Haplotype genotype, e.g. HLA-A*02:01.",
"allOf": [
{
"$ref": "#/$defs/Biomarker"
},
{
"properties": {
"biomarker_type": {
"const": "Haplotype genotype"
},
"genes": {
"type": "array",
"maxItems": 0
},
"allele": {
"type": "null"
},
"location": {
"type": "array",
"maxItems": 0
},
"copyChange": {
"type": "null"
},
"function": {
"type": "null"
}
}
}
]
},
"Homologous Recombination": {
"description": "Homologous recombination status.",
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{
"$ref": "#/$defs/Biomarker"
},
{
"properties": {
"biomarker_type": {
"const": "Homologous recombination"
},
"extensions": {
"type": "array",
"items": {
"anyOf": [
{
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "status"
},
"value": {
"type": "string"
}
}
}
]
},
"allOf": [
{
"contains": {
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "status"
},
"value": {
"type": "string"
}
}
}
}
]
},
"genes": {
"type": "array",
"maxItems": 0
},
"allele": {
"type": "null"
},
"location": {
"type": "array",
"maxItems": 0
},
"copyChange": {
"type": "null"
},
"function": {
"type": "null"
}
}
}
]
},
"Microsatellite Stability": {
"description": "Microsatellite instability status.",
"allOf": [
{
"$ref": "#/$defs/Biomarker"
},
{
"properties": {
"biomarker_type": {
"const": "Microsatellite stability"
},
"extensions": {
"type": "array",
"items": {
"anyOf": [
{
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "status"
},
"value": {
"enum": [
"Microsatellite instability-high (MSI-H)",
"Microsatellite instability-low (MSI-L)",
"Microsatellite stable (MSS)"
]
}
}
}
]
},
"allOf": [
{
"contains": {
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "status"
},
"value": {
"enum": [
"Microsatellite instability-high (MSI-H)",
"Microsatellite instability-low (MSI-L)",
"Microsatellite stable (MSS)"
]
}
}
}
}
]
},
"genes": {
"type": "array",
"maxItems": 0
},
"allele": {
"type": "null"
},
"location": {
"type": "array",
"maxItems": 0
},
"copyChange": {
"type": "null"
},
"function": {
"type": "null"
}
}
}
]
},
"Mismatch Repair": {
"description": "Mismatch repair status.",
"allOf": [
{
"$ref": "#/$defs/Biomarker"
},
{
"properties": {
"biomarker_type": {
"const": "Mismatch repair"
},
"extensions": {
"type": "array",
"items": {
"anyOf": [
{
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "status"
},
"value": {
"enum": [
"Deficient",
"Proficient"
]
}
}
}
]
},
"allOf": [
{
"contains": {
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "status"
},
"value": {
"enum": [
"Deficient",
"Proficient"
]
}
}
}
}
]
},
"genes": {
"type": "array",
"maxItems": 0
},
"allele": {
"type": "null"
},
"location": {
"type": "array",
"maxItems": 0
},
"copyChange": {
"type": "null"
},
"function": {
"type": "null"
}
}
}
]
},
"Protein expression": {
"description": "Protein expression, e.g. PD-L1 TPS >= 1%.",
"allOf": [
{
"$ref": "#/$defs/Biomarker"
},
{
"properties": {
"biomarker_type": {
"const": "Protein expression"
},
"extensions": {
"type": "array",
"items": {
"anyOf": [
{
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "marker"
},
"value": {
"type": "string"
}
}
},
{
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "unit"
},
"value": {
"type": "string"
}
}
},
{
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "equality"
},
"value": {
"enum": [
"=",
">=",
"<=",
"<",
">"
]
}
}
},
{
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "value"
},
"value": {
"type": [
"number",
"string"
]
}
}
}
]
},
"allOf": [
{
"contains": {
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "marker"
},
"value": {
"type": "string"
}
}
}
},
{
"contains": {
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "unit"
},
"value": {
"type": "string"
}
}
}
},
{
"contains": {
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "equality"
},
"value": {
"enum": [
"=",
">=",
"<=",
"<",
">"
]
}
}
}
},
{
"contains": {
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "value"
},
"value": {
"type": [
"number",
"string"
]
}
}
}
}
]
},
"genes": {
"type": "array",
"maxItems": 0
},
"allele": {
"type": "null"
},
"location": {
"type": "array",
"maxItems": 0
},
"copyChange": {
"type": "null"
},
"function": {
"type": "null"
}
}
}
]
},
"Rearrangement": {
"description": "Chromosomal rearrangement that is neither a gene fusion nor a translocation (see `Gene fusion`, `Translocation`). Shares `Rearrangement base`'s shape.",
"allOf": [
{
"$ref": "#/$defs/Rearrangement base"
},
{
"properties": {
"biomarker_type": {
"const": "Rearrangement"
},
"genes": {
"type": "array",
"maxItems": 2
},
"location": {
"type": "array",
"maxItems": 0
}
}
}
]
},
"Rearrangement base": {
"description": "Structural shape shared by `Rearrangement`, `Translocation`, and `Gene fusion`: no allele, copy change, or function consequence, and no extensions besides `biomarker_type`. Each subtype sets its own `location` constraint.",
"allOf": [
{
"$ref": "#/$defs/Biomarker"
},
{
"properties": {
"allele": {
"type": "null"
},
"copyChange": {
"type": "null"
},
"function": {
"type": "null"
}
}
}
]
},
"Translocation": {
"description": "Chromosomal translocation between one or two partner genes. Shares `Rearrangement base`'s shape.",
"allOf": [
{
"$ref": "#/$defs/Rearrangement base"
},
{
"properties": {
"biomarker_type": {
"const": "Translocation"
},
"genes": {
"type": "array",
"maxItems": 2
},
"location": {
"type": "array",
"maxItems": 2
}
}
}
]
},
"Somatic Variant": {
"description": "Somatic variant in a single gene.",
"allOf": [
{
"$ref": "#/$defs/Biomarker"
},
{
"properties": {
"biomarker_type": {
"const": "Somatic variant"
},
"extensions": {
"type": "array",
"items": {
"anyOf": [
{
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "chromosome"
},
"value": {
"type": "string"
}
}
},
{
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "start_position"
},
"value": {
"type": [
"integer",
"null"
]
}
}
},
{
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "end_position"
},
"value": {
"type": [
"integer",
"null"
]
}
}
},
{
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "reference_allele"
},
"value": {
"type": [
"string",
"null"
]
}
}
},
{
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "alternate_allele"
},
"value": {
"type": [
"string",
"null"
]
}
}
},
{
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "cdna_change"
},
"value": {
"type": [
"string",
"null"
]
}
}
},
{
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "protein_change"
},
"value": {
"type": [
"string",
"null"
]
}
}
},
{
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "variant_annotation"
},
"value": {
"type": [
"string",
"null"
]
}
}
},
{
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "exon"
},
"value": {
"type": [
"integer",
"string",
"null"
]
}
}
},
{
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "hgvsg"
},
"value": {
"type": [
"string",
"null"
]
}
}
},
{
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "hgvsc"
},
"value": {
"type": [
"string",
"null"
]
}
}
},
{
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "rsid"
},
"value": {
"type": [
"string",
"null"
]
}
}
},
{
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "requires_oncogenic"
},
"value": {
"type": "boolean"
}
}
}
]
},
"allOf": [
{
"contains": {
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "chromosome"
},
"value": {
"type": "string"
}
}
}
},
{
"contains": {
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "start_position"
},
"value": {
"type": [
"integer",
"null"
]
}
}
}
},
{
"contains": {
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "end_position"
},
"value": {
"type": [
"integer",
"null"
]
}
}
}
},
{
"contains": {
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "reference_allele"
},
"value": {
"type": [
"string",
"null"
]
}
}
}
},
{
"contains": {
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "alternate_allele"
},
"value": {
"type": [
"string",
"null"
]
}
}
}
},
{
"contains": {
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "cdna_change"
},
"value": {
"type": [
"string",
"null"
]
}
}
}
},
{
"contains": {
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "protein_change"
},
"value": {
"type": [
"string",
"null"
]
}
}
}
},
{
"contains": {
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "variant_annotation"
},
"value": {
"type": [
"string",
"null"
]
}
}
}
},
{
"contains": {
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "exon"
},
"value": {
"type": [
"integer",
"string",
"null"
]
}
}
}
},
{
"contains": {
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "hgvsg"
},
"value": {
"type": [
"string",
"null"
]
}
}
}
},
{
"contains": {
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "hgvsc"
},
"value": {
"type": [
"string",
"null"
]
}
}
}
}
]
},
"genes": {
"type": "array",
"minItems": 1,
"maxItems": 1
},
"copyChange": {
"type": "null"
}
}
}
]
},
"Tumor mutational burden": {
"description": "Tumor mutational burden classification.",
"allOf": [
{
"$ref": "#/$defs/Biomarker"
},
{
"properties": {
"biomarker_type": {
"const": "Tumor mutational burden"
},
"extensions": {
"type": "array",
"items": {
"anyOf": [
{
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "classification"
},
"value": {
"type": "string"
}
}
},
{
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "minimum_mutations"
},
"value": {
"type": [
"number",
"null"
]
}
}
},
{
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "minimum_mutations_per_megabase"
},
"value": {
"type": [
"number",
"null"
]
}
}
}
]
},
"allOf": [
{
"contains": {
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "classification"
},
"value": {
"type": "string"
}
}
}
},
{
"contains": {
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "minimum_mutations"
},
"value": {
"type": [
"number",
"null"
]
}
}
}
},
{
"contains": {
"$ref": "extension.schema.json",
"properties": {
"name": {
"const": "minimum_mutations_per_megabase"
},
"value": {
"type": [
"number",
"null"
]
}
}
}
}
]
},
"genes": {
"type": "array",
"maxItems": 0
},
"allele": {
"type": "null"
},
"location": {
"type": "array",
"maxItems": 0
},
"copyChange": {
"type": "null"
},
"function": {
"type": "null"
}
}
}
]
},
"Wild type": {
"description": "Absence of variants in a gene.",
"allOf": [
{
"$ref": "#/$defs/Biomarker"
},
{
"properties": {
"biomarker_type": {
"const": "Wild type"
},
"genes": {
"type": "array",
"minItems": 1,
"maxItems": 1
},
"allele": {
"type": "null"
},
"location": {
"type": "array",
"minItems": 1,
"maxItems": 1
},
"copyChange": {
"type": "null"
},
"function": {
"type": "null"
}
}
}
]
}
}
}