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Adding example for gene panel creation
This adds an example for the creation of a gene panel, by intersecting gene Ids and selected CNV types. Applied at the /biosamples (or /individuals, /analyses...) entry type the aggregation will report the number of samples affected by e.g. a high-level deletion involving CDKN2A.
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‎docs/aggregations.md‎

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@@ -460,8 +460,7 @@ the `results` section.
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},
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{
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"count": 339,
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"ids": [
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"[P18M, P10Y)"],
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"ids": ["[P18M, P10Y)"],
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"names": ["1.5 to 10 years"]
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},
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{
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]
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```
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=== "Gene Panel Aggregations - `aggr5`"
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#### Request
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This requests aggregates sets of genes and the types of variants they're affected
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by with. The `CancerPanelGeneIds` aggregation term is defined in the `/aggregation_terms` endpoint and provides a list of genes that are part of a cancer panel. The `VariantVRSCNVtype` aggregation term is also defined in the `/aggregation_terms` endpoint and provides a list of variant types (e.g., high-level loss, high-level gain) that are associated with the genes in the cancer panel.
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As above, the `selectors` modifiers would not be needed if already indicated
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in the respective aggregation term definitions.
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```json
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"aggregators" : [
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{
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"requestId": "aggr5",
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"aggregationTerms": [
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{
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"id": "CancerPanelGeneIds",
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"label": "Cancer Panel Genes",
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"selectors": [
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{"value": "CDKN2A"},
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{"value": "TP53"},
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{"value": "EGFR"},
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{"value": "MYCN"}
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]
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},
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{
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"id": "VariantVRSCNVtype",
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"selectors": [
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{"label": "high-level loss", "value": "EFO:0020073"
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},
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{"label": "high-level gain", "value": "EFO:0030072"
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}
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]
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}
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]
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}
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]
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```
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#### Response
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This aggregation response is a two-dimensional aggregation of the counts of samples with specific gene variants (high-level loss or gain) for a set of cancer panel genes. The `categoriesAndValues` section provides the counts for each combination of gene and variant type.
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This represents a typical application for generating a "gene panel dashboard".
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```json
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"resultsAggregation": [
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{
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"requestId": "aggr5",
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"aggregationTerms": [
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{"id": "CancerPanelGeneIds", "label": "Cancer Panel Genes"},
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{"id": "VariantVRSCNVtype"}
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],
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"categoriesAndValues": [
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{
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"count": 277,
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"ids": ["CDKN2A", "EFO:0020073"],
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"names": ["CDKN2A", "high-level loss"]
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},
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{
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"count": 0,
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"ids": ["CDKN2A", "EFO:0030072"],
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"names": ["CDKN2A", "high-level gain"]
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},
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{
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"count": 68,
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"ids": ["TP53", "EFO:0020073"],
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"names": ["TP53", "high-level loss"]
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},
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{
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"count": 4,
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"ids": ["TP53", "EFO:0030072"],
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"names": ["TP53", "high-level gain"]
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},
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{
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"count": 0,
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"ids": ["EGFR", "EFO:0020073"],
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"names": ["EGFR", "high-level loss"]
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},
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{
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"count": 161,
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"ids": ["EGFR", "EFO:0030072"],
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"names": ["EGFR", "high-level gain"]
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},
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{
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"count": 2,
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"ids": ["MYCN", "EFO:0020073"],
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"names": ["MYCN", "high-level loss"]
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},
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{
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"count": 88,
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"ids": ["MYCN", "EFO:0030072"],
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"names": ["MYCN", "high-level gain"]
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}
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],
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}
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]
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```
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‎framework/json/requests/examples-sections/aggregationTerms-example.json‎

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}
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],
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"requestId": "aggr4"
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},
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{
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"aggregationTerms": [
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{
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"id": "CancerPanelGeneIds",
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"label": "Cancer Panel Genes",
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"selectors": [
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{
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"value": "CDKN2A"
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},
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{
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"value": "TP53"
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},
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{
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"value": "EGFR"
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},
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{
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"value": "MYCN"
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}
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]
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},
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{
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"id": "VariantVRSCNVtype",
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"selectors": [
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{
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"label": "high-level loss",
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"value": "EFO:0020073"
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},
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{
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"label": "high-level gain",
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"value": "EFO:0030072"
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}
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]
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}
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],
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"requestId": "aggr5"
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}
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]
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}

‎framework/json/responses/examples-fullDocuments/beaconAggregationTermsResponse-example.json‎

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}
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]
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},
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{
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"description": "Aggregation by the gene identifiers of the genomic variants. The gene identifiers are selected from a predefined list of cancer related genes. The gene identifiers are represented as HGNC gene symbols. Note: The very limited gene list serves as example for usually more extended gene panels.",
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"id": "CancerPanelGeneIds",
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"label": "Selected cancer related genes",
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"modelProperty": "genomicVariant.molecularAttributes.geneIds",
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"selectors": [
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{
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"value": "CDKN2A"
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},
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{
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"value": "TP53"
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},
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{
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"value": "EGFR"
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},
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{
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"value": "MYCN"
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}
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]
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},
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{
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"description": "Aggregation by the copy number variation (CNV) types of the genomic variants. The CNV types are selected VRS \"high level\" types.",
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"id": "VariantVRShighLevelCNVtypes",
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"label": "CNV types indicating a high-level gain or loss, respectively",
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"modelProperty": "genomicVariant.variation.copyChange",
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"selectors": [
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{
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"label": "high-level loss",
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"value": "EFO:0020073"
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},
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{
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"label": "high-level gain",
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"value": "EFO:0030072"
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}
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]
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},
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{
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"description": "Aggregation by the karyotypic sex of the individuals. The karyotypic sex is determined by the chromosomal composition of the individual.",
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"id": "KaryotypicSex",

‎framework/json/responses/examples-sections/beaconAggregationResults-examples.json‎

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],
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"requestId": "aggr4"
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},
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{
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"aggregationTerms": [
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{
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"id": "CancerPanelGeneIds",
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"label": "Cancer Panel Genes"
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},
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{
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"id": "VariantVRSCNVtype"
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}
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],
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"categoriesAndValues": [
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{
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"count": 277,
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"ids": [
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"CDKN2A",
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"EFO:0020073"
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],
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"names": [
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"CDKN2A",
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"high-level loss"
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]
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},
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{
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"count": 0,
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"ids": [
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"CDKN2A",
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"EFO:0030072"
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],
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"names": [
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"CDKN2A",
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"high-level gain"
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]
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},
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{
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"count": 68,
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"ids": [
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"TP53",
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"EFO:0020073"
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],
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"names": [
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"TP53",
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"high-level loss"
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]
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},
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{
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"count": 4,
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"ids": [
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"TP53",
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"EFO:0030072"
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],
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"names": [
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"TP53",
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"high-level gain"
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]
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},
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{
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"count": 0,
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"ids": [
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"EGFR",
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"EFO:0020073"
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],
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"names": [
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"EGFR",
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"high-level loss"
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]
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},
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{
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"count": 161,
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"ids": [
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"EGFR",
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"EFO:0030072"
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],
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"names": [
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"EGFR",
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"high-level gain"
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]
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},
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{
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"count": 2,
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"ids": [
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"MYCN",
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"EFO:0020073"
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],
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"names": [
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"MYCN",
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"high-level loss"
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]
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},
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{
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"count": 88,
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"ids": [
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"MYCN",
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"EFO:0030072"
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],
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"names": [
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"MYCN",
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"high-level gain"
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]
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}
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],
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"requestId": "aggr5"
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},
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{
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"aggregationTerms": [
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{
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}
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],
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"anyValueCount": 3456,
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"requestId": "aggr5"
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"requestId": "aggr6"
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},
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{
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"aggregationTerms": [
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}
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],
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"distinctValuesCount": 243062,
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"requestId": "aggr6"
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"requestId": "aggr7"
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}
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]
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}

‎framework/src/requests/examples-sections/aggregationTerms-example.yaml‎

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label: 60 years and older
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sortOrder: 4
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- requestId: aggr5
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aggregationTerms:
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- id: CancerPanelGeneIds
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label: Cancer Panel Genes
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selectors:
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- value: CDKN2A
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- value: TP53
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- value: EGFR
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- value: MYCN
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- id: VariantVRSCNVtype
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selectors:
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- value: EFO:0020073
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label: high-level loss
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- value: EFO:0030072
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label: high-level gain
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‎framework/src/responses/examples-fullDocuments/beaconAggregationTermsResponse-example.yaml‎

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label: 65 years and older
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sortOrder: 2
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- id: CancerPanelGeneIds
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label: Selected cancer related genes
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modelProperty: genomicVariant.molecularAttributes.geneIds
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description: >-
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Aggregation by the gene identifiers of the genomic variants. The gene
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identifiers are selected from a predefined list of cancer related genes.
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The gene identifiers are represented as HGNC gene symbols.
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Note: The very limited gene list serves as example for usually more extended
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gene panels.
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selectors:
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- value: CDKN2A
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- value: TP53
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- value: EGFR
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- value: MYCN
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- id: VariantVRShighLevelCNVtypes
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label: CNV types indicating a high-level gain or loss, respectively
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modelProperty: genomicVariant.variation.copyChange
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description: >-
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Aggregation by the copy number variation (CNV) types of the genomic
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variants. The CNV types are selected VRS "high level" types.
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selectors:
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- value: EFO:0020073
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label: high-level loss
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- value: EFO:0030072
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label: high-level gain
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- id: KaryotypicSex
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label: karyotypic sex
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modelProperty: individual.karyotypicSex

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