https://progenetix.org/_next/static/chunks/pages/search-76b73abe1d008349.js

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The query is against the\nexamplez collection and can be modified e.g. through changing the position\nparameters or data source.\n',img:"/img/BeaconBracketQuery-limited-match-graphics.png",parameters:{referenceName:{isHidden:!1,defaultValue:"refseq:NC_000009.12"},start:{isHidden:!1,defaultValue:"21000001,21975098"},end:{isHidden:!1,defaultValue:"21967753,23000000"},variantType:{isHidden:!1,defaultValue:"EFO:0030067"},alternateBases:{isHidden:!0},referenceBases:{isHidden:!0},allTermsFilters:{isHidden:!1,defaultValue:["NCIT:C3058"]},analysisOperation:{isHidden:!0},sex:{isHidden:!1}}},{label:"SNV Example",note:"Example for specific EIF4A1 mutation",description:"This example shows a core Beacon query, against a specific\nmutation in the EIF4A1 gene, in the DIPG childhood brain tumor dataset.\n",parameters:{referenceName:{isHidden:!1,defaultValue:"refseq:NC_000017.11"},start:{isHidden:!1,defaultValue:7577121},variantType:{isHidden:!1,defaultValue:"SO:0001059"},alternateBases:{isHidden:!1,defaultValue:"A"},referenceBases:{isHidden:!1,defaultValue:"G"}}},{label:"Range Example",note:"Example for EIF4A1 transcript region matches (precise variants)",description:'As in the standard SNV query, this example shows a Beacon query against\nmutations in the `EIF4A1` gene in the DIPG childhood brain tumor dataset.\nHowever, this range + wildcard query will return any variant with\nalternate bases (indicated through "N").\nSince parameters will be interpreted using an "AND" paradigm, either <i>Alternate\nBases</i> OR <i>Variant Type</i> should be specified.\nThe exact variants which were being found can be retrieved through the variant\nhandover [H—>O] link.\n',parameters:{datasetIds:{isHidden:!1},referenceName:{isHidden:!1,defaultValue:"refseq:NC_000017.11"},start:{isHidden:!1,defaultValue:7572826},end:{isHidden:!1,defaultValue:7579005},variantType:{isHidden:!1,defaultValue:"SO:0001059"},alternateBases:{isHidden:!1,defaultValue:""},referenceBases:{isHidden:!1,defaultValue:""}},img:"/img/BeaconRangeQuery-graphics.png"},{label:"Gene Match",note:"Where supported beacons can discover variants overlap with the region of a known gene.\n",description:"Beacons in v2 can support the discovery of variants with overlap with the\ngenomic location of a gene, indicated by its symbol (e.g. `CDK2`). Additional\nparameters can _optionally_ be used to make matches more specific:\n- `variantMinLength` and `variantMaxLength` to limit matched CNV sizes\n- `genomicAlleleShortForm` (e.g. `V600E` with `BRAF`)\n- `variantType` and `alternateBases` to specify variants\nWhile it is not _per se_ necessary to use a filter, this example contains\na disease match filter since running against large databases such as Progenetix\nmight lead to technical problems.\n",img:"/img/BeaconGeneQuery-graphics.png",parameters:{geneId:{isHidden:!1,defaultValue:"CDK2"},referenceName:{isHidden:!0},start:{isHidden:!0},end:{isHidden:!0},variantMinLength:{isHidden:!1,defaultValue:1e4},variantMaxLength:{isHidden:!1,defaultValue:3e6},variantType:{isHidden:!1,defaultValue:"EFO:0030070"},alternateBases:{isHidden:!1},referenceBases:{isHidden:!0},allTermsFilters:{isHidden:!1,defaultValue:["pgx:icdom-85003"]}}},{label:"Identifier Example",note:"Samples can be identified through identifiers.",description:"This example retrieves _HeLa_ instances - including cell lines derived from\n_HeLa_ - by _HeLa's_ _cellosaurus_ identifier `cellosaurus:CVCL_0030`.\n",parameters:{aminoacidChange:{isHidden:!0},geneId:{isHidden:!0},referenceName:{isHidden:!0},start:{isHidden:!0},end:{isHidden:!0},variantType:{isHidden:!0},alternateBases:{isHidden:!0},referenceBases:{isHidden:!0},allTermsFilters:{isHidden:!1,defaultValue:["cellosaurus:CVCL_0030"]}}},{label:"Variant Short Form Example",note:"This is an experimental example for short form vbariant(s) support.",description:"This example shows a short form version of the CDKN2A deleti

1on example.\n",parameters:{variantQueryDigests:{isHidden:!1,defaultValue:"9:21000001-21975098--21967753-24000000:DEL"},variantType:{isHidden:!0},allTermsFilters:{isHidden:!1,defaultValue:["NCIT:C3058"]},aminoacidChange:{isHidden:!0},geneId:{isHidden:!0},referenceName:{isHidden:!0},start:{isHidden:!0},end:{isHidden:!0},alternateBases:{isHidden:!0},referenceBases:{isHidden:!0}}},{label:"Fusion Example",note:"This is an experimental example for a fusion query (by positions).\nhttp://progenetix.org/beacon/g_variants/?referenceName=8&mateName=12&start=45100000&end=47300000&mateStart=26200000&mateEnd=35600000&variantType=SO:0000806\n",description:"This is an experimental example for a fusion query (by positions).\n",img:"/img/BeaconFusionQuery-graphics.png",parameters:{variantType:{isHidden:!1,defaultValue:"SO:0000806"},allTermsFilters:{isHidden:!1},referenceName:{isHidden:!1,defaultValue:"refseq:NC_000008.11"},mateName:{isHidden:!1,defaultValue:"refseq:NC_000012.12"},start:{isHidden:!1,defaultValue:451e5},end:{isHidden:!1,defaultValue:473e5},mateStart:{isHidden:!1,defaultValue:262e5},mateEnd:{isHidden:!1,defaultValue:356e5}}}]];e.exports=n.length<=1?n[0]:n},16288:(e,n,a)=>{"use strict";a.d(n,{EJ:()=>s,FO:()=>d,Gr:()=>c,SK:()=>l,pM:()=>o,so:()=>i});var r=a(53020),t=a(26514);function s(e){var n=e.href,a=e.label,s=e.onClick;return(0,t.jsxs)("a",{href:n,onClick:s,children:[a," ",(0,t.jsx)(r.AnD,{className:"icon has-text-grey-light is-small"})]})}function c(e){var n=e.href,a=e.label,s=e.onClick;return(0,t.jsxs)("a",{href:n,rel:"noreferrer",target:"_blank",onClick:s,children:[a," ",(0,t.jsx)(r.EQc,{className:"icon has-text-info is-small"})]})}function 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1on matches.",description:'This example shows the query for CNV deletion variants overlapping the\nCDKN2A gene\'s coding region with at least a single base, but limited\nto "focal" hits (here i.e. <= ~2Mbp in size). The query is against the\nexamplez collection and can be modified e.g. through changing the position\nparameters or data source.\n',img:"/img/BeaconBracketQuery-limited-match-graphics.png",parameters:{referenceName:{isHidden:!1,defaultValue:"refseq:NC_000009.12"},start:{isHidden:!1,defaultValue:"21000001,21975098"},end:{isHidden:!1,defaultValue:"21967753,23000000"},variantType:{isHidden:!1,defaultValue:"EFO:0030067"},alternateBases:{isHidden:!0},referenceBases:{isHidden:!0},allTermsFilters:{isHidden:!1,defaultValue:["NCIT:C3058"]},analysisOperation:{isHidden:!0},sex:{isHidden:!1}}},{label:"SNV Example",note:"Example for specific EIF4A1 mutation",description:"This example shows a core Beacon query, against a specific\nmutation in the EIF4A1 gene, in the DIPG childhood brain tumor dataset.\n",parameters:{referenceName:{isHidden:!1,defaultValue:"refseq:NC_000017.11"},start:{isHidden:!1,defaultValue:7577121},variantType:{isHidden:!1,defaultValue:"SO:0001059"},alternateBases:{isHidden:!1,defaultValue:"A"},referenceBases:{isHidden:!1,defaultValue:"G"}}},{label:"Range Example",note:"Example for EIF4A1 transcript region matches (precise variants)",description:'As in the standard SNV query, this example shows a Beacon query against\nmutations in the `EIF4A1` gene in the DIPG childhood brain tumor dataset.\nHowever, this range + wildcard query will return any variant with\nalternate bases (indicated through "N").\nSince parameters will be interpreted using an "AND" paradigm, either <i>Alternate\nBases</i> OR <i>Variant Type</i> should be specified.\nThe exact variants which were being found can be retrieved through the variant\nhandover [H—>O] link.\n',parameters:{datasetIds:{isHidden:!1},referenceName:{isHidden:!1,defaultValue:"refseq:NC_000017.11"},start:{isHidden:!1,defaultValue:7572826},end:{isHidden:!1,defaultValue:7579005},variantType:{isHidden:!1,defaultValue:"SO:0001059"},alternateBases:{isHidden:!1,defaultValue:""},referenceBases:{isHidden:!1,defaultValue:""}},img:"/img/BeaconRangeQuery-graphics.png"},{label:"Gene Match",note:"Where supported beacons can discover variants overlap with the region of a known gene.\n",description:"Beacons in v2 can support the discovery of variants with overlap with the\ngenomic location of a gene, indicated by its symbol (e.g. `CDK2`). Additional\nparameters can _optionally_ be used to make matches more specific:\n- `variantMinLength` and `variantMaxLength` to limit matched CNV sizes\n- `genomicAlleleShortForm` (e.g. `V600E` with `BRAF`)\n- `variantType` and `alternateBases` to specify variants\n",img:"/img/BeaconGeneQuery-graphics.png",parameters:{geneId:{isHidden:!1,defaultValue:"CDK2"},referenceName:{isHidden:!0},start:{isHidden:!0},end:{isHidden:!0},variantMinLength:{isHidden:!1,defaultValue:1e4},variantMaxLength:{isHidden:!1,defaultValue:5e6},variantType:{isHidden:!1,defaultValue:"EFO:0030070"},alternateBases:{isHidden:!1},referenceBases:{isHidden:!0}}},{label:"Identifier - HeLa",note:"Samples can be identified through identifiers.",description:"This example retrieves _HeLa_ instances - including cell lines derived from\n_HeLa_ - by _HeLa's_ _cellosaurus_ identifier `cellosaurus:CVCL_0030`.\n",parameters:{aminoacidChange:{isHidden:!0},geneId:{isHidden:!0},referenceName:{isHidden:!0},start:{isHidden:!0},end:{isHidden:!0},variantType:{isHidden:!0},alternateBases:{isHidden:!0},referenceBases:{isHidden:!0},allTermsFilters:{isHidden:!1,defaultValue:["cellosaurus:CVCL_0030"]}}},{label:"Variant Short Form Example",note:"This is an experimental example for short form vbariant(s) support.",description:"This example shows a short form version of the CDKN2A deletion example.\n",parameters:{variantQueryDigests:{isHidden:!1,defaultValue:"9:21000001-21975098--21967753-24000000:DEL"},variantType:{isHidden:!0},allTermsFilters:{isHidden:!1,defaultValue:["NCIT:C3058"]},aminoacidChange:{isHidden:!0},geneId:{isHidden:!0},referenceName:{isHidden:!0},start:{isHidden:!0},end:{isHidden:!0},alternateBases:{isHidden:!0},referenceBases:{isHidden:!0}}},{label:"Fusion Example",note:"This is an experimental example for a fusion query (by positions).\nhttp://progenetix.org/beacon/g_variants/?referenceName=8&mateName=12&start=45100000&end=47300000&mateStart=26200000&mateEnd=35600000&variantType=SO:0000806\n",description:"This is an experimental example for a fusion query (by positions).\n",img:"/img/BeaconFusionQuery-graphics.png",parameters:{variantType:{isHidden:!1,defaultValue:"SO:0000806"},allTermsFilters:{isHidden:!1},referenceName:{isHidden:!1,defaultValue:"refseq:NC_000008.11"},mateName:{isHidden:!1,defaultValue:"refseq:NC_000012.12"},start:{isHidden:!1,defaultValue:451e5},end:{isHidden:!1,defaultValue:473e5},mateStart:{isHidden:!1,defaultValue:262e5},mateEnd:{isHidden:!1,defaultValue:356e5}}}]];e.exports=n.length<=1?n[0]:n},59628:e=>{let n=[[{label:"CNV (Bracket)",infoText:"Query using 2 `start` and 2 `end` values to find (structural) variants with\nsome fuzziness for their start and end.\n",description:"Typically CNV Queries are performed as **Beacon Bracket Queries**. These allow\nthe specification of sequence _ranges_ for both `start` and `end` positions of a\ngenomic variation since one usually wants to query for _similar_ structural\nvariants affecting a genomic region but potentially differing in their exact\nsize.\nSee also the [Beacon documentation](https://docs.genomebeacons.org/variant-queries/#beacon-bracket-queries) for more information.\n",img:"/img/BeaconBracketQuery-l

1imited-match-graphics.png",parameters:{aminoacidChange:{isHidden:!0},geneId:{isHidden:!0},genomicAlleleShortForm:{isHidden:!0},referenceName:{placeholder:"refseq:NC_000009.12",isHidden:!1},start:{placeholder:"21000001-21975098",isHidden:!1},end:{isHidden:!1,placeholder:"21967753-23000000"},variantType:{isHidden:!1,placeholder:"EFO:0030067 (DEL)"},alternateBases:{isHidden:!0},referenceBases:{isHidden:!0},variantMinLength:{isHidden:!0},variantMaxLength:{isHidden:!0},allTermsFilters:{isHidden:!1}},examples:[]},{label:"Range",infoText:"Query for variants with overlap to a genomic range",description:"**Beacon Range Queries** are supposed to return matches of any variant with\nat least partial overlap of the _sequence range_ specified by `reference_name`,\n`start` and `end` parameters. Additionally results might be restricted to\nvariants matching a given size range, variant type or base composition. \nSee also the [Beacon documentation](https://docs.genomebeacons.org/variant-queries/#beacon-range-queries) for more information.\n",img:"/img/BeaconRangeQuery-graphics.png",parameters:{referenceName:{isHidden:!1},geneId:{isHidden:!0},genomicAlleleShortForm:{isHidden:!0},aminoacidChange:{isHidden:!0},start:{isHidden:!1},end:{isHidden:!1},variantType:{isHidden:!1},alternateBases:{isHidden:!1},referenceBases:{isHidden:!1}},examples:[]},{label:"Gene ID",infoText:"",description:"**Gene Queries** are in essence a variation of Range Queries in which the\ncoordinates are replaced by the HGNC gene symbol. It is left to the implementation\nif the matching is done on variants annotated for the gene symbol or if a\npositional translation is being applied (and to which parameters - e.g. extend\nof coding region ...).\nSee also the [Beacon documentation](https://docs.genomebeacons.org/variant-queries/#beacon-geneid-queries) for more information.    \n",img:"/img/BeaconGeneQuery-graphics.png",parameters:{aminoacidChange:{isHidden:!0},geneId:{isHidden:!1},genomicAlleleShortForm:{isHidden:!0},referenceName:{isHidden:!0},start:{isHidden:!0},end:{isHidden:!0},variantMinLength:{isHidden:!1},variantMaxLength:{isHidden:!1},variantType:{isHidden:!1},alternateBases:{isHidden:!1},referenceBases:{isHidden:!1},sex:{isHidden:!1}},examples:[]},{label:"Sequence",infoText:'This represents the inputs for a "classic" Beacon SNV query',description:'**Sequence Queries** explore the existence of a specified sequence at a given\ngenomic position. Such queries correspond to the original Beacon queries\n("Allele Requests") and are used to match short, precisely defined genomic\nvariants such as SNVs and INDELs.\nSee also the [Beacon documentation](https://docs.genomebeacons.org/variant-queries/#beacon-sequence-queries) for more information.\n',parameters:{referenceName:{isHidden:!1},geneId:{isHidden:!0},genomicAlleleShortForm:{isHidden:!0},aminoacidChange:{isHidden:!0},start:{isHidden:!1},end:{isHidden:!0},variantType:{defaultValue:"SO:0001059"},alternateBases:{isHidden:!1},referenceBases:{isHidden:!1},variantMinLength:{isHidden:!0},variantMaxLength:{isHidden:!0}},examples:[],img:!1},{label:"Sample Data",infoText:"",description:'This template provides a variety of fields _excluding genomic variant parameters_\nfor the purpose to identify samples matchinng a single or several phenotypic\nor other properties. While here multiple (autocomplete) input fields are presented for convenience\nto facilitate complex queries, in the end all values are combined as a list of Beacon `filters`\nattributes (_i.e._ one can just add all of them to teh "Filters" field).\nSee also the [Beacon `filters` documentation](https://docs.genomebeacons.org/filters/#using-filters-in-queries) for more information.        \n',img:!1,parameters:{referenceName:{isHidden:!0},start:{isHidden:!0},end:{isHidden:!0},variantType:{isHidden:!0},alternateBases:{isHidden:!0},referenceBases:{isHidden:!0},bioontology:{isHidden:!1},clinicalClasses:{isHidden:!1},accessid:{isHidden:!0},allTermsFilters:{isHidden:!1},includeDescendantTerms:{isHidden:!1},sex:{isHidden:!1},materialtype:{isHidden:!1},referenceid:{isHidden:!1},cohorts:{isHidden:!0}},examples:[]},{label:"Short Form",infoText:"This example shows a short form version of the CDKN2A deleti

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