Variant Curation is available for public use. To register, create an account via "Login", and then contact our VCI helpdesk at vci@clinicalgenome.org.
\nGene Curation is currently restricted to ClinGen curators. To collaborate on gene curation contact clingen@clinicalgenome.org
\n\n
Any user may explore the demo version of the ClinGen interfaces by registering using the "Login" button, found in the header at curation-test.clinicalgenome.org. If you have questions about the demo site, please email us at clingen-helpdesk@lists.stanford.edu
\n\n Curious about how our ClinGen gene curation systems work?
\n See our latest peer-reviewed publication in the Annual Review of Biomedical Data Science:\n
\n Wright MW et al. Generating Clinical-Grade Gene-Disease Validity Classifications Through the ClinGen Data Platforms.
\n 2024 Aug;7(1):31-50. PMID: 38663031\n
\n The ClinGen variant curation process combines clinical, genetic, population, and functional evidence with expert review to classify variants into 1 of 5 categories according to the ACMG guidelines .\n
\nPathogenic • Likely Pathogenic • Uncertain • Likely Benign • Benign
\n\n Learn more\n
\n\n The ClinGen gene curation process combines an appraisal of genetic and experimental data in the scientific literature with expert review to classify gene-disease pairs into 1 of 6 categories according to ClinGen's Gene-Disease Clinical Validity Classification framework.\n
\nDefinitive • Strong • Moderate • Limited • Disputed • Refuted
\n\n Learn more\n
\nClinGen is a National Institutes of Health (NIH)-funded resource dedicated to building an authoritative central resource that defines the clinical relevance of genes and variants for use in precision medicine and research. One of the key goals of ClinGen is to implement an evidence-based consensus for curating genes and variants. For more information on the ClinGen resource, please visit the ClinGen portal at clinicalgenome.org
\n\n Please close any other VCI/GCI tabs you have open before you switch affiliations. \n Keeping work open in other tabs when you switch affiliations can potentially lead\n to your curations being attributed to the wrong affiliation.\n
\n| \n {column.render('Header')}\n \n {column.isSorted\n ? column.isSortedDesc\n ? | \n ))}\n
|---|
| \n {cell.render('Cell')}\n | \n )\n })}\n
No Interpretations yet!
\n }\n\n // linked to the statusFilter react-select component. Sets filters to selected values.\n function handleStatusChange(e) {\n let statuses = []\n for (let i in e) {\n let status = e[i]\n statuses.push(status.value)\n }\n setstatusFilters(statuses)\n }\n}\n\n\nconst mapDispatchToProps = dispatch => ({\n updateVariant: variant => dispatch(updateVariant(variant))\n})\n\nexport default connect(mapDispatchToProps)(Table);","import { convertDiseasePKToMondoId, isFreeTextDisease } from '../utilities/diseaseUtilities';\nimport { getFormattedDateTime } from '../utilities/dateTimeUtilities';\nimport { RestAPI as API } from '@aws-amplify/api-rest';\nimport { API_NAME } from '../utils';\n\n// curationType can be 'variant' or 'gene'.\n// If all interpretations are desired, getAllInterps = false.\n// else if only user's interpretations are desired, getAllInterps = true.\n// auth from redux store. Not used when getAllInterps is true, only needed for filtering for user data.\nexport async function get_interpretations(curationType, getAllInterps, auth, requestRecycler) {\n // Create URL for GET call based on table type (variant vs. gene)\n let url = ''\n if (curationType === 'variant') {\n url = `/interpretations`\n }\n else if (curationType === 'gene') {\n url = '/gdms'\n }\n\n // filter if only user's interpretations are wanted.\n if (!getAllInterps) {\n // If an affiliation is selected, get those interpretations.\n // TODO: Otherwise, get user's created interpretations that have no affiliation.\n // ^^ Look into range query to do this.\n if (auth.currentAffiliation !== null) {\n url += `?affiliation=${auth.currentAffiliation.affiliation_id}`\n }\n else {\n url += `?submitted_by=${auth.PK}`\n // url += `?submitted_by=${props.auth.PK}&affiliation=null`\n // url += `?submitted_by=7b555d35-5431-4f10-b760-6e6f6d0c3ebf` // variant Check\n // url += `?submitted_by=59dc49a3-92fa-442f-8fa9-043094fe7b7c` // gene check\n }\n\n if (curationType === 'variant') {\n url += `&action=myinterpretations`\n }\n\n if (curationType === 'gene') {\n url += `&action=mygdms`;\n }\n }\n\n // Retrieves, relabels, and sorts the data.\n async function fetch() {\n const data = await requestRecycler.capture(API.get(API_NAME, url));\n const updatedData = data.map((item) => {\n // if item.disease is PK (VCI table)\n const diseaseDisplayText = typeof item.disease === 'string' ? (\n // `${item.diseaseTerm || ''}${!isFreeTextDisease(item.disease) ? ` (${convertDiseasePKToMondoId(item.disease)})` : ''}`\n !item.disease && !item.diseaseTerm\n ? '--'\n : `${item.diseaseTerm || ''}${item.disease && !isFreeTextDisease(item.disease) ? ` (${convertDiseasePKToMondoId(item.disease)})` : ''}`\n )\n : null;\n\n const modeInheritanceDisplayText = item.modeInheritance ? item.modeInheritance.replace(/ *\\([^)]*\\) */g, \"\") : '';\n const pathogenicityDisplayText = item.alteredClassification ? item.alteredClassification.split('-')[0] : (item.autoClassification ? item.autoClassification.split('-')[0] : '');\n const variantIdDisplayText = item.carId && item.clinvarVariantId \n ? `${item.carId},${item.clinvarVariantId}` \n : `${item.carId || ''}${item.clinvarVariantId || ''}`;\n // Created by - Uncommented for alphatest, needs to be reimplemented at a later time\n // const submitted_by_displayText = getUserName(item.submitted_by);\n // const created_by_displayText = `${submitted_by_displayText}${item.affiliation ? ` (${getAffiliationName(item.affiliation)})` : ''}`;\n let showPathogenicity = true;\n\n if (curationType === 'variant') {\n if (item.snapshotStatuses && item.snapshotStatuses.length === 0 || item.status && item.status.toLowerCase() === \"in progress\") {\n showPathogenicity = false;\n }\n return {\n variant: (item.preferredTitle || '--'), // check that variantData[idx] is defined\n variantPK: item.variant, // for displaying link to interpretation page\n variantId: variantIdDisplayText,\n interpretationPK: item.PK, // for displaying link to interpretation page while specifying the interpretation PK\n disease_modeInheritance: `${diseaseDisplayText || '--'} / ${modeInheritanceDisplayText || '--'}`,\n snapshot: item.snapshotStatuses && item.snapshotStatuses.length ? item.snapshotStatuses : item, // for displaying all matching statuses\n pathogenicity: showPathogenicity ? pathogenicityDisplayText : '--',\n criteria: item.criteria || 'None',\n date_created: getFormattedDateTime(item.date_created, 'LLL', true),\n last_modified: item.last_modified\n // created_by: created_by_displayText\n }\n }\n else if (curationType === 'gene') {\n if (item.snapshotStatuses && item.snapshotStatuses.length === 0) {\n showPathogenicity = false;\n }\n let classification = item.alteredClassification && item.alteredClassification !== 'No Modification' ? item.alteredClassification : item.autoClassification;\n \n return {\n gene: (item.gene.PK ? item.gene.PK : (item.gene || '--')),\n gdmPK: item.PK, // for displaying link to gdm page\n disease_modeInheritance: `${diseaseDisplayText || '--'} / ${modeInheritanceDisplayText || '--'}`,\n classification: showPathogenicity ? classification : '--',\n snapshot: item.snapshotStatuses && item.snapshotStatuses.length ? item.snapshotStatuses : item, // for displaying all matching statuses\n date_created: getFormattedDateTime(item.date_created, 'LLL', true),\n last_modified: item.last_modified\n }\n }\n else return {}\n });\n\n return updatedData;\n }\n const results = await fetch();\n return results;\n}\n","import React from 'react';\nimport { connect } from 'react-redux';\nimport { Nav } from 'react-bootstrap';\nimport { useHistory } from 'react-router-dom';\nimport { FontAwesomeIcon } from '@fortawesome/react-fontawesome'\nimport { faList, faTable, faHome } from '@fortawesome/free-solid-svg-icons'\n\n\nfunction TableNavBar(props) {\n const { auth } = props;\n const history = useHistory();\n return (\n \n );\n}\n\nconst mapStateToProps = (state) => ({\n auth: state.auth,\n})\n\nexport default connect(mapStateToProps)(TableNavBar);\n","import React, { useState, useEffect } from 'react';\nimport Table from '../components/InterpretationsTable';\nimport { connect } from 'react-redux';\nimport { Row, Col } from 'react-bootstrap';\nimport { get_interpretations } from '../helpers/get_interpretations';\nimport TableNavBar from '../components/common/TableNavBar'\nimport { useAmplifyAPIRequestRecycler, AmplifyAPIRequestRecycler } from '../utilities/fetchUtilities';\n\nfunction Dashboard(props) {\n const requestRecycler = useAmplifyAPIRequestRecycler();\n\n // column names of variant and gene tables.\n const variantHeadersValue = [\n { key: 'variant', text: 'Variant', sort: true },\n { key: 'variantId', text: 'Variant ID(s)', sort: true },\n { key: 'disease_modeInheritance', text: 'Disease/Mode of Inheritance', sort: true },\n { key: 'status', text: 'Status', sort: true },\n { key: 'pathogenicity', text: 'Classification', sort: true },\n { key: 'criteria', text: 'Met Criteria', sort: true },\n { key: 'date_created', text: 'Date Created', sort: true },\n { key: 'last_modified', text: 'Last Modified', sort: true },\n ]\n const geneHeadersValue = [\n { key: 'gene', text: 'Gene', sort: true },\n { key: 'disease_modeInheritance', text: 'Disease/Mode of Inheritance', sort: true },\n { key: 'status', text: 'Status', sort: true },\n { key: 'classification', text: 'Classification', sort: true },\n { key: 'date_created', text: 'Date Created', sort: true },\n { key: 'last_modified', text: 'Last Modified', sort: true }\n ]\n\n const [variantTableTitle, setVariantTableTitle] = useState('');\n const [geneTableTitle, setGeneTableTitle] = useState('');\n const [variantTableData, setVariantTableData] = useState([]);\n const [variantTableLoading, setVariantTableLoading] = useState(false);\n const [geneTableData, setGeneTableData] = useState([]);\n const [geneTableLoading, setGeneTableLoading] = useState(false);\n\n// Gets the data for both tables.\n useEffect(() => {\n setVariantTableLoading(true);\n setGeneTableLoading(true);\n async function fetch() {\n let [variants, genes] = await Promise.all([\n get_interpretations('variant', false, props.auth, requestRecycler),\n get_interpretations('gene', false, props.auth, requestRecycler)\n ]);\n if (auth.currentAffiliation) {\n setVariantTableTitle('My Affiliation\\'s Variant Interpretations');\n setGeneTableTitle('My Affiliation\\'s Gene-Disease Records');\n } else {\n setVariantTableTitle('My Variant Interpretations');\n setGeneTableTitle('My Gene-Disease Records');\n }\n\n if (variants) {\n setVariantTableData(variants);\n }\n if (genes) {\n setGeneTableData(genes)\n }\n setVariantTableLoading(false);\n setGeneTableLoading(false)\n }\n fetch().catch(AmplifyAPIRequestRecycler.defaultCatch);\n }, [requestRecycler, props.auth])\n\n const { auth } = props;\n\n return (\n <>\n{variantType}
\nBelow is the data from OLS for the ID you submitted. Select "Save" below if it is the correct disease, otherwise revise your search above:
\n {displayObsoleteDiseaseIcon(retrievedDisease.term, \"gdm\")}\n {retrievedDisease.term}\n\n Note: We strongly encourage use of an allowed MONDO ontology term and therefore specific database\n identifier for a disease. If you have searched and there is no appropriate database identifier you may\n contact us at clingen-helpdesk@lists.stanford.edu and/or\n create a term using free text.\n
\nUse of free text could result in different terms being used for the same disease. Please make certain there is no\n appropriate ontology term before applying a free text disease name.\n
\nEither HPO term(s) or a definition is required to describe this disease (both fields may be used).
\nSearch HPO-Browser
\n \nNote: When curating as part of an affiliation, only affiliation specification documents are shown
\nCurrently saved to Interpretation: {previouslySavedCspec.label}
\n : previouslySavedCspec ?Disease: {disease.diseaseLabel} ({disease.diseaseId})
\n {disease.modesOfInheritance.map((moi, moiIndex) => (\n\n Mode of Inheritance: {moi.label} ({moi.id})\n
\n ))}\n{subTitle}
\n\n