@erosolaraijs/cure 1.0.0

package/dist/integrations/ehr/fhir.js.map

@@ -0,0 +1 @@
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package/dist/integrations/genomics/genomicPlatforms.d.ts

@@ -0,0 +1,362 @@
+/**
+ * Genomic Testing Platform Integrations
+ *
+ * Connects to major genomic testing providers:
+ * - Foundation Medicine (FoundationOne CDx, FoundationOne Liquid CDx)
+ * - Guardant Health (Guardant360, GuardantOMNI)
+ * - Tempus (xT, xF, xR panels)
+ * - Caris Life Sciences (Caris Molecular Intelligence)
+ * - NeoGenomics
+ *
+ * All data handling complies with HIPAA and CAP/CLIA requirements.
+ */
+import { EventEmitter } from 'events';
+export interface GenomicTestOrder {
+    orderId: string;
+    patientId: string;
+    testType: string;
+    panelName: string;
+    specimenType: 'tissue' | 'blood' | 'bone-marrow' | 'other';
+    specimenId?: string;
+    orderDate: Date;
+    clinicalIndication: string;
+    icdCodes: string[];
+    orderingPhysician: {
+        name: string;
+        npi: string;
+        facility: string;
+    };
+    status: 'ordered' | 'specimen-received' | 'in-process' | 'completed' | 'failed' | 'cancelled';
+}
+export interface GenomicTestResult {
+    reportId: string;
+    orderId: string;
+    patientId: string;
+    testType: string;
+    panelName: string;
+    specimenInfo: {
+        type: 'tissue' | 'blood' | 'bone-marrow' | 'other';
+        site?: string;
+        collectionDate: Date;
+        tumorPurity?: number;
+        cellularity?: number;
+    };
+    reportDate: Date;
+    variants: GenomicVariant[];
+    copyNumberAlterations: CopyNumberAlteration[];
+    fusions: GeneFusion[];
+    biomarkers: GenomicBiomarker[];
+    therapyMatches: TherapyMatch[];
+    clinicalTrialMatches: ClinicalTrialMatch[];
+    signatures?: {
+        microsatelliteInstability?: MSIResult;
+        tumorMutationalBurden?: TMBResult;
+        homologousRecombinationDeficiency?: HRDResult;
+        lossOfHeterozygosity?: LOHResult;
+    };
+    qualityMetrics: {
+        meanCoverage?: number;
+        percentBases100x?: number;
+        tumorFraction?: number;
+        contamination?: number;
+        mappingRate?: number;
+    };
+    reportPdf?: string;
+    rawData?: {
+        vcfUrl?: string;
+        bamUrl?: string;
+        fastqUrl?: string;
+    };
+}
+export interface GenomicVariant {
+    gene: string;
+    hgvsC?: string;
+    hgvsP?: string;
+    transcript?: string;
+    chromosome?: string;
+    position?: number;
+    refAllele?: string;
+    altAllele?: string;
+    variantType: 'SNV' | 'insertion' | 'deletion' | 'indel' | 'MNV' | 'complex';
+    variantAlleleFrequency: number;
+    coverage?: number;
+    zygosity?: 'heterozygous' | 'homozygous' | 'hemizygous';
+    clinicalSignificance: 'pathogenic' | 'likely-pathogenic' | 'vus' | 'likely-benign' | 'benign';
+    tier?: 'I' | 'II' | 'III' | 'IV';
+    oncogenicity?: 'oncogenic' | 'likely-oncogenic' | 'vus' | 'likely-neutral' | 'neutral';
+    functionalEffect?: 'loss-of-function' | 'gain-of-function' | 'switch-of-function' | 'unknown';
+    somaticStatus?: 'somatic' | 'germline' | 'unknown';
+    actionability?: {
+        level: 'FDA-approved' | 'clinical-guideline' | 'clinical-evidence' | 'preclinical';
+        therapies: string[];
+        evidence: string[];
+    };
+    annotations?: {
+        cosmic?: string;
+        dbSNP?: string;
+        clinVar?: string;
+        gnomAD?: {
+            frequency: number;
+            popMax?: number;
+        };
+        oncokb?: {
+            level: string;
+            description: string;
+        };
+    };
+}
+export interface CopyNumberAlteration {
+    gene: string;
+    chromosome?: string;
+    startPosition?: number;
+    endPosition?: number;
+    type: 'amplification' | 'gain' | 'loss' | 'deep-deletion';
+    copyNumber?: number;
+    logRatio?: number;
+    clinicalSignificance: 'pathogenic' | 'likely-pathogenic' | 'vus' | 'likely-benign' | 'benign';
+    actionability?: {
+        level: 'FDA-approved' | 'clinical-guideline' | 'clinical-evidence' | 'preclinical';
+        therapies: string[];
+    };
+}
+export interface GeneFusion {
+    gene5Prime: string;
+    gene3Prime: string;
+    fusionName: string;
+    breakpoint5Prime?: string;
+    breakpoint3Prime?: string;
+    readsSupporting?: number;
+    inFrame?: boolean;
+    clinicalSignificance: 'pathogenic' | 'likely-pathogenic' | 'vus';
+    actionability?: {
+        level: 'FDA-approved' | 'clinical-guideline' | 'clinical-evidence' | 'preclinical';
+        therapies: string[];
+    };
+}
+export interface GenomicBiomarker {
+    name: string;
+    value: number | string;
+    unit?: string;
+    status: 'positive' | 'negative' | 'equivocal' | 'indeterminate';
+    threshold?: number;
+    method?: string;
+    clinicalImplication?: string;
+}
+export interface MSIResult {
+    status: 'MSI-H' | 'MSI-L' | 'MSS' | 'indeterminate';
+    score?: number;
+    markersAnalyzed?: number;
+    markersUnstable?: number;
+    method: 'NGS' | 'PCR' | 'IHC';
+}
+export interface TMBResult {
+    value: number;
+    unit: 'mutations/Mb';
+    status: 'high' | 'intermediate' | 'low';
+    threshold: number;
+    percentile?: number;
+}
+export interface HRDResult {
+    status: 'positive' | 'negative' | 'indeterminate';
+    score?: number;
+    components?: {
+        loh?: number;
+        tai?: number;
+        lst?: number;
+    };
+    brcaStatus?: 'BRCA1-mut' | 'BRCA2-mut' | 'BRCA-wt';
+}
+export interface LOHResult {
+    percentage: number;
+    status: 'high' | 'intermediate' | 'low';
+    genomeFraction?: number;
+}
+export interface TherapyMatch {
+    therapy: string;
+    drugs: string[];
+    biomarkers: string[];
+    evidenceLevel: 'FDA-approved' | 'NCCN-guideline' | 'clinical-evidence' | 'case-report' | 'preclinical';
+    cancerType: string;
+    approvalStatus?: string;
+    clinicalTrials?: string[];
+    responseRate?: number;
+    references: string[];
+}
+export interface ClinicalTrialMatch {
+    trialId: string;
+    title: string;
+    phase: 'I' | 'I/II' | 'II' | 'II/III' | 'III' | 'IV';
+    matchingBiomarkers: string[];
+    status: 'recruiting' | 'active-not-recruiting' | 'enrolling-by-invitation';
+    locations?: {
+        name: string;
+        city: string;
+        state: string;
+        country: string;
+    }[];
+    sponsor?: string;
+    drugs?: string[];
+}
+export interface GenomicPlatformConfig {
+    platform: 'foundation-medicine' | 'guardant' | 'tempus' | 'caris' | 'neogenomics' | 'generic';
+    apiBaseUrl: string;
+    apiKey?: string;
+    clientId?: string;
+    clientSecret?: string;
+    organizationId?: string;
+    webhookUrl?: string;
+    timeout?: number;
+}
+export declare abstract class GenomicPlatformClient extends EventEmitter {
+    protected config: GenomicPlatformConfig;
+    protected accessToken?: string;
+    protected tokenExpiry?: Date;
+    constructor(config: GenomicPlatformConfig);
+    abstract authenticate(): Promise<void>;
+    abstract submitOrder(order: GenomicTestOrder): Promise<{
+        orderId: string;
+        status: string;
+    }>;
+    abstract getOrderStatus(orderId: string): Promise<GenomicTestOrder>;
+    abstract getResults(orderId: string): Promise<GenomicTestResult>;
+    abstract listPatientResults(patientId: string): Promise<GenomicTestResult[]>;
+    protected httpRequest(url: string, options: {
+        method: string;
+        headers?: Record<string, string>;
+        body?: string;
+    }): Promise<string>;
+    protected getAuthHeaders(): Promise<Record<string, string>>;
+}
+export declare class FoundationMedicineClient extends GenomicPlatformClient {
+    constructor(config: Omit<GenomicPlatformConfig, 'platform'>);
+    authenticate(): Promise<void>;
+    submitOrder(order: GenomicTestOrder): Promise<{
+        orderId: string;
+        status: string;
+    }>;
+    getOrderStatus(orderId: string): Promise<GenomicTestOrder>;
+    getResults(orderId: string): Promise<GenomicTestResult>;
+    listPatientResults(patientId: string): Promise<GenomicTestResult[]>;
+    /**
+     * Get FoundationOne CDx specific data
+     */
+    getFoundationOneCDxReport(orderId: string): Promise<{
+        variants: GenomicVariant[];
+        cnvs: CopyNumberAlteration[];
+        fusions: GeneFusion[];
+        msi: MSIResult;
+        tmb: TMBResult;
+        loh: LOHResult;
+        therapies: TherapyMatch[];
+    }>;
+    private mapToFMIOrder;
+    private mapPanelToFMICode;
+    private mapFromFMIOrder;
+    private mapFMICodeToPanel;
+    private mapFMIStatus;
+    private mapFromFMIReport;
+    private mapVariantType;
+    private mapPathogenicity;
+    private mapTier;
+}
+export declare class GuardantHealthClient extends GenomicPlatformClient {
+    constructor(config: Omit<GenomicPlatformConfig, 'platform'>);
+    authenticate(): Promise<void>;
+    submitOrder(order: GenomicTestOrder): Promise<{
+        orderId: string;
+        status: string;
+    }>;
+    getOrderStatus(orderId: string): Promise<GenomicTestOrder>;
+    getResults(orderId: string): Promise<GenomicTestResult>;
+    listPatientResults(patientId: string): Promise<GenomicTestResult[]>;
+    /**
+     * Get Guardant360 specific metrics including ctDNA fraction
+     */
+    getGuardant360Metrics(orderId: string): Promise<{
+        ctDNAFraction: number;
+        maxMAF: number;
+        somatic: GenomicVariant[];
+        clonalHematopoiesis: GenomicVariant[];
+        msi: MSIResult;
+    }>;
+    private mapPanelToGuardantTest;
+    private mapFromGuardantOrder;
+    private mapGuardantStatus;
+    private mapFromGuardantReport;
+}
+export declare class TempusClient extends GenomicPlatformClient {
+    constructor(config: Omit<GenomicPlatformConfig, 'platform'>);
+    authenticate(): Promise<void>;
+    submitOrder(order: GenomicTestOrder): Promise<{
+        orderId: string;
+        status: string;
+    }>;
+    getOrderStatus(orderId: string): Promise<GenomicTestOrder>;
+    getResults(orderId: string): Promise<GenomicTestResult>;
+    listPatientResults(patientId: string): Promise<GenomicTestResult[]>;
+    /**
+     * Get Tempus xT/xF specific analysis including RNA expression
+     */
+    getTempusAnalysis(orderId: string): Promise<{
+        dnaFindings: GenomicVariant[];
+        rnaExpression?: {
+            gene: string;
+            zscore: number;
+            percentile: number;
+        }[];
+        immuneProfile?: {
+            pdl1: {
+                score: number;
+                method: string;
+            };
+            tils: number;
+            immuneScore: number;
+        };
+        hrd: HRDResult;
+    }>;
+    private mapPanelToTempusCode;
+    private mapFromTempusOrder;
+    private mapTempusCodeToPanel;
+    private mapTempusStatus;
+    private mapFromTempusReport;
+}
+export declare class UnifiedGenomicsService {
+    private clients;
+    /**
+     * Register a genomic platform client
+     */
+    registerClient(name: string, client: GenomicPlatformClient): void;
+    /**
+     * Get results from all platforms for a patient
+     */
+    getAllPatientResults(patientId: string): Promise<{
+        platform: string;
+        results: GenomicTestResult[];
+    }[]>;
+    /**
+     * Aggregate and deduplicate variants across all platforms
+     */
+    getAggregatedVariants(patientId: string): Promise<{
+        variants: GenomicVariant[];
+        cnvs: CopyNumberAlteration[];
+        fusions: GeneFusion[];
+        biomarkers: {
+            msi?: MSIResult;
+            tmb?: TMBResult;
+            hrd?: HRDResult;
+            pdl1?: {
+                score: number;
+                scoreType: string;
+            };
+        };
+    }>;
+    /**
+     * Match patient genomics to actionable therapies
+     */
+    matchToTherapies(patientId: string, cancerType: string): Promise<TherapyMatch[]>;
+    private getFDAApprovedMatches;
+    private getNCCNMatches;
+}
+export declare function createGenomicClient(config: GenomicPlatformConfig): GenomicPlatformClient;
+export default UnifiedGenomicsService;
+//# sourceMappingURL=genomicPlatforms.d.ts.map

package/dist/integrations/genomics/genomicPlatforms.d.ts.map

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