Platform Overview

VariantMiner is a comprehensive clinical variant analysis platform designed for genomic data processing and interpretation. It provides a complete workflow from VCF file upload to clinical report generation, making it an essential tool for clinical laboratories, genetic counselors, and researchers working with genomic data.

What is VariantMiner?

VariantMiner addresses the key challenges in clinical genomics:

• Data Volume Management: Efficiently handles millions of genetic variants per sample through optimized database storage and querying

• Complex Interpretation: Provides intuitive tools for variant pathogenicity assessment using ACMG guidelines

• Workflow Integration: Unifies the entire process from raw data to clinical reporting in one platform

• Standardization: Generates FHIR-compliant clinical reports for seamless EHR integration

• Multi-tenancy: Supports multiple organizations with isolated workspaces for data security

Core Features

File Management

• Support for VCF (Variant Call Format) and BAM files

• Automated background processing with status tracking

• Integration with multiple storage backends (local, cloud, DNAnexus)

• Real-time processing status updates

Sample & Subject Management

• Complete patient (subject) and sample tracking

• Flexible metadata storage

• File-to-sample associations with role definitions

• Multi-sample analysis support

Order Processing

• Streamlined analysis request workflow

• Multi-step order creation wizard

• Proband sample designation for family studies

• Automated workflow state tracking

Variant Analysis

• High-performance variant browsing with advanced filtering

• Customizable column views and saved filters

• ACMG-based pathogenicity classification

• Collaborative commenting system

• Integration with external variant databases

Clinical Reports

• Professional clinical report generation

• Variant selection and interpretation workflow

• FHIR R4 compliant output

• Customizable report templates

Organization & Workspace Management

• Multi-tenant architecture for laboratory networks

• Hierarchical organization and workspace structure

• Granular role-based access control

• Invitation system for user onboarding

Who Uses VariantMiner?

Clinical Laboratories

• Process patient samples for genetic testing

• Generate clinical reports for physicians

• Manage laboratory workflows and quality control

Genetic Counselors

• Interpret variant significance

• Create patient reports

• Collaborate with laboratory teams

Researchers

• Analyze research cohorts

• Investigate variant-disease associations

• Manage large-scale genomic datasets

Laboratory Directors

• Oversee laboratory operations

• Manage user access and permissions

• Monitor processing workflows

Technology Stack

VariantMiner is built using modern web technologies:

• Backend: FastAPI (Python) for high-performance APIs

• Frontend: HTMX and Alpine.js for dynamic, responsive interfaces

• Database: PostgreSQL for application data, SQLite for variant storage

• Authentication: Supabase-based user management

• Deployment: Docker containerization for easy deployment

Security & Compliance

• Role-based access control (RBAC) at organization and workspace levels

• Complete audit logging of all user activities

• Data isolation through workspace containers

• Support for HIPAA-compliant deployments

• Secure authentication with JWT tokens

Getting Started

To begin using VariantMiner:

1. Log in to your account

2. Explore the dashboard

3. Understand your organization structure

4. Set up your workspace

5. Upload your first VCF file

---

Ready to get started? Continue to System Requirements to ensure your environment is properly configured.