Creating Reports

Clinical reports in VariantMiner transform your variant analysis into professional, FHIR-compliant documents suitable for clinical decision-making and EHR integration. This guide walks you through the complete report creation process.

Report Overview

What is a Clinical Report?

A clinical report in VariantMiner is a structured document that contains:

• Selected variants from your analysis

• Clinical interpretations and significance assessments

• Patient information and context

• Laboratory details and methodology

• Actionable recommendations for clinicians

• FHIR R4 compliance for EHR integration

Types of Reports

VariantMiner supports several report types:

• Germline Reports: Constitutional variant analysis

• Somatic Reports: Tumor-specific variant analysis

• Pharmacogenomics Reports: Drug response predictions

• Carrier Screening Reports: Reproductive risk assessment

• Research Reports: Non-clinical research findings

Starting a New Report

Access Methods

From Variant Browser:

1. Filter variants to your analysis set

2. Select variants of interest

3. Click "Add to Report" button

4. Choose "Create New Report"

The Reports dashboard showing existing reports and create options

From Reports Dashboard:

1. Navigate to "Reports" in the main menu

2. Click "Create New Report"

3. Select report type and template

4. Begin variant selection process

From Orders:

1. Open a completed analysis order

2. Go to "Reports" tab

3. Click "Generate Report"

4. Follow guided report creation

Report Templates

Choose from available templates:

• Standard Clinical Report: General-purpose clinical reporting

• Cancer Panel Report: Oncology-focused analysis

• Exome Analysis Report: Whole exome sequencing results

• Targeted Panel Report: Gene panel analysis

• Custom Template: Institution-specific formats

Report Configuration

Basic Information

Report Metadata:

• Report Title: Descriptive title for the report

• Report Type: Select appropriate clinical context

• Laboratory Information: Performing laboratory details

• Ordering Physician: Requesting clinician information

• Report Date: Analysis completion date

• Report ID: Unique identifier for tracking

Patient Information:

• Patient Demographics: Name, DOB, gender, MRN

• Clinical Indication: Reason for testing

• Family History: Relevant family medical history

• Previous Testing: Prior genetic testing results

• Consent Status: Testing consent documentation

Analysis Parameters

Document the analysis methodology:

Technical Details:

• Sequencing Platform: Technology used for sequencing

• Analysis Pipeline: Bioinformatics workflow

• Reference Genome: Genome build (GRCh37/38)

• Coverage Metrics: Mean coverage, coverage uniformity

• Quality Thresholds: Variant calling parameters

Scope of Analysis:

• Genes Analyzed: Complete gene list or panel description

• Variant Types: SNVs, indels, CNVs analyzed

• Regions Covered: Exonic, intronic, regulatory regions

• Limitations: Technical or analytical limitations

Variant Selection

Selection Criteria

Choose variants based on clinical relevance:

Primary Findings:

• Pathogenic variants: Clearly disease-causing

• Likely pathogenic variants: Probably disease-causing

• Variants of uncertain significance: Clinical correlation needed

• Pharmacogenomic variants: Drug response implications

Secondary Findings:

• Incidental findings: Medically actionable variants in other genes

• Carrier status: Recessive disease variants

• Risk factors: Variants conferring disease predisposition

Variant Prioritization

Use systematic approaches to prioritize variants:

Clinical Relevance:

• Disease association strength

• Phenotype matching

• Mode of inheritance

• Penetrance and expressivity

Quality Metrics:

• Variant quality scores

• Read depth and coverage

• Allele balance

• Strand bias

Population Frequency:

• Rarity in control populations

• Ethnicity-matched frequencies

• Disease-specific frequencies

• Family segregation data

Adding Variants to Reports

From Variant Browser:

1. Apply filters to identify candidate variants

2. Review individual variant details

3. Select checkbox for relevant variants

4. Click "Add Selected to Report"

5. Choose existing report or create new one

Direct Variant Addition:

1. In the variant detail view

2. Click "Add to Report" button

3. Select target report from dropdown

4. Variant is immediately added to report

Bulk Import:

1. Upload variant list (VCF or text format)

2. System validates variants against analysis

3. Confirm variants to include in report

4. Variants added with default interpretations

Variant Interpretation

Clinical Significance Assessment

For each variant in the report, provide:

ACMG Classification:

• Select appropriate pathogenicity level

• Document supporting evidence criteria

• Justify classification rationale

• Reference supporting literature

Clinical Interpretation:

Example Interpretation:
"This variant is classified as Likely Pathogenic based on:
- Absence from population databases (PM2)
- Computational predictions support pathogenic effect (PP3)
- Located in well-established functional domain (PM1)
- Previous reports of pathogenicity in ClinVar (PP5)"

Functional Assessment:

• Predicted protein consequence

• Domain/region importance

• Conservation analysis

• Structural modeling results

Medical Recommendations

Provide actionable clinical guidance:

Diagnostic Implications:

• Confirms clinical diagnosis

• Suggests differential diagnoses

• Requires additional testing

• Rules out suspected conditions

Management Recommendations:

• Surveillance protocols

• Preventive measures

• Treatment modifications

• Specialist referrals

Family Testing:

• Cascade screening recommendations

• Reproductive counseling

• Predictive testing options

• Risk assessment for relatives

Report Sections

Executive Summary

Concise overview of key findings:

• Primary diagnostic findings

• Clinical significance summary

• Immediate recommendations

• Next steps for patient care

Methodology

Detailed technical information:

• Sample processing procedures

• Sequencing methodology

• Bioinformatics analysis pipeline

• Quality control measures

• Analytical sensitivity and specificity

Results

Comprehensive variant findings:

Preview of a clinical report showing variant findings and interpretations

Table Format:

Gene	Variant	Classification	Interpretation	Recommendation
BRCA1	c.185delAG	Pathogenic	Disease-causing	Genetic counseling
CHEK2	c.1100delC	Likely Pathogenic	Probably pathogenic	Family screening

Detailed Descriptions: For each significant variant:

• Full variant nomenclature (HGVS)

• Population frequency data

• Clinical significance assessment

• Supporting evidence summary

• Medical recommendations

Interpretation and Recommendations

Clinical context and guidance:

• Overall diagnostic assessment

• Clinical correlation requirements

• Management recommendations

• Surveillance protocols

• Family testing recommendations

• Limitations of analysis

Appendices

Supporting information:

• Gene descriptions and disease associations

• Methodology details

• Quality metrics

• References and citations

• Glossary of terms

Quality Control

Report Review Process

Implement quality control measures:

Technical Review:

• Variant calling accuracy

• Classification appropriateness

• Methodology documentation

• Data integrity checks

Clinical Review:

• Medical interpretation accuracy

• Recommendation appropriateness

• Literature support

• Clinical correlation

Administrative Review:

• Patient information accuracy

• Report formatting

• Regulatory compliance

• Approval signatures

Validation Steps

Before finalizing reports:

1. Verify patient identity and demographics

2. Confirm variant accuracy against raw data

3. Validate classifications using current guidelines

4. Review recommendations for clinical appropriateness

5. Check formatting and professional presentation

Report Formats

FHIR R4 Output

Generate standardized FHIR reports:

• DiagnosticReport resource: Main report structure

• Observation resources: Individual variant findings

• Patient resource: Patient demographics

• Organization resource: Laboratory information

• Practitioner resource: Reporting professionals

PDF Generation

Professional PDF reports include:

• Institution branding and logos

• Structured layout with clear sections

• Tables and formatted variant data

• Electronic signatures

• Page numbering and headers

Export Options

Additional export formats:

• HTML: Web-viewable reports

• XML: Structured data exchange

• JSON: API-compatible format

• CSV: Spreadsheet-compatible data

Collaborative Reporting

Multi-User Workflow

Support team-based reporting:

• Draft Reports: Work-in-progress sharing

• Review Assignments: Assign reviewers by role

• Comment System: Internal discussion threads

• Approval Workflow: Sequential approval process

• Version Control: Track report changes

Role-Based Access

Control report access:

• Authors: Create and edit reports

• Reviewers: Review and comment on reports

• Approvers: Final approval authority

• Viewers: Read-only access to completed reports

Report Management

Report Lifecycle

Track reports through their lifecycle:

• Draft: Under development

• Review: Under review by team

• Approved: Ready for delivery

• Delivered: Sent to ordering physician

• Archived: Historical record

Version Control

Maintain report history:

• Version Numbers: Sequential versioning

• Change Tracking: What changed between versions

• Approval History: Who approved each version

• Amendment Process: Procedure for report corrections

Delivery and Distribution

Manage report distribution:

• Secure Delivery: Encrypted transmission

• Delivery Confirmation: Receipt tracking

• Access Logs: Who accessed reports and when

• Retention Policies: How long to retain reports

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Report created successfully? Continue to Adding Variants to Reports to learn about managing variants within your clinical reports.