---
title: Understanding Reports
---

# Understanding Reports

Learn about the different types of reports generated by ZaroPGx and how to interpret them.

## Report Types

### PDF Clinical Report
The primary clinical report in PDF format, designed for healthcare providers.

**Sections:**
- **Executive Summary**: Key findings and actionable recommendations
- **Gene Analysis**: Detailed results for each pharmacogene
- **Clinical Guidelines**: CPIC-based recommendations
- **Technical Details**: Methodology and parameters used
- **References**: Scientific citations and sources

### Interactive HTML Report
A comprehensive web-based report with interactive features.

**Features:**
- **Interactive Tables**: Sortable, filterable results
- **Visualizations**: Charts, graphs, and diagrams
- **Detailed Annotations**: Gene-specific information and explanations
- **Export Options**: Download data in various formats
- **Search Functionality**: Find specific genes or variants

### Raw Data Files
Original outputs from analysis tools for further processing.

**File Types:**
- **PharmCAT HTML**: Original PharmCAT report
- **PharmCAT JSON**: Machine-readable results
- **PharmCAT TSV**: Tab-separated data for spreadsheets
- **VCF Files**: Processed variant calls

## Report Structure

### Executive Summary

**Key Components:**
- **Patient Information**: Sample identifier and analysis date
- **Critical Findings**: High-priority pharmacogenomic results
- **Actionable Recommendations**: Clinical actions to consider
- **Risk Assessment**: Overall risk profile for drug metabolism

**Example:**
```
EXECUTIVE SUMMARY
================

Patient ID: SAMPLE_001
Analysis Date: 2024-01-15
Reference Genome: GRCh38

CRITICAL FINDINGS:
- CYP2D6: Poor Metabolizer (*4/*4)
- CYP2C19: Intermediate Metabolizer (*1/*2)
- TPMT: Normal Metabolizer (*1/*1)

ACTIONABLE RECOMMENDATIONS:
- Avoid codeine and tramadol (CYP2D6 poor metabolizer)
- Consider reduced dosing for clopidogrel (CYP2C19 intermediate)
- Standard dosing appropriate for azathioprine (TPMT normal)
```

### Gene Analysis Section

**For Each Pharmacogene:**
- **Diplotype**: Star allele combination (e.g., *1/*2)
- **Phenotype**: Functional classification (e.g., Intermediate Metabolizer)
- **Activity Score**: Quantitative measure of enzyme activity
- **Clinical Significance**: Impact on drug metabolism
- **Drug Interactions**: Affected medications
- **Recommendations**: Specific dosing guidance

**Example Gene Entry:**
```
CYP2D6 Analysis
===============

Diplotype: *4/*4
Phenotype: Poor Metabolizer
Activity Score: 0.0
Confidence: High

Clinical Significance:
- Significantly reduced enzyme activity
- Increased risk of adverse effects with standard dosing
- May require alternative medications

Affected Drugs:
- Codeine: Avoid (increased risk of toxicity)
- Tramadol: Avoid (increased risk of toxicity)
- Metoprolol: Consider reduced dosing
- Fluoxetine: Consider reduced dosing

Recommendations:
- Avoid codeine and tramadol
- Use alternative analgesics
- Consider reduced dosing for other CYP2D6 substrates
- Monitor for adverse effects
```

## Understanding Star Alleles

### Star Allele Notation

**Format**: `*1/*2` (diplotype) or `*1` (haplotype)

**Common Alleles:**
- **`*1`**: Reference (wild-type) allele
- **`*2`, `*3`, `*4`, etc.**: Variant alleles
- **`*N`**: Novel or undefined alleles
- **`*`**: No call or failed analysis

**Examples:**
- `*1/*1`: Homozygous reference (normal metabolizer)
- `*1/*2`: Heterozygous variant (intermediate metabolizer)
- `*2/*2`: Homozygous variant (poor metabolizer)
- `*1/*17`: Duplication (ultrarapid metabolizer)

### Phenotype Classifications

**Normal Metabolizer (NM):**
- Standard enzyme activity
- Normal drug processing
- Standard dosing appropriate

**Intermediate Metabolizer (IM):**
- Reduced enzyme activity
- Slower drug processing
- May require dose adjustment

**Poor Metabolizer (PM):**
- Significantly reduced activity
- Very slow drug processing
- Often requires alternative medications

**Rapid Metabolizer (RM):**
- Increased enzyme activity
- Faster drug processing
- May require higher doses

**Ultrarapid Metabolizer (UM):**
- Very high enzyme activity
- Very fast drug processing
- Often requires alternative medications

## Clinical Recommendations

### Recommendation Levels

**Green (No Action):**
- Standard dosing appropriate
- No special monitoring required
- Normal drug response expected

**Yellow (Consider Alternative):**
- Consider dose adjustment
- Monitor for efficacy/adverse effects
- May require alternative medications

**Red (Avoid or Extreme Caution):**
- Avoid medication if possible
- Use only with extreme caution
- Consider alternative treatments

**Blue (Additional Monitoring):**
- Standard dosing may be appropriate
- Monitor closely for effects
- Consider therapeutic drug monitoring

### CPIC Guidelines

**Clinical Pharmacogenomics Implementation Consortium (CPIC) Guidelines:**
- Evidence-based recommendations
- Regularly updated with new evidence
- Graded by strength of evidence
- Specific to gene-drug pairs

**Guideline Levels:**
- **Level 1A**: Strong evidence, high confidence
- **Level 1B**: Strong evidence, moderate confidence
- **Level 2A**: Moderate evidence, high confidence
- **Level 2B**: Moderate evidence, moderate confidence
- **Level 3**: Weak evidence, low confidence

## Quality Metrics

### Confidence Scores

**High Confidence (≥90%):**
- Strong evidence for genotype
- Multiple supporting variants
- High-quality sequencing data

**Moderate Confidence (70-89%):**
- Good evidence for genotype
- Some supporting variants
- Good-quality sequencing data

**Low Confidence (<70%):**
- Weak evidence for genotype
- Few supporting variants
- Poor-quality sequencing data

### Coverage Information

**Coverage Depth:**
- **High Coverage (≥30x)**: Reliable genotype calls
- **Medium Coverage (10-29x)**: Generally reliable
- **Low Coverage (<10x)**: May be unreliable

**Coverage Breadth:**
- **Complete**: All target regions covered
- **Partial**: Some regions missing
- **Incomplete**: Many regions missing

## Interpreting Results

### Key Considerations

**Clinical Context:**
- Consider patient's current medications
- Review medical history
- Assess drug-drug interactions
- Consider other genetic factors

**Limitations:**
- Results are based on current knowledge
- New variants may not be detected
- Phenotype predictions are probabilistic
- Clinical response may vary

**Action Items:**
- Review with healthcare provider
- Update medication list
- Consider genetic counseling
- Monitor for drug effects

### Common Scenarios

**CYP2D6 Poor Metabolizer:**
- Avoid codeine, tramadol
- Consider alternative analgesics
- Monitor for adverse effects
- May require dose adjustment for other drugs

**CYP2C19 Intermediate Metabolizer:**
- Consider reduced clopidogrel dosing
- Monitor for efficacy
- May require alternative antiplatelet therapy
- Consider genetic testing for family members

**TPMT Poor Metabolizer:**
- Avoid azathioprine, mercaptopurine
- Use alternative immunosuppressants
- Monitor for bone marrow toxicity
- Consider genetic testing for family members

## Export and Integration

### FHIR Export

**Fast Healthcare Interoperability Resources (FHIR):**
- Standard format for healthcare data
- Compatible with EHR systems
- Includes structured pharmacogenomic data
- Supports clinical decision support

**Export Process:**
1. Generate report
2. Convert to FHIR format
3. Export to FHIR server
4. Integrate with EHR system

### Data Formats

**JSON Export:**
- Machine-readable format
- Includes all analysis results
- Compatible with other tools
- Suitable for further processing

**CSV Export:**
- Spreadsheet-compatible format
- Includes key results
- Easy to import into databases
- Suitable for bulk analysis

## Troubleshooting Reports

### Common Issues

**Missing Genes:**
- Check file coverage
- Verify reference genome
- Review analysis logs
- Consider alternative tools

**Low Confidence Results:**
- Check sequencing quality
- Review coverage depth
- Consider additional analysis
- Consult with geneticist

**Inconsistent Results:**
- Compare with other tools
- Check analysis parameters
- Review variant calls
- Consider manual inspection

### Getting Help

**Documentation:**
- Review this guide
- Check tool-specific documentation
- Consult CPIC guidelines
- Review scientific literature

**Support:**
- Check system logs
- Review error messages
- Contact support team
- Join community discussions

## Next Steps

- **Learn about usage**: {doc}`usage`
- **Understand file formats**: {doc}`file-formats`
- **Configure advanced settings**: {doc}`../advanced-configuration`
- **Troubleshoot issues**: {doc}`troubleshooting`