Custom Genome Browser for Clinical Diagnostics Lab
Tailored visualization tool enhances workflow for NIPT, congenital anomaly, and familial genome testing
Client Overview
A regional diagnostics laboratory specializing in prenatal and genetic testing needed a custom genome browser tailored to their specific clinical workflows. Generic tools didn't meet their unique requirements for NIPT analysis, congenital anomaly detection, and familial variant interpretation.
The Challenge
Workflow-Specific Requirements
Each test type (NIPT, congenital anomaly, familial genome) required different visualization modes, annotation tracks, and interpretation workflows. Generic genome browsers forced scientists to adapt their workflow to the tool.
NIPT-Specific Visualization
NIPT analysis requires chromosome-level copy number visualization with Z-score plots and fetal fraction estimates. Standard browsers lacked these specialized views.
Family Pedigree Integration
Familial testing required viewing variants across multiple family members simultaneously with inheritance pattern visualization. No existing tool provided this integrated view.
Clinical Reporting Needs
Lab scientists needed to annotate variants, add clinical interpretations, and generate reports directly from the browser. Switching between tools was inefficient.
Data Privacy & Security
Patient genomic data required strict access controls, audit trails, and compliance with local data protection regulations.
Our Approach: Customer-Centric Design
We worked closely with the lab team to understand their daily workflows and pain points, then built a custom solution tailored to their specific needs.
1. Requirements Gathering
Conducted on-site observations and interviews:
- Shadowed lab scientists during variant review sessions
- Documented step-by-step workflows for each test type
- Identified bottlenecks and inefficiencies in current process
- Gathered wish-list features from clinical geneticists
- Understood reporting requirements and turnaround time constraints
2. NIPT-Specific Features
Chromosome Copy Number View:
- Z-Score Plots: Chromosome-level visualization with automated aneuploidy detection
- Fetal Fraction Display: Prominent display of fetal fraction with quality flags
- Reference Ranges: Customizable thresholds based on lab's validation data
- Batch Comparison: Compare current sample against recent controls
Quality Control Dashboard:
- Read depth metrics across chromosomes
- GC bias visualization
- Automated QC pass/fail indicators
- Flagging of samples requiring repeat testing
3. Congenital Anomaly Testing Features
CNV Detection & Visualization:
- Segmentation View: Clear visualization of copy number segments
- Gene Content: Automatic annotation of genes within CNV regions
- OMIM Integration: Direct links to disease associations
- DGV Comparison: Overlay with Database of Genomic Variants
Pathogenicity Assessment:
- ACMG classification criteria checklist
- Population frequency from gnomAD
- ClinVar annotations with conflict resolution
- Literature references from PubMed
4. Familial Genome Analysis Features
Multi-Sample View:
- Pedigree Visualization: Interactive family tree with genotypes
- Segregation Analysis: Automatic inheritance pattern detection
- Shared Variants: Highlight variants segregating with disease
- Compound Heterozygotes: Identify gene pairs with biallelic variants
Filtering Workflows:
- Preset filters for dominant, recessive, X-linked patterns
- Custom filter builder for complex scenarios
- Save and share filter configurations
- Undo/redo filter operations
5. Clinical Workflow Integration
Annotation & Interpretation:
- In-Browser Notes: Add comments and interpretations directly on variants
- Classification System: ACMG/AMP variant classification with evidence tracking
- Collaboration: Tag colleagues for review, discussion threads
- Version History: Track interpretation changes over time
Report Generation:
- One-click report generation with lab's template
- Automatic inclusion of relevant variants and interpretations
- Customizable report sections
- Export to PDF with embedded IGV snapshots
6. User Experience Design
Focused on making the tool intuitive for lab scientists:
- Test-Type Modes: One-click switch between NIPT, CNV, and familial analysis modes
- Keyboard Shortcuts: Power users can navigate entirely via keyboard
- Customizable Layouts: Save preferred track arrangements and panel configurations
- Responsive Design: Works on lab workstations and tablets for bedside consultations
- Minimal Training: Intuitive interface required < 2 hours training
Technology Stack:
Implementation & Deployment
Discovery Phase (Week 1-2)
On-site workflow observation, requirements gathering, mockup design and feedback sessions with lab team.
Development Sprint 1 (Week 3-6)
Built core genome browser with NIPT-specific features. Weekly demos and feedback incorporation.
Development Sprint 2 (Week 7-10)
Added CNV analysis and familial genome features. Integrated with lab's LIMS system.
Testing & Refinement (Week 11-12)
Parallel testing with real cases, bug fixes, performance optimization, user training.
Deployment & Support (Week 13+)
Production deployment, ongoing support, feature enhancements based on user feedback.
Results & Impact
Faster Variant Review
Variant interpretation time reduced by 40%. Scientists can review more cases per day without compromising quality.
Improved Accuracy
Integrated ACMG criteria and automated checks reduced classification errors. Fewer cases requiring re-review.
Better Collaboration
In-browser discussion threads improved communication between lab scientists and clinical geneticists.
100% Adoption
All 12 lab scientists and 3 clinical geneticists adopted the tool within 2 weeks. Replaced all previous tools.
Before vs After
| Metric | Before | After |
|---|---|---|
| NIPT Review Time | 15 minutes/case | 8 minutes/case |
| CNV Analysis Time | 45 minutes/case | 25 minutes/case |
| Familial Analysis Time | 2 hours/family | 1.2 hours/family |
| Report Generation | 30 minutes | 5 minutes |
| Tools Used | 5 different tools | 1 integrated platform |
Customer Service & Support
Our commitment extended beyond initial deployment:
Ongoing Support
- Dedicated Support Channel: WhatsApp group for quick questions and issues
- Monthly Check-ins: Regular calls to gather feedback and discuss enhancements
- Feature Requests: Prioritized roadmap based on lab's evolving needs
- Training Updates: Sessions for new staff members
- Bug Fixes: 24-hour response time for critical issues
Continuous Improvement
Post-deployment enhancements based on user feedback:
- Added batch processing for high-volume NIPT days
- Integrated with lab's billing system for automated invoicing
- Built mobile app for on-call geneticists
- Added machine learning-based variant prioritization
- Implemented advanced search across historical cases
SyncBio didn't just build us a genome browser—they built exactly what we needed. They took the time to understand our workflows, watched us work, and designed a tool that feels like it was made by someone who does this job every day. Our team loves it, and we're much more efficient now.
Need a Custom Solution?
Let SyncBio build tailored software that fits your exact workflow and requirements.
Discuss Your Project