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Rare Disease Genome Analysis Guide
Authorities and Responsibilities
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Background
Bioinformatics pipeline
Variant prioritisation approaches
Additional information
Release notes
Rare Disease Genome Analysis Guide
Background
Background
Pipeline Overview
Purpose
Scope
Target Audience
Authorities and Responsibilities
Bioinformatics pipeline
Bioinformatics pipeline
Genome alignment and variant detection
Genome alignment and variant detection
Overview
de novo variant detection
Mitochondrial variant detection
Quality control and genomic identity checks
Quality control and genomic identity checks
Genomic and data checks
SNP identity checks (Sample Matching Service)
Quality control
Case flags in the CIP-API and Interpretation Portal
Variant prioritisation approaches
Variant prioritisation approaches
Pre-interpretation review and virtual gene panel assignment
PanelApp
PanelApp
Overview
Use of virtual gene panels
PanelApp criteria for diagnostic grade 'green' genes
Small variant tiering
Small variant tiering
Overview
Tiers
Tiering algorithm
Filter status
Population frequency
Predicted functional impact
Segregation with disease
Variants with pathogenic/likely pathogenic disease associations
Variant inclusion list
Variant exclusion list
Penetrance modes
Additional notes
Copy number variant tiering
Copy number variant tiering
Overview
Sample quality control
CNV frequency annotation
Detection of CNVs between 2-10kb
Measurement of uncertainty of CNV breakpoints
Short tandem repeats
Short tandem repeats
Overview
STR tiering
Measurement of uncertainty of STR allele sizing
STR visualisation
Exomiser
Exomiser
Overview
Exomiser implementation in Genomics England Rare Disease pipeline
Validation of Exomiser performance
Exomiser configuration
Exomiser database versions
Uniparental disomy
Additional information
Additional information
Abbreviations and Glossary
Software and Database Versions
Pipeline sensitivity and precision
Coverage profile data
Clinical Interpretation Portal-API
Decision Support Systems (DSS)
GMS interpretation portal
Genome data available through IGV.js
Limitations of the Rare Disease bioinformatics pipeline
Links to supporting documentation
Feedback
Release notes
Authorities and Responsibilities
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