NGS analysis using LOVD+ - MolMed · Ivo Fokkema Claudia Ruivenkamp NGS analysis using LOVD+ -...
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Ivo Fokkema Claudia Ruivenkamp NGS analysis using LOVD + - introducon Johan den Dunnen
Transcript of NGS analysis using LOVD+ - MolMed · Ivo Fokkema Claudia Ruivenkamp NGS analysis using LOVD+ -...
Ivo Fokkema
Claudia Ruivenkamp
NGS analysis using LOVD+ - introduction
Johan den Dunnen
© Claudia Ruivenkamp, Johan den Dunnen, Ivo FokkemaLOVD+
Based on LOVD v3 platform
• VCF file (genomic variants) loaded intoannotation tool, like Ensembl VEP• Maps variants to selected transcripts• Adds annotations
• LOVD+ pre-filters annotated VCF file and imports data• Analyze results using customizable analyses• Used in accredited diagnostic labs
NGS analysis using LOVD+
© Claudia Ruivenkamp, Johan den Dunnen, Ivo FokkemaLOVD+
• Supports trio-analysis• Multi-sample VCF file or genotype of the parents in annotation• Complex family structures also possible, separate VCF files
• Pre-set inheritance based filtering• De novo, X-linked, recessive, imprinting
• Analysis of whole exome or using gene panels• Create gene panels with full history or define quick custom panels
• Link to third party software• e.g. Alamut, genome browsers, OMIM, LOVD search
Analysis NGS data
© Claudia Ruivenkamp, Johan den Dunnen, Ivo FokkemaLOVD+
View samples
Samples loaded for analysis;
analysis based on gene panels
© Claudia Ruivenkamp, Johan den Dunnen, Ivo Fokkema
Gene panel design
LOVD+
Simple forms for
gene panel design
NOTE: whether variants are linked to
a gene is defined during
variant annotation.
VEP uses a gene +/- 5000 bp.
© Claudia Ruivenkamp, Johan den Dunnen, Ivo Fokkema
Gene panel design
LOVD+
LOVD+ provides full
gene panel history
NOTE: whether variants are linked to
a gene is defined during
variant annotation.
VEP uses a gene +/- 5000 bp.
© Claudia Ruivenkamp, Johan den Dunnen, Ivo Fokkema
Individual’s analysis view
LOVD+
© Claudia Ruivenkamp, Johan den Dunnen, Ivo Fokkema
Details WES data
QC check
Details NGS
LOVD+
© Claudia Ruivenkamp, Johan den Dunnen, Ivo Fokkema
Details WES data
Details NGS
LOVD+
coverage
© Claudia Ruivenkamp, Johan den Dunnen, Ivo Fokkema
Details WES data
Details NGS
LOVD+
Informationand controls
© Claudia Ruivenkamp, Johan den Dunnen, Ivo Fokkema
• 3 standard inheritance patterns (de novo, X-linked, recessive)• Stringent variant filtering
Gene panel analysis
LOVD+
pane selected
tabular display of analyses
© Claudia Ruivenkamp, Johan den Dunnen, Ivo Fokkema
Imprinted genes
Separate analysis for variants in imprinted genes
LOVD+
© Claudia Ruivenkamp, Johan den Dunnen, Ivo Fokkema
Variant coloring
LOVD+
Variants colored based on predicted effect• red = nonsense, frame shift, splicing• orange = missense, in-frame coding• green = silent, in UTR, intronic• blue = more than 1 predicted effect
© Claudia Ruivenkamp, Johan den Dunnen, Ivo Fokkema
Variant details
LOVD+
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© Claudia Ruivenkamp, Johan den Dunnen, Ivo Fokkema
User levels
- Different user levels- Read only account- Analyzer (for this demo)- Manager- Administrator
- Higher user levels...- May confirm analyses and select a final classification- May add, remove or customize fields and change settings- May create more users- May monitor progress of data imports
LOVD+
© Claudia Ruivenkamp, Johan den Dunnen, Ivo Fokkema
Open source
- Open source software- See: www.lovd.nl/plus/- Preparing new release- Preparing documentation
- Support- May be required for
- Installation, customization or handling different file formats- Training- Adding / modifying analyses
- Offered by:
LOVD+
© Claudia Ruivenkamp, Johan den Dunnen, Ivo Fokkema
LOVD+ practical
http://courses.lovd.nl/LOVD+/
Practical at the Documentation tab
Username: demo# (# = your participant ID)Password: demo
LOVD+
Ivo Fokkema
Claudia Ruivenkamp
Questions ?
Johan den Dunnen
