Variant interpretation with theAlamut® Software Suite
Presenters: André Blavier, Alexandros Hatzoglou
Company
• Established in 2007
• Based in Rouen, Normandie, France
• Software company focused onmedical molecular genetics
• Participant in
• (Medical Devices)
VEP Training Course - Heraklion 2016
The Alamut® Software Suite
Sequencer Alignment Variant Detection Annotation Filtering Interpretation
Reporting
DNA Reads Variants Mutations
VEP Training Course - Heraklion 2016
Alamut Batch
Sequencer Alignment Variant Detection Annotation Filtering Interpretation
Reporting
DNA Reads Variants Mutations
VEP Training Course - Heraklion 2016
High-throughput variant annotation engine for NGS analysis
Raw VariantsChr3:37055960 G>A
…
Gene: MLH1Transcript: NM_000249.3Exon: 9Coding Effect: MissenseNomen: p.(Ala239Thr)…
Alamut Batch
VEP Training Course - Heraklion 2016
Distinctive features
• Uses high-quality Alamut® database• Supports LRGs and RefSeqGenes• Extensive annotation set• Splicing predictions• GUI (Windows) and command-line (Linux,
Windows)
Alamut Focus
Sequencer Alignment Variant Detection Annotation Filtering Interpretation
Reporting
DNA Reads Variants Mutations
VEP Training Course - Heraklion 2016
Interactive variant filtration
AnnotatedVariants
CandidateVariants
Alamut Focus
VEP Training Course - Heraklion 2016
Alamut Focus
VEP Training Course - Heraklion 2016
Alamut Focus
VEP Training Course - Heraklion 2016
Alamut Focus
VEP Training Course - Heraklion 2016
Alamut Focus
VEP Training Course - Heraklion 2016
Alamut Focus
VEP Training Course - Heraklion 2016
Alamut Focus
VEP Training Course - Heraklion 2016
Alamut Focus
VEP Training Course - Heraklion 2016
Alamut Focus
VEP Training Course - Heraklion 2016
Distinctive features
• Supports interactive/exploratory filtration• Clinically oriented• Built-in inheritance models• Linked to Alamut Batch & Alamut Visual
Alamut Visual
Sequencer Alignment Variant Detection Annotation Filtering Interpretation
Reporting
DNA Reads Variants Mutations
VEP Training Course - Heraklion 2016
Decision-support system for variant interpretation
Alamut Visual
VEP Training Course - Heraklion 2016
Visual interface
Publicbiological data
Predictionalgorithms
Privatedata
Variant management ReportingLocal database Shared database
AlamutDatabase
Alamut Visual – Data Sources
VEP Training Course - Heraklion 2016
RefSeq dbSNP
-Genome-Transcripts
HUGO
InterPro
DomainsVariants
Genes-Proteins-Missense variants
+OrthologuesLSDBs
Abstracts
Conservation
Mutations
NHLBI GO ESPExAC
VEP Training Course - Heraklion 2016
Ref. Genome
Conservation
Ref. transcripts
dbSNPvariations
ESP, ExACvariations
HGMD, ClinVarmutations
Proteindomains
Orthologues
VEP Training Course - Heraklion 2016
Please navigate to:training.interactive-biosoftware.com/heraklion
VEP Training Course - Heraklion 2016
www.interactive-biosoftware.com