Genomic data interpretation solution: Alamut …bioinfo.univ-rouen.fr/seqbio2018/slides/seqbio2018...Alamut database HUGO Genes PUBMED Abstracts UCSC GENOME BIOINFORMATICS Conservation

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Dr. André Blavier, MD-MSScientific Director - Interactive Biosoftware, a SOPHiA GENETICS company    

Genomic data interpretation solution:Alamut powered by SOPHiA 

• Variability of the human genome

• Rarity of disease-causing variants

• Limited understanding of molecular mechanisms

→ Interpretation is challenging1/3 of ClinVar variants classified as “Uncertain Significance”

The interpretation challenges

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Diving deep into genomic variants

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AlignmentAlignment VariantCallingVariantCalling AnnotationAnnotation FilteringFiltering ReportingReporting

Secondary Analysis

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Tertiary Analysis

Alamut offerings

PrimaryAnalysis

SequencerSequencer

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Alamut database

HUGOGenes

PUBMEDAbstracts

UCSC GENOME BIOINFORMATICSConservation

NCBIREFSEQ

ENSEMBL

GenomeTranscripts DBSNP

GNOMADNHLBI GO ESP1000GCLINVARCOSMIC

Variants

EMBL-EBIINTERPROENSEMBL

DomainsOrthologues

LOVDLSDBs

UNIPROTProteins

Missense variants

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AlignmentAlignment VariantCallingVariantCalling AnnotationAnnotation FilteringFiltering ReportingReporting

PrimaryAnalysis

Secondary Analysis

……

Tertiary Analysis

Alamut offerings

SequencerSequencer

Advanced variant exploration

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Graphic interface

Publicbiological data

Local database

Alamut Genova

Predictionalgorithms

Private data

ReportingVariant datamanagement Shared database

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Main features

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Full genome browser

Covering the entire human genome

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Full genome browser• Structural variants, CNVs• Intergenic annotations, e.g. regulatory features

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Full genome browser

• Mitochondrial genome

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Gene view

Redesigned to make it better

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New splicing track and predictions

SPiCE (Leman et al. NAR 2018) - soon available

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Implementation of ACMG/AMP guidelines

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3D protein visualization

Toward protein level predictions

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Comprehensive report_1

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Comprehensive report_2

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Benefits

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