Variant interpretation with the Alamut® Software Suite · 2016-11-09 · Alamut Batch Sequencer...

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Variant interpretation with the Alamut® Software Suite Presenters: André Blavier, Alexandros Hatzoglou

Transcript of Variant interpretation with the Alamut® Software Suite · 2016-11-09 · Alamut Batch Sequencer...

Page 1: Variant interpretation with the Alamut® Software Suite · 2016-11-09 · Alamut Batch Sequencer Alignment Variant Detection Annotation Filtering Interpretation Reporting DNA Reads

Variant interpretation with theAlamut® Software Suite

Presenters: André Blavier, Alexandros Hatzoglou

Page 2: Variant interpretation with the Alamut® Software Suite · 2016-11-09 · Alamut Batch Sequencer Alignment Variant Detection Annotation Filtering Interpretation Reporting DNA Reads

Company

• Established in 2007

• Based in Rouen, Normandie, France

• Software company focused onmedical molecular genetics

• Participant in

• (Medical Devices)

VEP Training Course - Heraklion 2016

Page 3: Variant interpretation with the Alamut® Software Suite · 2016-11-09 · Alamut Batch Sequencer Alignment Variant Detection Annotation Filtering Interpretation Reporting DNA Reads

The Alamut® Software Suite

Sequencer Alignment Variant Detection Annotation Filtering Interpretation

Reporting

DNA Reads Variants Mutations

VEP Training Course - Heraklion 2016

Page 4: Variant interpretation with the Alamut® Software Suite · 2016-11-09 · Alamut Batch Sequencer Alignment Variant Detection Annotation Filtering Interpretation Reporting DNA Reads

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)…

Page 5: Variant interpretation with the Alamut® Software Suite · 2016-11-09 · Alamut Batch Sequencer Alignment Variant Detection Annotation Filtering Interpretation Reporting DNA Reads

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)

Page 6: Variant interpretation with the Alamut® Software Suite · 2016-11-09 · Alamut Batch Sequencer Alignment Variant Detection Annotation Filtering Interpretation Reporting DNA Reads

Alamut Focus

Sequencer Alignment Variant Detection Annotation Filtering Interpretation

Reporting

DNA Reads Variants Mutations

VEP Training Course - Heraklion 2016

Interactive variant filtration

AnnotatedVariants

CandidateVariants

Page 7: Variant interpretation with the Alamut® Software Suite · 2016-11-09 · Alamut Batch Sequencer Alignment Variant Detection Annotation Filtering Interpretation Reporting DNA Reads

Alamut Focus

VEP Training Course - Heraklion 2016

Page 8: Variant interpretation with the Alamut® Software Suite · 2016-11-09 · Alamut Batch Sequencer Alignment Variant Detection Annotation Filtering Interpretation Reporting DNA Reads

Alamut Focus

VEP Training Course - Heraklion 2016

Page 9: Variant interpretation with the Alamut® Software Suite · 2016-11-09 · Alamut Batch Sequencer Alignment Variant Detection Annotation Filtering Interpretation Reporting DNA Reads

Alamut Focus

VEP Training Course - Heraklion 2016

Page 10: Variant interpretation with the Alamut® Software Suite · 2016-11-09 · Alamut Batch Sequencer Alignment Variant Detection Annotation Filtering Interpretation Reporting DNA Reads

Alamut Focus

VEP Training Course - Heraklion 2016

Page 11: Variant interpretation with the Alamut® Software Suite · 2016-11-09 · Alamut Batch Sequencer Alignment Variant Detection Annotation Filtering Interpretation Reporting DNA Reads

Alamut Focus

VEP Training Course - Heraklion 2016

Page 12: Variant interpretation with the Alamut® Software Suite · 2016-11-09 · Alamut Batch Sequencer Alignment Variant Detection Annotation Filtering Interpretation Reporting DNA Reads

Alamut Focus

VEP Training Course - Heraklion 2016

Page 13: Variant interpretation with the Alamut® Software Suite · 2016-11-09 · Alamut Batch Sequencer Alignment Variant Detection Annotation Filtering Interpretation Reporting DNA Reads

Alamut Focus

VEP Training Course - Heraklion 2016

Page 14: Variant interpretation with the Alamut® Software Suite · 2016-11-09 · Alamut Batch Sequencer Alignment Variant Detection Annotation Filtering Interpretation Reporting DNA Reads

Alamut Focus

VEP Training Course - Heraklion 2016

Page 15: Variant interpretation with the Alamut® Software Suite · 2016-11-09 · Alamut Batch Sequencer Alignment Variant Detection Annotation Filtering Interpretation Reporting DNA Reads

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

Page 16: Variant interpretation with the Alamut® Software Suite · 2016-11-09 · Alamut Batch Sequencer Alignment Variant Detection Annotation Filtering Interpretation Reporting DNA Reads

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

Page 17: Variant interpretation with the Alamut® Software Suite · 2016-11-09 · Alamut Batch Sequencer Alignment Variant Detection Annotation Filtering Interpretation Reporting DNA Reads

Alamut Visual

VEP Training Course - Heraklion 2016

Visual interface

Publicbiological data

Predictionalgorithms

Privatedata

Variant management ReportingLocal database Shared database

Page 18: Variant interpretation with the Alamut® Software Suite · 2016-11-09 · Alamut Batch Sequencer Alignment Variant Detection Annotation Filtering Interpretation Reporting DNA Reads

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

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VEP Training Course - Heraklion 2016

Ref. Genome

Conservation

Ref. transcripts

dbSNPvariations

ESP, ExACvariations

HGMD, ClinVarmutations

Proteindomains

Orthologues

Page 20: Variant interpretation with the Alamut® Software Suite · 2016-11-09 · Alamut Batch Sequencer Alignment Variant Detection Annotation Filtering Interpretation Reporting DNA Reads

VEP Training Course - Heraklion 2016

Please navigate to:training.interactive-biosoftware.com/heraklion

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VEP Training Course - Heraklion 2016

www.interactive-biosoftware.com


Assassins of Alamut by James Boschert

Assassins of Alamut by James Boschert

ESMO Virtual Advanced Course on Biomarkers for Precision ......20’ Clinical Variant Interpretation, Antoine Italiano, FR 20’ Harmonizing variant interpretation, Alex H. Wagner,

ESMO Virtual Advanced Course on Biomarkers for Precision ......20’ Clinical Variant Interpretation, Antoine Italiano, FR 20’ Harmonizing variant interpretation, Alex H. Wagner,

THE ASSASSINS OF ALAMUT

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Summary of Interpretation of sequence variants schemes ... Moore... · – Alamut predictions suggest that the nucleotide change is unlikely to affect splicing but this is not definitive.

Summary of Interpretation of sequence variants schemes ... Moore... · – Alamut predictions suggest that the nucleotide change is unlikely to affect splicing but this is not definitive.

Variant Interpretation for Cancer Consortium (VICC) · 2020-01-22 · genomicsandhealth.org Mul0ple groups are now curang clinical interpretaons for cancer variants – Problem too

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Interpreting NGS Data - Agilent · PR7000-0663 What You’ll Learn Today Variant Call Format •Components •Format types Recommendations for NGS Interpretation Publicly available

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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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An Investigation into Eco-tourism Potential of the Alamut Region … · Keywords: Ecotourism, SWOT, Strategic factors, Alamut, weighted score. Introduction . Today the subject of

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DEVELOPER DATA SHEET - Bluefish444 Epoch... · DEVELOPER DATA SHEET A VARIANT B VARIANT C VARIANT D VARIANT E VARIANT X ... Neutron Full-height - LTC I/O / RS-422 EB3007X Epoch |

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Genome analysis and knowledge-driven variant interpretation with … · 2020. 1. 1. · SOFTWARE Open Access Genome analysis and knowledge-driven variant interpretation with TGex

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Hands-on Workshop Variant Interpretation and Classificationvariantworkshop.org/igv/AMP 2019 Routbort - Variant Interpretation and Classification.pdfStart up IGV, display a test message

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4,400 117,000 130M...Chapter Bioinformatics Workflows for Genomic Variant Discovery, Interpretation and Prioritization Osman Ugur Sezerman, Ege Ulgen, Nogayhan Seymen

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Progress of the InSiGHT Mismatch Repair Gene Database and Variant Interpretation Committee - Application of Classification Rules and Dissemination of Results - Finlay Macrae

Progress of the InSiGHT Mismatch Repair Gene Database and Variant Interpretation Committee - Application of Classification Rules and Dissemination of Results - Finlay Macrae

Challenges and complexities in the interpretation of ... · Challenges and complexities in the interpretation of mitochondrial DNA ... >1500 mtDNA genomes ... • Variant interpretation

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Alamut® Batch 1.8 User Manual - Interactive Biosoftware · 2017-10-12 · Alamut® Batch 1.8 User Manual 3 Product description Alamut Batch is a high-throughput annotation engine

Alamut® Batch 1.8 User Manual - Interactive Biosoftware · 2017-10-12 · Alamut® Batch 1.8 User Manual 3 Product description Alamut Batch is a high-throughput annotation engine

PANDA: pathway and annotation explorer for visualizing and ... · Keywords Pathway, Visualization, Genomics, User interface, Data integration, Variant interpretation, Annotation and

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Variant Detection & Interpretation in a diagnostic context · Variant Detection & Interpretation in a diagnostic context Christian Gilissen c.gilissen@gen.umcn.nl 28-05-2013

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A lam ut G e nov Us r M - interactive-biosoftware.com · Alamut ® Genova is a component of the Alamut ® Software Suite, a set of applications dedicated to genomic variant annotation,

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F-4 Phantom II Variant by Variant (1)

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Güvercinin Gerdanlığı Alamut

Güvercinin Gerdanlığı Alamut