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in a quality perspective

in a quality perspective. Alamut. Gene browser over 18,000+ human protein-coding genes Advanced visualization of gene-related annotations Integration of prediction tools Variant management and reporting HGVS nomenclature compliancy. Alamut. Ref . Genome. Conservation.

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in a quality perspective

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  1. in a quality perspective UK NEQAS UV Participants Meeting 2013

  2. Alamut • Gene browser over 18,000+ human protein-coding genes • Advanced visualization of gene-related annotations • Integration of prediction tools • Variant management and reporting • HGVS nomenclature compliancy UK NEQAS UV Participants Meeting 2013

  3. Alamut Ref. Genome Conservation Ref. transcripts dbSNP variations ESP variations HGMD mutations Proteindomains Orthologues UK NEQAS UV Participants Meeting 2013

  4. Data Sources dbSNP NHLBI GO ESP RefSeq InterPro -Genome -Transcripts Domains Variants LSDBs +Orthologues Conservation Genes HUGO -Proteins -Missense variants Mutations Alamut Database Abstracts UK NEQAS UV Participants Meeting 2013

  5. MissensePredictions UK NEQAS UV Participants Meeting 2013

  6. SplicingPredictions UK NEQAS UV Participants Meeting 2013

  7. ExerciseCriticalJudgment! • Software = Program code + Data UK NEQAS UV Participants Meeting 2013

  8. ExerciseCriticalJudgment! • Software = Program code + bugs + Data + errors UK NEQAS UV Participants Meeting 2013

  9. ExerciseCriticalJudgment! • Software = Program code + bugs + Data + errors UK NEQAS UV Participants Meeting 2013

  10. Data • dbSNP is not a database of polymorphisms • Conservation scores depend on sequences and alignment algorithms • Transcripts can be misplaced (very unusual) • Protein domains are mostly predicted • Orthologues are mostly computed UK NEQAS UV Participants Meeting 2013

  11. MissensePredictions • WhyAlign GVGD, PolyPhen-2, SIFT, MutationTaster? • Reputation • Automatability • Right to use in commercial software • Complexalgorithmsbased on AA physico-chemicalproperties, AA conservation, protein structure, and more • Predictions ±stronglydepend on Alamut-suppliedorthologuealignment UK NEQAS UV Participants Meeting 2013

  12. SplicingPredictions • Why SSF, MaxEnt, NNSPLICE, GeneSplicer, HSF? • ditto • Simple algorithms based on sequence • MaxEnt often considered as the most accurate • (Splicing regulation predictions: for experts only!) UK NEQAS UV Participants Meeting 2013

  13. Quality Contribution • Up-to-date data • Visual feedback • HGVS nomenclature (when in doubt check with Mutalyzer) • Manually-curated orthologue alignments • NGS alignment and coverage visualization UK NEQAS UV Participants Meeting 2013

  14. NGS AlignmentViewer UK NEQAS UV Participants Meeting 2013

  15. Alamut / CMGS-VKGL Guidelines • 3.3 Variant Nomenclature • 3.4 Variant Submission • 4.1 LSDBs • 4.2 SNP Databases • 4.7 Species Conservation • 4.8 MissensePredictions • 4.9 Splice Site Predictions • 4.14 InterpretationProcessStandardization • 5.1 ReportingVariants • 5.4 Variant Classification UK NEQAS UV Participants Meeting 2013

  16. 34 labs UK NEQAS UV Participants Meeting 2013

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