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Published byJob Horatio Rich Modified over 8 years ago
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Variant Prioritization in Disease Studies
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1. Remove common SNPs Credit: goldenhelix.com
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2. Remove common exonic SNPs (from large WES studies) Credit: goldenhelix.com
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3. Select amino acid changing variants Credit: goldenhelix.com
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4. Find variants that have potential functional effect Credit: goldenhelix.com
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Predicting functional effects Conservation across species Amino acid properties Protein structure Transmembrane regions, signal peptides etc.
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Annovar: Annotate variants with all these annotations http://www.openbioinformatics.org/annovar/ Web version: http://wannovar.usc.edu/
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Web ANNOVAR - basic
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Web ANNOVAR - Advanced
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Most times that’s still not enough to find a causative variant If the list is still too large and/or no obvious candidate variant stands out… Then we go ‘digging’ in the context of existing knowledge about genes, their product functions and known involvement in phenotypes and diseases…
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Typical questions bioinformaticists ask (or should): Is the variant in a known disease gene? Is it in a gene involved in a related disease? Does the gene have a function that coincides with the pathology, biochemistry, etc? Is the gene product in a pathway associated with the disease? But that’s a lot of literature and databases to sift through!
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Semantic database for disease genomics (my personal project) The dream: ASSIMILATE millions of biomedical and genetic facts and their inter-relations into a database in a way a biologist thinks about them Enable simultaneous querying across those facts from multiple knowledge domains in the way a biologist would Report relevant results along with their meaning
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The B.O.R.G. (BioOntological Relationship Graph) “Resistance is futile, your data will be assimilated…”
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Disease-specific semantic model For guilt by association or indirect association
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Known disease gene
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Potential novel disease gene
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THE BORG “Resistance is futile… You WILL be assimilated…”
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THANK YOU (Please fill out the feedback form) Assessment reports due 22 March junaid@sanbi.ac.za
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