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Genomic Variant Analysis and Prioritization: Tools and Resources

Explore the world of genomic variant analysis with this comprehensive guide that provides an overview of data mining, sequence information mapping, phenotypic information, and literature prediction programs. Learn about gene prediction, promoter prediction, functional prediction, and structural prediction, as well as variant annotation and prioritization. Discover various tools and resources, such as genome browsers, ENSEMBL, UCSC, ENSEMBL Tools, Assembly Converter, and DECIPHER, that can assist in genomic variant analysis. Gain insights into mutation and polymorphism databases, prediction programs, splicing finder programs, and batch annotators for gene panel and whole exome sequencing.

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Genomic Variant Analysis and Prioritization: Tools and Resources

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  1. Data mining

  2. Data mining • Sequence information • Mapping information • Phenotypic information • Literature • Prediction programs • Gene prediction • Promotor prediction • Functional prediction • Structural prediction • Variant annotation

  3. http://www.ncbi.nlm.nih.gov/

  4. Genome browsers • ENSEMBL: http://www.ensembl.org/index.html • UCSC : http://genome.ucsc.edu/

  5. http://www.ensembl.org/index.html

  6. Ensembl Tools

  7. http://genome.ucsc.edu/

  8. Assembly converter

  9. http://dgv.tcag.ca/dgv/app/home

  10. https://decipher.sanger.ac.uk/

  11. Genomic variant analysis • Genomic variants • Mutation: literature, HGMD, gene specific databases • Polymorphism: dbSNP, EVS, ExAC • Prediction programs

  12. http://www.ncbi.nlm.nih.gov/SNP/

  13. http://evs.gs.washington.edu/EVS/

  14. ExAC (http://exac.broadinstitute.org/)

  15. ExAC

  16. Kaviar: http://db.systemsbiology.net/kaviar/

  17. Kaviar: http://db.systemsbiology.net/kaviar/

  18. http://sift.jcvi.org/

  19. CFTR: p.N1303K

  20. CFTR: p.N1303K

  21. Polyphenhttp://genetics.bwh.harvard.edu/pph2/

  22. Mutation Taster http://www.mutationtaster.org/

  23. But beware……!!!!! There are many examples of known pathogenic variants predicted to be benign and vice versa

  24. Human Splicing Finderhttp://www.umd.be/HSF/

  25. Splice Site Predictionhttp://www.fruitfly.org/seq_tools/splice.html

  26. Splice finder programs GeneSplicer http://www.cbcb.umd.edu/software/GeneSplicer/gene_spl.shtml Netgene http://www.cbs.dtu.dk/services/NetGene2/

  27. http://scholar.google.be

  28. Batch Annotators & Prioritization Gene Panel / Whole Exome Sequencing • Large amounts of variants (50-50,000) • Needed information for interpretation: • Location w.r.t. gene (intron/exon/splicing) • Effect on CDS (synonymous/stop-gain/frameshift/...) • Severity of the effect • Function of gene w.r.t. phenotype Example Applications: wANNOVAR: http://wannovar.usc.edu SeattleSeq: http://snp.gs.washington.edu/SeattleSeqAnnotation141/ VEP: http://www.ensembl.org/Tools/VEP VariantDB: http://biomina.be/apps/variantdb eXtasy: http://extasy.esat.kuleuven.be/ Exomiser: http://www.sanger.ac.uk/science/tools/exomiser

  29. VEP

  30. Batch Annotators: wAnnovar

  31. NCBI http://www.ncbi.nlm.nih.gov/ Ensembl http://www.ensemble.org/index.html UCSC http://genome.ucsc.edu/ Genatlas http://genatlas.medecine.univ-paris5.fr/ PolyPhen http://genetics.bwh.harvard.edu/pph2/ SIFT http://sift.jcvi.org/ Mutation taster http://www.mutationtaster.org/ Splice prediction http://www.umd.be/HSF/ http://www.fruitfly.org/seq_tools/splice.html http://www.cbs.dtu.dk/services/NetGene2/ DECIPHER https://decipher.sanger.ac.uk/

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