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Fundamentals of Exome Analysis
- 1. Fundamentals of Analysis of Exomes Diego Forero, MD, PhD Assistant Professor Director, Laboratory of NeuroPsychiatric Genetics Director, Medical Research Office School of Medicine Antonio Nariño University Bogotá, Colombia Editor, hum-molgen.org diego.forero@uan.edu.co
- 2. CAUSAL GENES FOR MENDELIAN DISORDERS Mendelian Autosomal Sex-linked Total Disorders Causal Gene 3.175 266 3.441 Known Causal Gene 1.633 140 1.773 Unknown Online Mendelian Inheritance in Man
- 3. Exomes: Publication Trends 600 Total: 925 (Oct 2012) 500 400 Papers 300 200 100 0 2005 2006 2007 2008 2009 2010 2011 2012 2013 Year 2013: ~ 800 papers 2014: ~ 1200 papers Forero DA, 2012
- 5. Majewski, J Med Genet 2011
- 6. Majewski, J Med Genet 2011
- 7. From Data Generation to Data Analysis
- 8. A timeline illustrating technological breakthroughs and hallmark publications for Mendelian disease gene identification Gilissen, Genom Biol 2011
- 9. A timeline illustrating technological breakthroughs and hallmark publications for Mendelian disease gene identification Gilissen, Genom Biol 2011
- 10. First Published Exome "We focus here on the variants in a person’s ‘exome,’ which is the set of exons in a genome..." Ng, PLoS Genet 2008
- 11. A representation of the relationship between the size of the mutational target and the frequency of disease for disorders caused by de novo mutations Gilissen, Genom Biol 2011
- 12. Majewski, J Med Genet 2011
- 13. Strategies for finding disease-causing rare variants using exome sequencing Bamshad, Nat Rev Genet 2011
- 14. Typical heuristic filtering applied to exome sequencing projects aimed at novel gene discovery for Mendelian disorders Stitziel, Genom Biol 2011
- 15. Mean number of coding variants in two populations Bamshad, Nat Rev Genet 2011
- 16. First identification of the causal gene for a monogenic disorder by exome sequencing Freeman–Sheldon syndrome (MYH3) Ng, Nature 2009
- 17. Exome Analysis for One Patient Perrault syndrome (HSD17B4) Pierce, Am J Hum Genet 2010
- 18. Useful In Silico Tools VarSifter http://research.nhgri.nih.gov/software/VarSifter/index.shtml Exome Variant Server (6503 exomes) http://evs.gs.washington.edu/EVS/ wANNOVAR http://wannovar.usc.edu/
- 19. Useful In Silico Tools Atlas2 Suite http://sourceforge.net/p/atlas2/wiki/Atlas2%20Suite/ IBD2 http://compbio.charite.de/contao/index.php/ibd2.html EVA http://plateforme-genomique-irib.univ-rouen.fr/EVA/index.php TREAT http://ndc.mayo.edu/mayo/research/biostat/stand-alone-packages.cfm KGGSeq http://statgenpro.psychiatry.hku.hk/limx/kggseq/
- 20. Exomes-Service Providers Axeq (USA) 50x; Illumina TrueSeq/HiSeq200. $2,300 USD per sample Macrogen (Korea) 50x; Illumina TrueSeq/HiSeq200. $2,499 USD per sample BaseClear (Netherlands) 30x; Nimblegen/Illumina. € 2,499 per sample PerkinElmer (USA) 30x; Agilent/Illumina. $3,500 USD per sample BGI Americas (USA) 30x; $3,500 USD per sample EdgeBio (USA) 50x; SOLiD 4. $5,500 USD per sample DNAVision (Belgium) 30x; Agilent/Illumina. 5,990 € per sample Knome (USA) 30x; Illumina. $8,750 USD per sample Source BioScience (UK) 50x; Agilent/Illumina. 5,850GBP per sample
- 21. Example of Data Provided http://www.ncbi.nlm.nih.gov/omim Need for in-house exome data. Possible Noise from dbSNP and OMIM Data from Human Gene Mutation Database?
- 22. Candidate genes prioritization Endeavour http://homes.esat.kuleuven.be/~bioiuser/endeavour/tool/endeavourweb.php ToppGene http://toppgene.cchmc.org/prioritization.jsp
- 23. Tools for mutation pathogenicity prediction Thusberg J, Olatubosun A, Vihinen M. Performance of mutation pathogenicity prediction methods on missense variants. Hum Mutat. 2011 Apr;32(4):358-68.
- 24. Tools for mutation pathogenicity prediction MutPred http://mutpred.mutdb.org/ SNPs&GO http://snps-and-go.biocomp.unibo.it/snps-and-go/ PolyPhen-2 http://genetics.bwh.harvard.edu/pph2/ SIFT http://sift.bii.a-star.edu.sg/
- 25. www.daforerog.co.cc “This is an excellent resource for anyone who is generally interested in how these technologies work”. Stephen Turner, PhD Center for Human Genetics Research, Vanderbilt University.