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Fundamentals of Analysis of Exomes
Diego Forero, MD, PhDAssistant Professor
Director, Laboratory of NeuroPsychiatric GeneticsDirector, Medical Research Office
School of MedicineAntonio Nariño University
Bogotá, ColombiaEditor, hum-molgen.org
Online Mendelian Inheritance in Man
Mendelian Disorders
Autosomal Sex-linked Total
Causal Gene Known
3.175 266 3.441
Causal Gene Unknown
1.633 140 1.773
CAUSAL GENES FOR MENDELIAN DISORDERS
0
100
200
300
400
500
600
2005 2006 2007 2008 2009 2010 2011 2012 2013
Year
Pa
pe
rs
2013: ~ 800 papers
2014: ~ 1200 papers
Forero DA, 2012
Exomes: Publication Trends
Total: 925 (Oct 2012)
GENOMICS: PLATFORMS
Majewski, J Med Genet 2011
Majewski, J Med Genet 2011
From Data Generation to Data Analysis
A timeline illustrating technological breakthroughs and hallmark publications for Mendelian disease gene
identification
Gilissen, Genom Biol 2011
A timeline illustrating technological breakthroughs and hallmark publications for Mendelian disease gene
identification
Gilissen, Genom Biol 2011
"We focus here on the variants in a person’s ‘exome,’ which is the set of exons in a genome..."
Ng, PLoS Genet 2008
First Published Exome
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
Majewski, J Med Genet 2011
Bamshad, Nat Rev Genet 2011
Strategies for finding disease-causing rare variants using exome sequencing
Typical heuristic filtering applied to exome sequencing projects aimed at novel gene discovery for Mendelian
disorders
Stitziel, Genom Biol 2011
Bamshad, Nat Rev Genet 2011
Mean number of coding variants in two populations
First identification of the causal gene for a monogenic disorder by exome sequencing
Freeman–Sheldon syndrome (MYH3)
Ng, Nature 2009
Pierce, Am J Hum Genet 2010
Exome Analysis for One Patient
Perrault syndrome (HSD17B4)
VarSifterhttp://research.nhgri.nih.gov/software/VarSifter/index.shtml
Exome Variant Server (6503 exomes)http://evs.gs.washington.edu/EVS/
wANNOVARhttp://wannovar.usc.edu/
Useful In Silico Tools
EVAhttp://plateforme-genomique-irib.univ-rouen.fr/EVA/index.php
TREAThttp://ndc.mayo.edu/mayo/research/biostat/stand-alone-packages.cfm
KGGSeqhttp://statgenpro.psychiatry.hku.hk/limx/kggseq/
Atlas2 Suite http://sourceforge.net/p/atlas2/wiki/Atlas2%20Suite/
IBD2http://compbio.charite.de/contao/index.php/ibd2.html
Useful In Silico Tools
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
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?
Example of Data Provided
Candidate genes prioritization
Endeavourhttp://homes.esat.kuleuven.be/~bioiuser/endeavour/tool/endeavourweb.php
ToppGenehttp://toppgene.cchmc.org/prioritization.jsp
Thusberg J, Olatubosun A, Vihinen M.Performance of mutation pathogenicity prediction methods on missense variants.
Hum Mutat. 2011 Apr;32(4):358-68.
Tools for mutation pathogenicity prediction
MutPredhttp://mutpred.mutdb.org/
SNPs&GOhttp://snps-and-go.biocomp.unibo.it/snps-and-go/
PolyPhen-2http://genetics.bwh.harvard.edu/pph2/
SIFThttp://sift.bii.a-star.edu.sg/
Tools for mutation pathogenicity prediction
www.daforerog.co.cc
“This is an excellent resource for anyone who is generally interested in how these technologies work”. Stephen Turner, PhDCenter for Human Genetics Research, Vanderbilt University.
www.daforerog.co.cc
