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Practical
MutationTaster & RegulationSpotter
Daniela Hombach & Jana Marie Schwarz
Exzellenzcluster NeuroCure Charité Universitätsmedizin Berlin
AG Translational Genomics
08.11.2017
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Rare diseases
7000 – 8000 rare diseases are known.
>> World-wide more than 300 Millions patients
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Rare diseases
Mendelian Complex
# loci one multiple (polygenic)
effect ofenvironment
small high
frequency in population
rare common
effect strong weak
example cystic fibrosis,hemophilia, PKU
allergy, cancer, diabetes
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MutationTaster
Single variant query VCF query
InDels, SNVs, introns, exons, coding and non-coding variants
Go to: www.mutationtaster.org
highly-parallel fashion (500,000 variants / hour)
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SOD1
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C[A/G]TGTTCATGAG….
causes ALS
transcript-based!
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Computer based classification
• „either-or“ decision
• automated classification by Bayes classifier
• simple handling• CPU/RAM friendly• Fast & robust results
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Subject: new message | important
sign up and win! Every click wins!
The best exclusive exciting HD videos online.
Shop now – cheap and easy.
Payments...
Our "Low Price Pharmacy Store" design sports a professional array of pharmaceuticals.
msg me with a valid email for an account
Bayes classifier: Spam E-Mails
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Subject: new message | important
sign up and win! Every click wins!
The best exclusive exciting HD videos online.
Shop now – cheap and easy.
Payments...
Our "Low Price Pharmacy Store" design sports a professional array of pharmaceuticals.
msg me with a valid email for an account
Bayes classifier: Spam E-Mails
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term / phrase spam ham
shop now ++ -
pharmacy ++ o
win ++ +
account o +
MutationTaster - ++
abstract - ++
Recognition by Bayes classifier
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Bayes classifier in MutationTaster
attribute disease mutation polymorphism
loss of splice site 49.5 % 0.06 %
amino acid exchangetransmembrane domain
7.3 % 4.5 %
loss of disulfide bridge 2.9 % 0.1 %
amino acid exchange Arg>His 2.3 % 2.4 %
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Bayes classifier in MutationTaster
• training witha) > 100,000 known disease mutations
Human Gene Mutation Database (HGMD)
b) > 6,000,000 harmless polymorphisms1000 Genomes Project (1000G)
• classification model:stores frequencies of of different values / test results
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VCF upload
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Example case: Whole Exome Sequencing
http://bit.ly/mt_exome
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Example case: Phenotype
Muscle cramps, Spasticity
Hyperreflexia
Muscle weakness, Fasciculations
Sleep apnea
http://bit.ly/mt_exome
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Example case: Phenotype
Amyotrophic lateral sclerosis (ALS)OMIM #105400
Muscle cramps, Spasticity
Hyperreflexia
Muscle weakness, Fasciculations
Sleep apnea
http://bit.ly/mt_exome
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Example case: WholeExome Sequencing
Amyotrophic lateral sclerosis (ALS)OMIM #105400
Exome from 1000G(HG00377)
with known diseasemutation from ClinVar
http://bit.ly/mt_exome
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VCF upload
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Analysis Settings
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Results
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Results: Overview
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Results: Overview
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Results: Overview
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Results: GeneDistiller
http://www.genedistiller.org
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Results: Overview
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Results: Details
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Results: Details
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Results: Details
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RegulationSpotter
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RegulationSpotter
• Extratranscriptic variants: located outside of known transcripts
• free, web-based tool
• InDels, SNVs
• hyperlinks to MutationTaster for intragenic variants
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RegulationSpotter
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RegulationSpotter – submit VCF file
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Example case: Phenotype
Corneal arcus, Xanthelasma
Coronary heartdisease
Hypercholesterolemia
Tendinous xanthomas
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Example case: Phenotype
Corneal arcus, Xanthelasma
Coronary heartdisease
Hypercholesterolemia
Tendinous xanthomas
Hypercholesterolemia (familial)OMIM #143890
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Example case: Previous examinations
Whole ExomeSequencingPanel Sequencing
Hypercholesterolemia (familial)OMIM #143890
Linkage Analysis:19:11,000,000-11,500,000
APOA2ITIH4PPP1R17GHREPHX2ABCA1LDLR
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Example case: Whole Genome Sequencing
1000G Genome(HG00101)
with known diseasemutation from ClinVar
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RegulationSpotter – submit VCF file
Analysis settings: Discard variants which appear more than 4 times in 1000G or 10 times in ExAC
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Example case: Whole Genome Sequencing
APOA2ITIH4PPP1R17GHREPHX2ABCA1LDLR
http://bit.ly/rs_genome
Linkage Analysis:19:11,000,000-11,500,000
1000G Genome(HG00101)
with known diseasemutation from ClinVar
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Filter: none
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Filter: needed for Genome
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Filter: needed for Genome
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Filter: regions
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Filter: candidate genes
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Example case: Whole Genome Sequencing
APOA2ITIH4PPIR17GHREPHX2ABCA1LDLR
http://bit.ly/rs_genome
Linkage Analysis:19:11,000,000-11,500,000
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Results
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Results - Filter: regions
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Results - Filter: regions
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Results – Details 19:11200032_112000034delCTC
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Results – Details 19:11200032_112000034delCTC
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Results – Details 19:11200032_112000034delCTC
-500/+50 bp around TSS
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Results – Details 19:11200032_112000034delCTC
found in at least 3 cell lines
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Results – Details 19:11200032_112000034delCTC
only meaningful modifications used for scoring
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Results – Details 19:11200032_112000034delCTC
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Results – Details Interaction
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Results – Score
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Results – Details intragenic variant
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Results – Details intragenic variant
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Results – view MutationTaster
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Thank you!
Contact:
Charité Translational Genomicshttps://translationalgenomics.charite.de/
mutationtaster.orgregulationspotter.org
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