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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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Page 1: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

Practical

MutationTaster & RegulationSpotter

Daniela Hombach & Jana Marie Schwarz

Exzellenzcluster NeuroCure Charité Universitätsmedizin Berlin

AG Translational Genomics

08.11.2017

Page 2: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

Rare diseases

7000 – 8000 rare diseases are known.

>> World-wide more than 300 Millions patients

Page 3: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

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

Page 4: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

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)

Page 5: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

SOD1

Page 6: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

C[A/G]TGTTCATGAG….

causes ALS

transcript-based!

Page 7: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin
Page 8: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

Computer based classification

• „either-or“ decision

• automated classification by Bayes classifier

• simple handling• CPU/RAM friendly• Fast & robust results

Page 9: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

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

Page 10: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

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

Page 11: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

term / phrase spam ham

shop now ++ -

pharmacy ++ o

win ++ +

account o +

MutationTaster - ++

abstract - ++

Recognition by Bayes classifier

Page 12: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

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 %

Page 13: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

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

Page 14: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

VCF upload

Page 15: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

Example case: Whole Exome Sequencing

http://bit.ly/mt_exome

Page 16: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin
Page 17: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

Example case: Phenotype

Muscle cramps, Spasticity

Hyperreflexia

Muscle weakness, Fasciculations

Sleep apnea

http://bit.ly/mt_exome

Page 18: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

Example case: Phenotype

Amyotrophic lateral sclerosis (ALS)OMIM #105400

Muscle cramps, Spasticity

Hyperreflexia

Muscle weakness, Fasciculations

Sleep apnea

http://bit.ly/mt_exome

Page 19: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

Example case: WholeExome Sequencing

Amyotrophic lateral sclerosis (ALS)OMIM #105400

Exome from 1000G(HG00377)

with known diseasemutation from ClinVar

http://bit.ly/mt_exome

Page 20: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

VCF upload

Page 21: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

Analysis Settings

Page 22: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

Results

Page 23: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

Results: Overview

Page 24: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

Results: Overview

Page 25: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

Results: Overview

Page 26: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

Results: GeneDistiller

http://www.genedistiller.org

Page 27: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

Results: Overview

Page 28: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

Results: Details

Page 29: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

Results: Details

Page 30: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

Results: Details

Page 31: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

RegulationSpotter

Page 32: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

RegulationSpotter

• Extratranscriptic variants: located outside of known transcripts

• free, web-based tool

• InDels, SNVs

• hyperlinks to MutationTaster for intragenic variants

Page 33: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

RegulationSpotter

Page 34: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

RegulationSpotter – submit VCF file

Page 35: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

Example case: Phenotype

Corneal arcus, Xanthelasma

Coronary heartdisease

Hypercholesterolemia

Tendinous xanthomas

Page 36: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

Example case: Phenotype

Corneal arcus, Xanthelasma

Coronary heartdisease

Hypercholesterolemia

Tendinous xanthomas

Hypercholesterolemia (familial)OMIM #143890

Page 37: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

Example case: Previous examinations

Whole ExomeSequencingPanel Sequencing

Hypercholesterolemia (familial)OMIM #143890

Linkage Analysis:19:11,000,000-11,500,000

APOA2ITIH4PPP1R17GHREPHX2ABCA1LDLR

Page 38: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

Example case: Whole Genome Sequencing

1000G Genome(HG00101)

with known diseasemutation from ClinVar

Page 39: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

RegulationSpotter – submit VCF file

Analysis settings: Discard variants which appear more than 4 times in 1000G or 10 times in ExAC

Page 40: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

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

Page 41: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

Filter: none

Page 42: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

Filter: needed for Genome

Page 43: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

Filter: needed for Genome

Page 44: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

Filter: regions

Page 45: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

Filter: candidate genes

Page 46: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

Example case: Whole Genome Sequencing

APOA2ITIH4PPIR17GHREPHX2ABCA1LDLR

http://bit.ly/rs_genome

Linkage Analysis:19:11,000,000-11,500,000

Page 47: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

Results

Page 48: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

Results - Filter: regions

Page 49: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

Results - Filter: regions

Page 50: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

Results – Details 19:11200032_112000034delCTC

Page 51: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

Results – Details 19:11200032_112000034delCTC

Page 52: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

Results – Details 19:11200032_112000034delCTC

-500/+50 bp around TSS

Page 53: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

Results – Details 19:11200032_112000034delCTC

found in at least 3 cell lines

Page 54: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

Results – Details 19:11200032_112000034delCTC

only meaningful modifications used for scoring

Page 55: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

Results – Details 19:11200032_112000034delCTC

Page 56: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

Results – Details Interaction

Page 57: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

Results – Score

Page 58: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

Results – Details intragenic variant

Page 59: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

Results – Details intragenic variant

Page 60: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

Results – view MutationTaster

Page 61: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin

Thank you!

Contact:

Charité Translational Genomicshttps://translationalgenomics.charite.de/

[email protected]

mutationtaster.orgregulationspotter.org

Page 62: MutationTaster & RegulationSpotter - Amazon S3€¦ · MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin