MutationTaster & RegulationSpotter

Transcription

1 Practical MutationTaster & RegulationSpotter Daniela Hombach & Jana Marie Schwarz Exzellenzcluster NeuroCure Charité Universitätsmedizin Berlin AG Translational Genomics

2 Rare diseases rare diseases are known. >> World-wide more than 300 Millions patients

3 Rare diseases Mendelian Complex # loci one multiple (polygenic) effect of environment frequency in population small rare high common effect strong weak example cystic fibrosis, hemophilia, PKU allergy, cancer, diabetes

4 MutationTaster Single variant query VCF query highly-parallel fashion (500,000 variants / hour) InDels, SNVs, introns, exons, coding and noncoding variants Go to:

5 SOD1

6 transcript-based! C[A/G]TGTTCATGAG. causes ALS

7

8 Computer based classification either-or decision automated classification by Bayes classifier simple handling CPU/RAM friendly Fast & robust results

9 Bayes classifier: Spam s 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 for an account

10 Bayes classifier: Spam s 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 for an account

11 Recognition by Bayes classifier term / phrase spam ham shop now ++ - pharmacy ++ o win ++ + account o + MutationTaster - ++ abstract - ++

12 Bayes classifier in MutationTaster attribute disease mutation polymorphism loss of splice site 49.5 % 0.06 % amino acid exchange transmembrane domain 7.3 % 4.5 % loss of disulfide bridge 2.9 % 0.1 % amino acid exchange Arg>His 2.3 % 2.4 %

13 Bayes classifier in MutationTaster training with a) > 100,000 known disease mutations Human Gene Mutation Database (HGMD) b) > 6,000,000 harmless polymorphisms 1000 Genomes Project (1000G) classification model: stores frequencies of of different values / test results

14 VCF upload

15 Example case: Whole Exome Sequencing

16

17 Example case: Phenotype Muscle weakness, Fasciculations Muscle cramps, Spasticity Hyperreflexia Sleep apnea

18 Example case: Phenotype Muscle weakness, Fasciculations Muscle cramps, Spasticity Hyperreflexia Sleep apnea Amyotrophic lateral sclerosis (ALS) OMIM #105400

19 Example case: WholeExome Sequencing Exome from 1000G (HG00377) with known disease mutation from ClinVar Amyotrophic lateral sclerosis (ALS) OMIM #105400

20 VCF upload

21 Analysis Settings

22 Results

23 Results: Overview

24 Results: Overview

25 Results: Overview

26 Results: GeneDistiller

27 Results: Overview

28 Results: Details

29 Results: Details

30 Results: Details

31 RegulationSpotter

32 RegulationSpotter Extratranscriptic variants: located outside of known transcripts free, web-based tool InDels, SNVs hyperlinks to MutationTaster for intragenic variants

33 RegulationSpotter

34 RegulationSpotter submit VCF file

35 Example case: Phenotype Hypercholesterolemia Corneal arcus, Xanthelasma Tendinous xanthomas Coronary heart disease

36 Example case: Phenotype Hypercholesterolemia Corneal arcus, Xanthelasma Tendinous xanthomas Coronary heart disease Hypercholesterolemia (familial) OMIM #143890

37 Example case: Previous examinations Panel Sequencing Whole Exome Sequencing Linkage Analysis: 19:11,000,000-11,500,000 APOA2 ITIH4 PPP1R17 GHR EPHX2 ABCA1 LDLR Hypercholesterolemia (familial) OMIM #143890

38 Example case: Whole Genome Sequencing 1000G Genome (HG00101) with known disease mutation from ClinVar

39 RegulationSpotter submit VCF file Analysis settings: Discard variants which appear more than 4 times in 1000G or 10 times in ExAC

40 Example case: Whole Genome Sequencing Linkage Analysis: 19:11,000,000-11,500,000 APOA2 ITIH4 PPP1R17 GHR EPHX2 ABCA1 LDLR 1000G Genome (HG00101) with known disease mutation from ClinVar

41 Filter: none

42 Filter: needed for Genome

43 Filter: needed for Genome

44 Filter: regions

45 Filter: candidate genes

46 Example case: Whole Genome Sequencing Linkage Analysis: 19:11,000,000-11,500,000 APOA2 ITIH4 PPIR17 GHR EPHX2 ABCA1 LDLR

47 Results

48 Results - Filter: regions

49 Results - Filter: regions

50 Results Details 19: _ delCTC

51 Results Details 19: _ delCTC

52 Results Details 19: _ delCTC -500/+50 bp around TSS

53 Results Details 19: _ delCTC found in at least 3 cell lines

54 Results Details 19: _ delCTC only meaningful modifications used for scoring

55 Results Details 19: _ delCTC

56 Results Details Interaction

57 Results Score

58 Results Details intragenic variant

59 Results Details intragenic variant

60 Results view MutationTaster

61 Thank you! Contact: Charité Translational Genomics mutationtaster.org regulationspotter.org

62