Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary

Integrative and translational analysis of thephenome

Robert Hoehndorf

Department of Physiology, Development and NeuroscienceUniversity of Cambridge

26 September 2012

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Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary

Translational research

National Cancer Institute:

Translational research transforms scientific discoveries arising fromlaboratory, clinical, or population studies into clinical applicationsto reduce [disease] incidence, morbidity, and mortality.

Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary

Genetic diseasesAlmost 4,000 genetic diseases in OMIM have an unknown molecular basis.

Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary

Genetic diseasesOrphaNet

5,917 orphan diseases

2,543 genes linked to 2,544 diseases

2,700 diseases indexed with clinical signs

Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary

Genetic diseasesAnimal models have been shown to be highly successful in studying human disease

Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary

Approach

Can we use phenotypes of mutant animal organisms to findcandidate genes for orphan diseases?

1 make animal and human phenotypes comparable

2 systematically analyze the phenome for possible causativemutations

3 evaluate using real biomedical data

Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary

Approach

Can we use phenotypes of mutant animal organisms to findcandidate genes for orphan diseases?

1 make animal and human phenotypes comparable

2 systematically analyze the phenome for possible causativemutations

3 evaluate using real biomedical data

Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary

Genetic diseasesPATO and the EQ method enable the integration of phenotype ontologies across species.

use of Entity-Quality definitions

homologous anatomical structures

integration based on species-independent ontologies

Gene OntologyChEBI, Protein ontology, Celltype ontology

Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary

Genetic diseasesIntegration of phenotypes enables direct comparison between species

Proximal fibular overgrowth(HPO):

E: Proximal epiphysis offibula (FMA)

Q: hypertrophic

Abnormal fibula morphology(MP):

E: fibula (MA)

Q: morphology (abnormal)

UBERON: fibula (MA) orthologous to Fibula (FMA)

FMA: Proximal epiphysis of fibula part-of Fibula

PATO: hypertrophic is-a morphology

Proximal fibular overgrowth is-a Abnormal fibula morphology

Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary

Genetic diseasesExperimental data can be integrated through ontologies and explored using automatedreasoning.

integration of phenotype ontologies

yeast, fly, slime mold, worm, fish, mouse, rat, human

ontology-based integration of phenotypes

mutant phenotypes for yeast, fly, slime mold, worm, fish,mouse, rathuman disease phenotypes from OMIM and OrphaNet

OWL ontology with more than 500,000 classes

OWL reasoner reveals connections between phenotypes

Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary

Genetic diseasesSemantic similarity over phenotype ontologies measures phenotypic similarity.

semantic similarity: metric based on information contained inthe axioms of an ontology

pairwise comparison of disease and animal phenotypes

sim(P,D) =

∑x∈Cl(P)∩Cl(D)

IC (x)

∑y∈Cl(P)∪Cl(D)

IC (y)

Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary

Genetic diseasesSimilarity-based comparison

Evaluation against known gene–disease associations:

OMIM

MGI

OrphaNet

Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary

Genetic diseasesOMIM phenotypes

AUC (OMIM): 0.78

AUC (MGI): 0.87

Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary

Genetic diseasesOrphaNet phenotypes

AUC (OrphaNet):0.73

AUC (OMIM): 0.76

AUC (MGI): 0.80

Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary

Genetic diseasesOntology-based integration and analysis can reveal disease genes for orphan diseases.

Adam19 and Fgf15 in mice are strong candidates forTetralogy of Fallot

Gene disease associations for orphan diseases

Slc34a1 (MGI:1345284) and Fanconi renotubular syndrome 1(OMIM:134600)

Disease pathways

Cytokine-cytokine receptor interaction pathway (ko04060) issignificantly correlated with Tetralogy of Fallot (p = 5 · 10−7,Wilcoxon signed-rank test)

Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary

Bassoe SyndromeSigns and symptoms

skeletal:

kyphosis, hypertensible joints, cubitus valgus

muscular:

hypotonia, muscle hypotrophy, amyotrophy

behavior:

abnormal gait, amimia

visual:

cataract, strabismus

reproductive:

hypogonadism, hypogenitalism, abnormal ovaries, hypoplastictestis, reduced fertility

Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary

Bassoe Syndromehttp://phenomebrowser.net

Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary

Bassoe SyndromeHIP1 knockout mice

Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary

Bassoe SyndromeHIP1 mouse phenotypes

Bassoe Syndrome:

kyphosis, hypertensiblejoints, cubitus valgus

amyotrophy, hypotonia,muscle hypotrophy

abnormal gait, amimia

cataract, strabismus

testicular atrophy,hypogonadism,hypogenitalism,abnormal ovaries,reduced fertility

Mouse phenotypes:

kyphosis, abnormal spine curvature,lordosis

abnormal muscle morphology

, musclehypotrophy, muscle wasting

abnormal gait, hypoactivity, tremors

,failure to thrive, ataxia

nuclear cataracts, microphthalmia

testicular atrophy, male infertility

,ovarian abnormalities, testiculardegeneration, increased apoptosis ofpostmeiotic spermatids, oligospermia

Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary

Bassoe SyndromeHIP1 mouse phenotypes

Bassoe Syndrome:

kyphosis, hypertensiblejoints, cubitus valgus

amyotrophy, hypotonia,muscle hypotrophy

abnormal gait, amimia

cataract, strabismus

testicular atrophy,hypogonadism,hypogenitalism,abnormal ovaries,reduced fertility

Mouse phenotypes:

kyphosis, abnormal spine curvature,lordosis

abnormal muscle morphology, musclehypotrophy, muscle wasting

abnormal gait, hypoactivity, tremors,failure to thrive, ataxia

nuclear cataracts, microphthalmia

testicular atrophy, male infertility,ovarian abnormalities, testiculardegeneration, increased apoptosis ofpostmeiotic spermatids, oligospermia

Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary

Bassoe Syndrome

Computational analysis of mouse phenotypes provides a strongindication that HIP1 may be involved in Bassoe syndrome.

Genetic diseasesROC analysis quantifies the performance of the approach.

Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary

Question

Is there a similarity between a knock-out/knock-down of a gene(through targeted mutation) and the inhibition/negative regulationof a gene (through a drug action)?

Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary

PhenomeNET compares phenotypes across species

Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary

Statistical testing to rank drug–disease pairs

one-sided Wilcoxon signed rank test

result: ranking of drugs for each disease based on p-value

Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary

Phenotype-based comparison can provide some informationabout drug indications

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AUC (CTD): 0.61AUC (FDA): 0.67

Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary

Future: phenotype-based drug repurposing

similarity between inhibition (drug action) andknock-out/knock-down (mutation)

effectsindicationstargets

combination with interaction networks

D inhibits G1 and G1 positively regulated G2 ⇒ D inhibits G2.

drug pathways

pharmacodynamicspharmacokineticsphysiological pathways

Pharmacogenomics databases

Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary

Aims: queries and integrated analysis

integrate and query knowledge in pharmacogenomics

identify aberrant pathways and patho-physiology underlyingdisease

identify drug pathways (pharmacokinetics andpharmacodynamics)

personalized treatment and dosage guidelines

Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary

Approach to data integration in pharmacogenomics

integration of databases containing drug, gene, genotype,disease and pathway information

DrugBank: drugs and drugs targetsPharmGKB: genotype and drug responsePathway Interaction Database: biological pathwaysCTD: toxicogenomics information (chemical–gene–disease)

Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary

Queries

What drugs can be used to treat parasitic infectious diseases(DOID:1398)?

Chloroquine

Arthemeter

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Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary

Queries

What drugs are effective for diseases affecting the joints(FMA:7490)?

Folic acid (for arthritis)

Chloroquine (for Chikungunya virus)

...

Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary

Queries

What genotypes are related to diseases affecting the joints(FMA:7490)?

RSID:rs70991108 (with arthritis)

RSID:rs1207421 (Osteoarthritis, Knee)

...

Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary

Queries

What genotypes are related to response to steroids(CHEBI:35341)?

RSID:rs45566039 (with estrogen)

RSID:rs1042713 (with budesonide)

...

Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary

Disease and drug pathwaysOntology enrichment analysis can identify over-represented ontology classes.

ontology-based, statistical approach to identify drug anddisease pathways

use graph structure of ontology to identify statistically over-and under-represented ontology classes

aims:

identify over-represented disease classes (in disease ontology)for genes in a pathway (disease pathways)identify over-represented chemical classes (from chemicalontology) for genes in a pathway (drug pathways)

Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary

Disease and drug pathwaysOntoFUNC enables enrichment analyses over OWL ontologies.

OntoFUNC: http://ontofunc.googlecode.com

based on FUNC (http://func.eva.mpg.de)

supports

hypergeometric testWilcoxon rank testbinomial testMcDonaldKreitman (2x2 contingency) testcorrection for multiple testing (FWER, FDR)

Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary

Disease and drug pathwaysOntoFUNC identifies disease classes that are enriched in pathways.

hypergeometric test over Disease Ontology

genes participating in pathway P vs. all other genes

carcinosarcoma (DOID:4236) and Zidovudine Pathway(PharmGKB:PA165859361) (p < 10−10).

mood disorder (DOID:3324) and Zidovudine Pathway(PharmGKB:PA165859361) (p < 0.01).

(All results at http://pharmgkb-owl.googlecode.com)

Species Inferred p-valueFish 1717 0.240Yeast 14047 0.162Fly 1633 0.041Worm 9221 0.003

Mouse 15693 7 · 10−5

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Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary

SummaryOntologies can be used to enable integrative biology.

1 integration of ontologies

2 integration of data through ontologies3 ontology-based data analysis

semantic similaritystatistical testsgraph-/network-based algorithms

4 quantitative evaluation on real biological data

Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary

Acknowledgements

George Gkoutos

Paul Schofield

Michel Dumontier

Heinrich Herre

Janet Kelso

DietrichRebholz-Schuhmann

Dan Cook

John Gennari

Anika Oellrich

Nico Adams

Bernard de Bono

Pierre Grenon

Midori Harris

Pascal Hitzler

Simon Jupp

Frank Loebe

Kay Pruefer

Gabrielle Rustici

Stefan Schulz

Robert Stevens

Sarala Wimalaratne

...

Introduction Animal and disease phenotypes Pharmacogenomics Pathways Summary

Thank you!

http://phenomebrowser.net