Genetics of Chiari Type 1 Malformation Christina Markunas Ph.D. Candidate Center for Human Genetics Duke University Medical Center.

Genetics of Chiari Type 1 Malformation

Christina Markunas

Ph.D. CandidateCenter for Human Genetics

Duke University Medical Center

Outline

• Brief genetics review

• Why study the genetics of a disease?

• Why do we think CM1/S has a genetic component?

• What genetic approaches can we take?

• Discuss previous and current genetic studies of CM1

Outline

• Brief genetics review

• Why study the genetics of a disease?

• Why do we think CM1/S has a genetic component?

• What genetic approaches can we take?

• Discuss previous and current genetic studies of CM1

Images from U.S. Department of Energy Genome Programs (http://genomics.energy.gov)

Genes

• Humans have >20,000 genes

• Instructions or blueprints for our body

• Receive ½ our genes from mom and ½ our genes from dad

• Genes produce proteins that help determine how we grow and develop

Why study the genetics of a disease?

• Development of genetic tests– More accurate and quicker diagnoses– Testing for at-risk family members

• Better understanding of disease mechanism

• Potential new therapies/treatments

Why do we think CM1 has a genetic component?

• Familial Clustering• Twin Studies• Co-segregation with known genetic syndromes• Heritability estimates of posterior fossa

measurements• Preliminary evidence from a linkage screen

Why do we think CM1 has a genetic component?

• Familial Clustering• Twin Studies• Co-segregation with known genetic syndromes• Heritability estimates of posterior fossa

measurements• Preliminary evidence from a linkage screen

Does the disorder run in families?

• We have 23 pairs of chromosomes– Receive ½ from mom

and ½ from dad• We have > 20,000 genes

Does the disorder run in families?

• We have 23 pairs of chromosomes– Receive ½ from mom

and ½ from dad• We have > 20,000 genes

Does the disorder run in families?

• We have 23 pairs of chromosomes– Receive ½ from mom

and ½ from dad• We have > 20,000 genes

Does the disorder run in families?

• We have 23 pairs of chromosomes– Receive ½ from mom

and ½ from dad• We have > 20,000 genes

Does the disorder run in families?

• We have 23 pairs of chromosomes– Receive ½ from mom

and ½ from dad• We have > 20,000 genes

Does the disorder run in families?

• We have 23 pairs of chromosomes– Receive ½ from mom

and ½ from dad• We have > 20,000 genes

Does the disorder run in families?

• We have 23 pairs of chromosomes– Receive ½ from mom

and ½ from dad• We have > 20,000 genes

Does the disorder run in families?

• We have 23 pairs of chromosomes– Receive ½ from mom

and ½ from dad• We have > 20,000 genes

CM1/S in Families

• Milhorat, et al. Neurosurgery 1999– 43/364 symptomatic patients (12%) reported that they

had ≥ 1 close relative with CM1/S

– An additional 72 patients (20%) reported that they had ≥ 1 close relative with symptoms similar to their own

• Additional studies– Speer, et al. Neurosurgical Focus 2000

– Szewka, et al. Pediatr.Neurol. 2006

– Boyles, et al. Am J Med Genet A 2006

• We have collected >100 CM1/S multiplex families

Why do we think CM1 has a genetic component?

• Familial Clustering• Twin Studies• Co-segregation with known genetic syndromes• Heritability estimates of posterior fossa

measurements• Preliminary evidence from a linkage screen

Twin Studies

• Same environment• Share all genes

• Same environment• Share ½ genes

Identical Fraternal

CM1 Twin Studies

• Higher concordance between 3 sets of identical twins compared to 3 sets of fraternal twins– Speer, et al. Journal of Genetic Counseling. 2003

• Concordance between identical twins and triplets– Atkinson, et al. Neurosurgery. 1998– Stovner, et al. Ann Neurol. 1992– Szewka, et al. Pediatr.Neurol. 2006– Cavendar, et al. J.Neurosurg. 1995

Why do we think CM1 has a genetic component?

• Familial Clustering• Twin Studies• Co-segregation with known genetic syndromes• Heritability estimates of posterior fossa

measurements• Preliminary evidence from a linkage screen

Co-segregation with known genetic syndromes

• Achondroplasia• Craniosynostosis• Paget’s Disease• Ehlers Danlos Syndrome• Marfan Syndrome• X-linked Aqueductal

Stenosis• Carpenter’s Syndrome• Cleidocranial Dysplasia• Empty Sella Turcica• Familial Osteosclerosis• Hajdu-Cheney Syndrome

• Hypophosphatemic Rickets• Klippel Feil• Marshall Smith Syndrome• Noonan Syndrome• Primary Basilar

Impression/Invagination• Renal-coloboma Syndrome• Spondylo-epiphyseal

Dysplasia Tarda• Williams-Beuren Syndrome

• Albright Hereditary Osteodystrophy (pseudohypoparathyroidism)

Speer, et al. Journal of Genetic Counseling 2003; Milhorat, et al. J.Neurosurg.Spine 2007.

Why do we think CM1 has a genetic component?

• Familial Clustering• Twin Studies• Co-segregation with known genetic syndromes• Heritability estimates of posterior fossa

measurements• Preliminary evidence from a linkage screen

It is probably more complex…

CM1

Outline

• Brief genetics review

• Why study the genetics of a disease?

• Why do we think CM1/S has a genetic component?

• What genetic approaches can we take?

• Discuss previous and current genetic studies of CM1

Genome Screens• Finding a gene is similar

to searching the US for a house without an address

• Must search genome by increments

• Enables geneticists to localize a gene to a small region on a single chromosome

Genetic Approach to a Disease

Genetic Approach to a Disease

Define the phenotype

Genetic Approach to a Disease

Define the phenotype

CM1/S

*Small Posterior Fossa*

1) Affected/Unaffected

2) PF Measures

Genetic Approach to a Disease

Define the phenotype

Look for evidence of a

genetic component

Perform Initial Analysis

CM1/S

*Small Posterior Fossa*

1) Affected/Unaffected

2) PF Measures

-Familial clustering

-Twin Studies

-Co-segregation with Genetic Syndromes

Linkage Analysis

Genetic Approach to a Disease

Define the phenotype

CM1/S

*Small Posterior Fossa*

1) Affected/Unaffected

2) PF Measures

Genetic Approach to a Disease

Define the phenotype

Look for evidence of a

genetic component

CM1/S

*Small Posterior Fossa*

1) Affected/Unaffected

2) PF Measures

Genetic Approach to a Disease

Define the phenotype

Look for evidence of a

genetic component

CM1/S

*Small Posterior Fossa*

1) Affected/Unaffected

2) PF Measures

-Familial clustering

-Twin Studies

-Co-segregation with Genetic Syndromes

Genetic Approach to a Disease

Define the phenotype

Look for evidence of a

genetic component

Design Study

CM1/S

*Small Posterior Fossa*

1) Affected/Unaffected

2) PF Measures

-Familial clustering

-Twin Studies

-Co-segregation with Genetic Syndromes

Genetic Approach to a Disease

Define the phenotype

Look for evidence of a

genetic component

Design Experiment

CM1/S

*Small Posterior Fossa*

1) Affected/Unaffected

2) PF Measures

-Familial clustering

-Twin Studies

-Co-segregation with Genetic Syndromes

-Family-based Study

-Genome Screen

Genetic Approach to a Disease

Define the phenotype

Look for evidence of a

genetic component

Design Experiment

Genotype population

CM1/S

*Small Posterior Fossa*

1) Affected/Unaffected

2) PF Measures

-Familial clustering

-Twin Studies

-Co-segregation with Genetic Syndromes

-Family-based Study

-Genome Screen

Genetic Approach to a Disease

Define the phenotype

Look for evidence of a

genetic component

Design Experiment

Genotype population

CM1/S

*Small Posterior Fossa*

1) Affected/Unaffected

2) PF Measures

-Familial clustering

-Twin Studies

-Co-segregation with Genetic Syndromes

-Family-based Study

-Genome Screen

Genotype using Illumina’s 610 chip

Genetic Approach to a Disease

Define the phenotype

Look for evidence of a

genetic component

Design Experiment

Genotype population

Perform Initial Analysis

CM1/S

*Small Posterior Fossa*

1) Affected/Unaffected

2) PF Measures

-Familial clustering

-Twin Studies

-Co-segregation with Genetic Syndromes

-Family-based Study

-Genome Screen

Genotype using Illumina’s 610 chip

Genetic Approach to a Disease

Define the phenotype

Look for evidence of a

genetic component

Design Experiment

Genotype population

Perform Initial Analysis

CM1/S

*Small Posterior Fossa*

1) Affected/Unaffected

2) PF Measures

-Familial clustering

-Twin Studies

-Co-segregation with Genetic Syndromes

-Family-based Study

-Genome Screen

Genotype using Illumina’s 610 chipLinkage Analysis

Genetic Approach to a Disease

Define the phenotype

Look for evidence of a

genetic component

Design Experiment

Genotype population

Perform Initial Analysis

Follow-up genomic

regions / genes

CM1/S

*Small Posterior Fossa*

1) Affected/Unaffected

2) PF Measures

-Familial clustering

-Twin Studies

-Co-segregation with Genetic Syndromes

-Family-based Study

-Genome Screen

Genotype using Illumina’s 610 chipLinkage Analysis

Genetic Approach to a Disease

Define the phenotype

Look for evidence of a

genetic component

Design Experiment

Genotype population

Perform Initial Analysis

Follow-up genomic

regions / genes

CM1/S

*Small Posterior Fossa*

1) Affected/Unaffected

2) PF Measures

-Familial clustering

-Twin Studies

-Co-segregation with Genetic Syndromes

-Family-based Study

-Genome Screen

Genotype using Illumina’s 610 chipLinkage Analysis-Fine-Mapping

-Sequencing

Genetic Approach to a Disease

Define the phenotype

Look for evidence of a

genetic component

Design Experiment

Replication

Genotype population

Perform Initial Analysis

Follow-up genomic

regions / genes

CM1/S

*Small Posterior Fossa*

1) Affected/Unaffected

2) PF Measures

-Familial clustering

-Twin Studies

-Co-segregation with Genetic Syndromes

-Family-based Study

-Genome Screen

Genotype using Illumina’s 610 chipLinkage Analysis-Fine-Mapping

-Sequencing

Genome Screen - Linkage

• We have 23 pairs of chromosomes– Receive ½ from mom

and ½ from dad• We have > 20,000 genes

Genome Screen - Linkage

• We have 23 pairs of chromosomes– Receive ½ from mom

and ½ from dad• We have > 20,000 genes

Follow-up

Follow-up : Association

Reduce Region of Interest

Genes

Follow-up : Association

CM1 No CM1

5/20 5/20

Gene is not important

Follow-up : AssociationCM1 No CM1

10/20 5/20

Gene may be important

Outline

• Brief genetics review

• Why study the genetics of a disease?

• Why do we think CM1/S has a genetic component?

• What genetic approaches can we take?

• Discuss previous and current genetic studies of CM1

Previous Linkage Screen – 23 families

A.L. Boyles, et al. Am J Med Genet A, Dec 15, 2006

Image from U.S. Department of Energy Genome Programs(http://genomics.energy.gov)

Heritability of PF Measures

Measurement h2 p-value

Left Herniation 0 0.5

Right Herniation 0 0.5

Max Herniation 0 0.5

Foramen Magnum 0.19 0.27

Tentorium 0.11 0.31

Supraoccipital 0.28 0.07

Tentorial Angle 0.10 0.39

Clivus 0.39 0.05

Basal Angle 0.51 0.01

PF Volume 0.96 0.0035

Cranial Volume 0.11 0.32

A.L. Boyles, et al. Am J Med Genet A , Dec 15, 2006

Current Ascertainment• Continued enrollment of CM1/S multiplex families (>100

families ascertained thus far)• Collecting:

– Medical records– Family history– Pre-surgical MRIs– Questionnaire

• Symptoms• Associated conditions• Disease onset• Pregnancy History

Current Genome Screen

• Phase I– 234 individuals from 40 CM1/S families– Genotyping and Quality Control: Complete– Analysis: In progress

• Phase II– Genotype another 240 individuals– Goal is to complete in the fall…

Posterior Fossa Measurements

• Collection of Pre-surgical MRIs– Collected > 200 so far– Measurements are in progress

• Goals:– Re-estimate heritability– Use as a phenotype– Identification of subtypes

Future Work

• Copy number variation

• Expression studies

Duplication Deletion

DNA RNA

Interested?

• Please pick up a study brochure after the session

• Feel free to contact the study coordinator with any questions:– Phone: 1-877-385-2626– Email: [email protected]

Acknowledgements

• Principal Investigator: Allison Ashley-Koch, Ph.D. • Principal Investigator: Simon Gregory, Ph.D.• Herbert Fuchs, M.D., Ph.D.• Gerald Grant, M.D.• David Enterline, M.D.• Heidi Cope, M.S., C.G.C.• Karen Soldano• Shonda Evans• Kaiti Dunlap

Funding provided by:

• National Institutes of Health (NINDS)

• Conquer Chiari