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					Genetics of Neurodevelopmental Disorders
AP Monaco

Neurodevelopmental Disorders
• • • • Autism Specific Language Impairment (SLI) Developmental Dyslexia Attention Deficit Hyperactivity Disorder

Summary of Talk
• Why we think autism has genetic origins. • Strategies to identify genes involved in autism. • What have we discovered thus far. • The Autism Genome Project. • The search for further autism susceptibility genes.

AUTISM: a severe neurodevelopmental
disorder
„…… an innate inability to form the usual biologically provided affective contact with people.’ Leo Kanner, 1943. Characterised by impairments in three principal areas: • Verbal and non-verbal communication • Reciprocal social interaction • Repetitive and stereotyped patterns of interests and behaviours Onset apparent before 3 years of age and persists throughout life Population prevalence of autism is ~17-61 per 10,000. Male to female ratio of ~4:1

Evidence for a genetic origin
• Large number of chromosome abnormalities associated with autism. • Familial clustering of autism is well above the normal population prevalence. • Twin based studies.

Twin Studies
• Identical twins share 100% of their genes. • Non-identical twins share on average 50% of their genes.
mother father mother father

child 1

child 2

child 3

child 4

Identical twins

Non-Identical twins

Twin Studies
Identical twins Non-Identical twins ? ?

60% concordance

affected unaffected

0-3% concordance

GENETIC FACTORS IN AUTISM
•Evidence from twin studies suggests a monozygotic (MZ) to dizygotic (DZ) concordance rate of 60%:0% (Bailey et al., 1995) •Heritability estimates of >90% •The rate among siblings of an autistic proband is ~3% •Autism is one of the most strongly genetic of the childhood-onset psychiatric disorders but no known mode of inheritance •Statistical modelling suggests the epistatic interaction of 3 genes, but possibly up to 10 loci •Family and twin studies indicate evidence for a broader autistic phenotype including combinations of milder but related social and/or communicative abnormalities in people of normal intelligence •MZ:DZ twin concordance rate for the broader phenotype ~92%:10%
The Wellcome Trust Centre for Human Genetics.

Finding autism susceptibility genes:

I.

Chromosome abnormalities

II.

Linkage Studies

III. Association Studies

The Human Genome
23 from mother

23 from father a human cell 23 pairs of chromosomes

a human

Finding autism susceptibility genes: I. Translocations
• Principle: To identify an individual (or several members of a family) with a chromosomal translocation and autism spectrum disorder.

23 pairs of chromosomes

Finding dyslexia susceptibility genes: I. Translocations
• Principle: To identify an individual (or several members of a family) with a chromosomal translocation and reading impairment.

Potential site for physical break in gene or regulatory element

23 pairs of chromosomes

Finding autism susceptibility genes: II. Linkage Studies
• Principle: To identify regions of the genome inherited more often than by chance in individuals with autism.
Family 1
mother father

Family 2
mother father

Family 3
mother father

.... Family 300

Linked to autism
child 1 child 2 child 1 child 2 child 1 child 2

Finding autism susceptibility genes: III. Association Studies
• Principle: To identify a genetic variant that is disproportionately more frequent in individuals with autism.
Examples of genetic variants: - microsatellites - single nucleotide polymorphisms (SNPs) - insertions and deletions (INDELS) - combinations of the above (haplotypes) Freq. (%) in controls 25 11 28 17 11 Freq. (%) in autistic cases 24 13 27 34 12

Variant 1 2 3 4 5

Finding dyslexia susceptibility genes: III. Association Studies
• Principle: To identify a genetic variant that is disproportionately more frequent in individuals with autism.
Examples of genetic variants: - microsatellites - single nucleotide polymorphisms (SNPs) - insertions and deletions (INDELS) - combinations of the above (haplotypes) Freq. (%) in controls 25 11 28 17 11 Freq. (%) in autistic cases 24 13 27 34 12

Variant 1 2 3 4 5

Associated to autism

THE INTERNATIONAL MOLECULAR GENETIC STUDY OF AUTISM CONSORTIUM (IMGSAC)
Initial aims:

Identify 200 multiplex families with two or more individuals with autism
Clear inclusion (ADI and ADOS) and exclusion criteria Carry out a genome screen for autism susceptibility loci.

340 families now identified through clinics internationally U.K, Italy, Denmark, France, Greece, Germany, The Netherlands, U.S.A.
The Wellcome Trust Centre for Human Genetics.

Autism Pathway
Normal
A Patient1 Patient2 A* Patient3 A* Patient4

B*

B

B*
C* C* C*

B*
C*

C
D

D*
E* E* E*

E
F

F*

GENOME SCREEN RESULTS
3.5

3

152 ASP
2.5

ASPEX MLS

2

219 ASP

1.5

1

0.5

0
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X

Chromosome
The Wellcome Trust Centre for Human Genetics.

AUTISM GENOME SCREEN RESULTS
8 genome screens for autism susceptibility loci carried out to date

MLS > 3.6 MLS > 2.2 MLS > 1

Genetic heterogeneity between studies? Some encouraging convergence of linkage findings eg chr 2, 7

The Wellcome Trust Centre for Human Genetics.

POSITIONAL CANDIDATE GENE SCREENING
Strategy depends on the model for autism susceptibility •Multiple rare variants model -Exhaustive Candidate gene screening -No clear aetiological mutations involved in the majority of families -Rare mutations identified: NLGN, NRXN, SHANK3 •Common Disease, Common Variant model -High Resolution SNP/haplotype association mapping -Regional or Whole Genome Association studies

The Wellcome Trust Centre for Human Genetics.

REGIONS FOR ILLUMINA SNP GENOTYPING
Chromosome 2, 219 ASP
3 2.5

Chromosome 7, 219 ASP
3

2

ASPEX MLS

3.5

2.5 1.5

2

3

1

ASPEX MLS
0 50 100

1.5

0.5

2.5

0 150

1 200 250 300

Position (cM )
0.5

ASPEX MLS

2
0 0 50 100 Position (cM) 150 200 250

1.5

1

0.5

0
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X

The Wellcome Trust Centre for Human Genetics.

Chromosome

International HapMap Project
• Genotyped individuals from four populations:
– – – – Yoruba (Nigerian) Japanese Han Chinese Utah (US) = CEPH samples:
• Northern and western European ancestry.

• PHASE I to genotype 1,000,000 SNPs • PHASE II to genotype 5,000,000 more SNPs

Summary Strategy Overview
• • Download CEPH HapMap genotypes. Process genotypes (filter & clean).

Summary Strategy Overview
• • • Download CEPH HapMap genotypes. Process genotypes (filter & clean). Create haplotype blocks:
– Regions of LOW recombinations.
LOW recombination HIGH recombination

Haploview Daly Lab at the Whitehead Institute

Summary Strategy Overview
• • • • Download CEPH HapMap genotypes. Process genotypes (filter & clean). Create haplotype blocks. Identify haplotype-tagging SNPs (htSNPs).

SNP number 1 ^ A C C C 2 3 ^ T A C A C C C A 4 ^ A G A A 5 6 7 8 9 G A A A C T T T T C T T A A G A G G A G Freq 0.75 0.10 0.08 0.06

1 Haplotype 2 number 3 4

Summary Strategy Overview
• • • • • Download CEPH HapMap genotypes. Process genotypes (filter & clean). Create haplotype blocks. Identify haplotype-tagging SNPs (htSNPs). Align haplotype blocks with genes.

Important Points:

Haplotype block not covering any gene, therefore less need to genotype htSNPs.

Gene not covered by haplotype block, so can not be tested.

Segments of genes not covered by haplotype block, so can not be tested.

Summary Strategy Overview
• • • • • • Download CEPH HapMap genotypes. Process genotypes (filter & clean). Create haplotype blocks. Identify haplotype-tagging SNPs (htSNPs). Align haplotype blocks with genes. Genotype 1536 htSNPs on the Illumina platform, utilising the GoldenGate assay, in the selected samples (cases and controls).

T/T G/G

G/C

A/C

A/T

G/C

T/T

T/C

A/C

Summary Strategy Overview
• • • • • • Download CEPH HapMap genotypes. Process genotypes (filter & clean). Create haplotype blocks. Identify haplotype-tagging SNPs (htSNPs). Align haplotype blocks with genes. Genotype 1536 htSNPs on the Illumina platform, utilising the GoldenGate assay, in the selected samples (cases and controls). Reconstruct haplotypes based on the htSNPs‟ genotypes.

T/T G/G

G/C

A/C

A/T

G/C

T/T

T/C

A/C

•

TGC 0.80 TCG 0.15 AGC 0.05

AT 0.60 AA 0.25 CT 0.15

AT 0.60 AA 0.25 CT 0.15

AT 0.60 AA 0.25 CT 0.15

Summary Strategy Overview
• • Download CEPH HapMap genotypes. Process genotypes (filter & clean).

•
• • •

Create haplotype blocks.
Identify haplotype-tagging SNPs (htSNPs). Align haplotype blocks with genes. Genotype 1536 htSNPs on the Illumina platform, utilising the GoldenGate assay, in the selected samples (cases and controls). Reconstruct haplotypes based on the htSNPs‟ genotypes. Test haplotypes for association to autism.
T/T G/G G/C A/C A/T G/C T/T T/C A/C

•

•

TGC 0.80 TCG 0.15 AGC 0.05

AT 0.60 AA 0.25 CT 0.15

AT 0.60 AA 0.25 CT 0.15

AT 0.60 AA 0.25 CT 0.15

0.021

association p-values

0.451

0.001

0.748

Summary Strategy Overview
• • Download CEPH HapMap genotypes. Process genotypes (filter & clean).

•
• • •

Create haplotype blocks.
Identify haplotype-tagging SNPs (htSNPs). Align haplotype blocks with genes. Genotype 1536 htSNPs on the Illumina platform, utilising the GoldenGate assay, in the selected samples (cases and controls). Reconstruct haplotypes based on the htSNPs‟ genotypes. Test haplotypes for association to autism.
T/T G/G G/C A/C A/T G/C T/T T/C A/C

•

•

TGC 0.80 TCG 0.15 AGC 0.05

AT 0.60 AA 0.25 CT 0.15

AT 0.60 AA 0.25 CT 0.15

AT 0.60 AA 0.25 CT 0.15

•

Attempt to replicate any significant results in INDEPENDENT samples.

0.021

association p-values

0.451

0.001

0.748

0.847

0.002

Autism Candidate Gene

Chromosome 7
Probands v/s unrelated controls (population-based analysis) Experiment-wise posterior probability of association
1.0
Strong evidence for association (90%) Positive evidence for association (75%)

0.8

IMMP2L

Posterior probability

0.0

0.2

0.4

0.6

PTPRZ1/2

NM015328

0

200

400 Block

600

800

Family Based Analysis
Probands v/s internal controls Experiment wise posterior probability of association
Strong evidence for association 90% Positive evidence for association 75%

0.8

1.0

LHFPL3

IMMP2L

Posterior probability

MUC3A/B

0.6

WNT16 CUTL1

0.0
0

0.2

0.4

200

400 Block

600

800

Summary of molecular genetics research
• Several groups have carried out genome screens for linkage

to autistic disorder.
• Encouraging convergent evidence for linkage in some

regions.
• Many candidate gene screening and association studies

have been carried out, but no etiological variants have been so far conclusively identified in the majority of families with autism.
• High density SNP genotyping for association to autism on

chromosome 7q and 2q have identified several positive risk haplotypes that need to be replicated.
The Wellcome Trust Centre for Human Genetics.

Autism Genome Project
• Genome-wide SNP genotypes (10k, 1M)

• Copy Number Variation (CNV)
• Linkage analyses

• Association analyses
• Trait subsets, endophenotypes, QTLs

Autism Genome Project
• Consortium of consortia
• • • • Autism Genetics Cooperative (AGC) Autism Genetics Research Exchange (AGRE) Collaborative Programs of Excellence in Autism (CPEA) International Molecular Genetic Studies of Autism Consortium (IMGSAC)

• Pool autism family samples, phenotype data and expertise • Phase I
• Genome-wide genotyping (10k) • Initial linkage analysis

• Phase II
• Association and Copy Number Variants

Autism Genome Project: Phase I
• ~1400 multiplex families • Affymetrix 10k SNP genotypes • Basic linkage analysis
• “autism” = affected (categorical Dx) • Narrow and broad autism and “heterogeneous ASDs”

• Copy Number Variation
• Use signal intensity data from adjacent/contiguous SNPs to infer copy number gains or losses

• Linkage analyses in data subsets
• Sex: Male-only, Female-containing • Ancestry: Western European • CNV: Removing CNV by different algorithms

Autism Genome Project Copy Number Variation and Genetic Linkage

Copy Number Variants
2p16 deletion: 2 affected siblings NRX1
17

17p12 dups: three families SMS, CMT

1q21 dups/dels: three families Previously implicated in MR
22

22q11.2 deletions: two families Interpretation complicated

1

2

17 de novo CNVs (10 found in both ASP) 18 CNVs overlap ASD-related rearrangements Numerous overlapping/recurrent CNVs Families with transmission of maternal 15q gains

Copy Number Variation and Autism Risk: De Novo Mutation vs. Inherited Risk

CNV in Simplex and Multiplex Autism Families

Sebat et al, Science 2007

Are CNVs more frequent in simplex families?

Sebat et al, Science 2007

Are autism associated CNVs more likely to be sporadic “mutations” or inherited risk factors?

AGP
Phase II Design

Summary
• • • • • • Autism has a complex genetic etiology CNV is a major class of autism risk and causation Need to clarify what is disease-related vs rare polymorphism New information from genetic linkage studies 11p and other regions targeted for candidate gene analysis Whole genome association (WGA) studies will (hopefully) identify common liability alleles – Common = common in the general population • WGA does not identify genes with rare or infrequent risk or causative alleles – Sequence (autism genomes?) • Higher resolution CNV analysis • Collaboration is important to make progress in such complex disorders

Acknowledgments Nuala Sykes Ines Sousa Alistair Pagnamenta Richard Holt Kirsty Wing Gaby Barnby Penny Farrar Elena Bonora Tom Scerri Elena Maestrini Andrew Morris Janine Lamb Tony Monaco Tony Bailey autism@well.ox.ac.uk Funding MRC, Wellcome Trust, NLM Family Foundation, Simons Foundation, EU
The Wellcome Trust Centre for Human Genetics.

International Molecular Genetic Study of Autism Consortium (IMGSAC)
http://www.well.ox.ac.uk/~maestrin/iat.html

• Denmark, Centre for Autisme, Bagsvaerd

• U.K.

• Dept of Psychiatry, University of
Oxford • Wellcome Trust Centre, Univ of Oxford • Institute of Psychiatry, London • University of Cambridge, Dept of
Psychiatry

• France, Hôpital La Grave, Toulouse • Germany, Molecular Genome Analysis,

Heidelberg Dept of Psychiatry, Frankfurt • Greece, Agia Sophia Children’s Hospital, Athens • Italy, University of Bologna • The Netherlands, Dept of Psychiatry, Utrecht

• Guy’s Hospital, London • University of Newcastle, School of

• U.S.A University of Chicago, Dept of

Clinical Medical Sciences • University of Manchester, School of Epidemiology & Health Science

Psychiatry UCLA Center for Neurobehavioural Genetics, Psychiatric Institute

• ECACC, Porton Down

Yale University University of Pittsburgh, Dept of

The Wellcome Trust Centre for Human Genetics.

Human Genetics and Biostatistics University of Michigan, Autism & Communicative Disorders Center

Autism Genome Project Genome-Wide Analysis of Linkage and Copy Number Variation
Autism Genome Project Consortium: Autism Genetics Collaborative (AGC) Autism Genetics Resource Exchange (AGRE) Collaborative Programs of Excellence in Autism (CPEA) International Molecular Genetics Study of Autism Consortium (IMGSAC)

Funding: UK: Medical Research Council USA: Autism Speaks Ireland:HRB Canada: Genome Canada


				
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