Transcript Genetics of Dyslexia

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
a human
23 pairs of chromosomes
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
.... Family 300
father
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)
Variant
Freq. (%) in
controls
Freq. (%) in
autistic cases
1
25
24
2
11
13
3
28
27
4
17
34
5
11
12
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)
Variant
Freq. (%) in
controls
Freq. (%) in
autistic cases
1
25
24
2
11
13
3
28
27
4
17
34
5
11
12
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
Patient1 Patient2
Normal
A
B*
A*
Patient3
A*
B*
B
C
C*
D
D*
Patient4
B*
C*
C*
C*
E
E*
E*
E*
F
F*
GENOME SCREEN RESULTS
3.5
3
152 ASP
ASPEX MLS
2.5
219 ASP
2
1.5
1
0.5
0
1
2
3
4
5
6
7
8
9
10
Chromosome
The Wellcome Trust Centre for Human Genetics.
11
12
13
14
15
16
17
18 19 20 21 22
X
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
Chrom os om e 2, 219 ASP
3
Chrom os om e 7, 219 ASP
2.5
3
2
ASPEX MLS
3.5
2.5
1.5
2
3
ASPEX MLS
1
0.5
2.5
1.5
1
0
0
50
100
150
200
250
300
Pos ition (cM )
ASPEX MLS
0.5
2
0
0
50
100
150
200
250
Position (cM)
1.5
1
0.5
0
1
2
3
4
5
6
7
8
9
10
Chromosome
The Wellcome Trust Centre for Human Genetics.
11
12
13
14
15
16
17
18 19 20 21 22
X
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.
Haploview
Daly Lab at the Whitehead Institute
LOW
HIGH
recombination
recombination
Summary Strategy Overview
•
Download CEPH HapMap genotypes.
•
Process genotypes (filter & clean).
•
Create haplotype blocks.
•
Identify haplotype-tagging SNPs (htSNPs).
SNP number
1
Haplotype 2
number 3
4
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
Freq
G
A
A
A
0.75
0.10
0.08
0.06
C
T
T
T
T
C
T
T
A
A
G
A
G
G
A
G
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
AT 0.60
AT 0.60
AT 0.60
TCG 0.15
AA 0.25
AA 0.25
AA 0.25
AGC 0.05
CT 0.15
CT 0.15
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
AT 0.60
AT 0.60
AT 0.60
TCG 0.15
AA 0.25
AA 0.25
AA 0.25
AGC 0.05
CT 0.15
CT 0.15
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.
•
Attempt to replicate any significant results
in INDEPENDENT samples.
T/T G/G
G/C
A/C
A/T
G/C
T/T
T/C
A/C
TGC 0.80
AT 0.60
AT 0.60
AT 0.60
TCG 0.15
AA 0.25
AA 0.25
AA 0.25
AGC 0.05
CT 0.15
CT 0.15
CT 0.15
0.021
0.847
association p-values
0.451
0.001
0.748
0.002
Autism Candidate Gene
Chromosome 7
1.0
Probands v/s unrelated controls (population-based analysis)
Experiment-wise posterior probability of association
Strong evidence for
association (90%)
0.8
IMMP2L
NM015328
0.2
0.4
0.6
PTPRZ1/2
0.0
Posterior probability
Positive evidence for
association (75%)
0
200
400
600
Bloc k
800
Family Based Analysis
1.0
Probands v/s internal controls
Experiment wise posterior probability of association
LHFPL3
IMMP2L
0.6
MUC3A/B
WNT16
0.2
0.4
CUTL1
0.0
Posterior probability
0.8
Strong evidence
for association
90%
Positive evidence
for association
75%
0
200
400
600
Bloc k
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
17p12 dups:
three families
SMS, CMT
2p16 deletion:
2 affected siblings
NRX1
17
1q21 dups/dels:
three families
Previously implicated in MR
22q11.2 deletions:
two families
Interpretation complicated
22
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
[email protected]
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
• Guy’s Hospital, London
• University of Newcastle, School of
Clinical Medical Sciences
• University of Manchester, School of
Epidemiology & Health Science
• ECACC, Porton Down
The Wellcome Trust Centre for Human Genetics.
• 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
• U.S.A
University of Chicago, Dept of
Psychiatry
UCLA Center for Neurobehavioural
Genetics, Psychiatric Institute
Yale University
University of Pittsburgh, Dept of
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