copy number variants in autism …what are we missing? lauren a. weiss dept. psychiatry institute...
TRANSCRIPT
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Copy Number Variants in Autism …what are we missing?
Lauren A. Weiss
Dept. PsychiatryInstitute for Human Genetics
Center for Neurobiology and Psychiatry
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Autism
• Specific impairment in:– Language and communication– Social skills– Restricted and repetitive behavior
• Clinically very heterogeneous– MR, epilepsy, hyperserotonemia, GI
problems, regression, savant skills, sensory hypersensitivity, head growth
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What we know
• A Pervasive Developmental Disorder– Prevalence of ASDs ~0.6%– 4:1 male to female ratio
• Estimates of >90% heritability – Siblings at increased risk– Large role for inherited genetics vs. sporadic
events and environmental factors– no genes identified in majority
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Known Genetic Causes of Autism
• Chromosomal/Structural variants associated with autism
• Rare mutations associated with autism
• Account for ~10%
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Structural Variants in Autism
• X chromosome (Turner, Klinefelter)
• FMR1 (Fragile X)
• 15q11-q13 duplication (PWS/AS)
• 7q11.23 (Williams Syndrome)
• 22q11.2 (diGeorge/VCFS)
• 22q13 (Phelan-McDermid syndrome)
• 17p11.2 (Smith-Magenis/Potocki-Lupski)
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Single Base Mutations in Autism
• NLGN3, NLGN4X
• MECP2 (Rett Syndrome)
• TSC1/2 (Tuberous Sclerosis)
• PTEN (Cowden Disease)
• SHANK3
• CACNA1C (Timothy Syndrome)
• DCHR7 (Smith-Lemli-Opitz Syndrome)
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Complex Genetics
disease
genes QTs environment
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Complex Genetics
Common
polymorphism
Rare
variant
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Study Design
>1000 multiplex families
Linkage analysis SNP/CNV association
IdentificationOf risk genes
In linkage/CNVregions
Replication studies
Follow up of autismrisk factors
CNV analysis
Validation andTyping of
CNVs
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Genome-Wide Association
• Common polymorphism
• Usually case-control– TDT for family-based association
T U
A 5 0
B 0 5
case control
A 0.61 0.28
B 0.39 0.72
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Genome-Wide Association
• Common polymorphism
• Usually case-control– TDT for family-based association
• LARGE sample size required– 1,000s to 10,000s
• MANY markers across the genome– 500,000 to 1,000,000
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Copy Number Variation
• Greater than 1 kb in/del– Normal copy number 2– Rare, common?
• Detection methods– Karyotype, CGH, FISH, MLPA, qPCR
• SNP arrays– Whole genome, small events, boundary
estimates
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Datasets
Broad Affy 5.0 AGRE 850 mpx
JHUAffy
5.0/500KNIMH 240 mpx
CHOP(linkage only)
Illumina HH550
AGRE 120 mpx
Many!(replication only)
Affy 5.0/500K, Sequenom
Varied 2400 trios
Site Platform Source N families
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Analysis Methods
• Genotype calling by Birdseed– Careful QC pipeline
• Linkage analysis in MERLIN
• Association analysis by TDT in PLINK
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Linkage Results
NP
L L
OD
Sco
re
3
2
1
0
•16,150 high quality markers in 878 multiplex families
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Top Linkage
Chr6 Chr15
Chr17 Chr20
Chr6 Chr15
Chr17 Chr20
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SNP Association Results
11 22 33 44 55 66 77 88 99 1010 1111 1212 1313 1414 15151616 18 18 20 20 2222
17 17 1919 2121 XX
6
5
4
3
2
1
-log 1
0P
chr
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Replication
• Top results (P < 10-4) into replication– Additional Affy microarray data– Sequenom genotyping (TaqMan)– extra cases vs. controls
• rs10513025 on 5p15 replicates P < 0.006– MAF 0.04, OR 0.5
• Combined P = 2 x 10-7
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Top Association
Chr5, kb
SEMA5A TAS2R1
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Top Association
Chr5, kb
SEMA5A TAS2R1
rs10513025 meta-P = 2 x 10-7
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SEMA5A Brain Expression
0
0.2
0.4
0.6
0.8
1
1.2
1.4
1.6
1.8
2
Control Autism
Fol
d E
xpre
ssio
n
P = 0.039
Control Autism
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SNP Results Summary
• Genome-wide significant linkage on 20p
• Association on 5p15 near SEMA5A– Replicated independently
• Very low/high frequency variation implicated
• More to find!
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Copy Number Analysis
Physical position (kb)
Chr 15 Duplications
Indi
vidu
al
mom
dad
autism
autism0
1
2
3
4
5
0
1
2
3
4
5
0
1
2
3
4
5
0
1
2
3
4
5
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16p11.2 microdeletion/duplication
SPNQPRT
c16orf54
MAZPRRT2
MVPCDIPT
c16orf53
KIF22SEZ6L2
ASPHD1
KCTD13LOC124446
TAOK2HIRIP3
CCDC95DOC2A
FAM57BALDOA
PPP4C
TBX6YPEL3
GDPD3
MAPK3 CORO1ABOLA2GIYD1/2SULT1A3/4
BOLA2GIYD1/2SULT1A3/4
29.5 29.6 29.7 29.8 29.9 30.0 30.1
29 29.5 30 30.5 31
16p11.2
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16p11.2 microdeletion/duplication
Sample Deletion Duplication
freqcase vs freqcontrol
P-valuedel+dup
AGRE
751 multiplex autism families
2814 controls
5 cases
3 controls
7 cases
0 controls
0.8% vs 0.1%
1.1 x 10-4
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16p11.2 microdeletion/duplication
Sample Deletion Duplication
freqcase vs freqcontrol
P-valuedel+dup
Children’s Hospital
512 DD/MR/ASD
434 congenital anomalies
(not including DD/MR/ASD)
5* cases
0 controls
4 cases
0 controls
1.6% vs. 0
7.1 x 10-3
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16p11.2 microdeletion/duplication
Sample Deletion Duplication
freqcase vs freqcontrol
P-valuedel+dup
deCODE
299 ASD cases
18,834 unscreened controls
5,019 psych/lang disorders
3 cases
2 controls
5 psych/
lang
0 cases
5 controls
1% vs. 0.01%
4.2 x 10-4
(0.1% in psych/lang)
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Copy Number Summary
• 16p11.2 microdeletion/duplication found in 1-2% of autism cases, <0.1% controls– Three independent samples– Large Icelandic population sample
• 0.1% in psych/lang disorder, 0.01% population
• 15q11-q13 duplications, including partial
• Follow-up and additional controls required for more common and inherited events
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• 16p11.2– Deletion, high penetrance, variable expression– Duplication, reduced penetrance, variable expression
• 15q13.3– Deletion, high penetrance, variable expression– Duplication, reduced penetrance, variable expression
• 1q21.1– Deletion, high penetrance, variable expression– Duplication, reduced penetrance, variable expression
Novel CNVs associated with autism
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• 16p11.2– Autism, PDD/Asperger’s, ADHD, MR/DD, epilepsy,
schizophrenia, bipolar disorder, dyslexia
• 15q13.3– Epilepsy, MR/DD, schizophrenia, autism, language
delay, dysmorphism
• 1q21.1– Micro/macrocephaly, MR/LD, autism, ADHD,
schizophrenia, epilepsy, dysmorphism, congenital anomalies, short stature
Novel CNVs associated with autism
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Structural Variants in Autism
• X chromosome (Turner, Klinefelter)
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Structural Variants in Autism
• X chromosome (Turner, Klinefelter)
• FMR1 (Fragile X)
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Structural Variants in Autism
• X chromosome (Turner, Klinefelter)
• FMR1 (Fragile X)
• 15q11-q13 duplication (PWS/AS)
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Structural Variants in Autism
• X chromosome (Turner, Klinefelter)
• FMR1 (Fragile X)
• 15q11-q13 duplication (PWS/AS)
• 7q11.23 (Williams Syndrome)
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Structural Variants in Autism
• X chromosome (Turner, Klinefelter)
• FMR1 (Fragile X)
• 15q11-q13 duplication (PWS/AS)
• 7q11.23 (Williams Syndrome)
• 22q11.2 (diGeorge/VCFS)
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Structural Variants in Autism
• X chromosome (Turner, Klinefelter)
• FMR1 (Fragile X)
• 15q11-q13 duplication (PWS/AS)
• 7q11.23 (Williams Syndrome)
• 22q11.2 (diGeorge/VCFS)
• 22q13 (Phelan-McDermid syndrome)
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Structural Variants in Autism
• X chromosome (Turner, Klinefelter)
• FMR1 (Fragile X)
• 15q11-q13 duplication (PWS/AS)
• 7q11.23 (Williams Syndrome)
• 22q11.2 (diGeorge/VCFS)
• 22q13 (Phelan-McDermid syndrome)
• 17p11.2 (Smith-Magenis/Potocki-Lupski)
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• Reverse genetic screen
• Common, small CNV associations?
Implications for CNV studies
Common
polymorphism
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Single Base Mutations in Autism
• NLGN3, NLGN4X
• MECP2 (Rett Syndrome)
• TSC1/2 (Tuberous Sclerosis)
• PTEN (Cowden Disease)
• SHANK3
• CACNA1C (Timothy Syndrome)
• DCHR7 (Smith-Lemli-Opitz Syndrome)
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• Are narrow phenotype definitions useful?
• Population re-sequencing?
• Genetic overlap (e.g. autoimmune syndromes)
• Meta-analysis?
Implications for SNP studies
Human Molecular Genetics, 2008, Vol. 17, Review Issue 2
Guillaume Lettre and John D. Rioux
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• Underlying QT– E.g. Diabetic retinopathy, neuropathy,
periodontal disease, nephropathy, cardiovascular disease, reproductive disorders
• Heritable modifiers?
Implications for Neurobiology
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Acknowledgements
• Mark Daly
• Pamela Sklar
• Aravinda Chakravarti
• Dan Arking
• AGP, CHOP, and replication groups
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