1. Copy number variations in
monozygotic twins
discordant for schizophrenia
Christina A. Castellani, Sujit Maiti, Kiran Kumar HB,
Richard L. O’Reilly and Shiva M. Singh
The University of Western Ontario

2. Schizophrenia, OMIM 181500
• > 1% of the population
• Characterized by a distortion of reality
• Heritability estimates of ~80%
• Significant disease heterogeneity
• Most cases singleton in the family
• Complex inheritance patterns
• Greatest risk is family history

3. Complex and Subjective diagnosis

4. Schizophrenia Inheritance

5. Search for genes: progress to date
• Chromosomal abnormalities (22q11, 1q42.1)
• Candidate gene approach (COMT, PRODH)
• Early linkage based on few markers (DTNBP1,
NRG1, DAOA)
• Genome wide association studies
(ZNF804A)
Despite increasing numbers (>6,000) of patients
and controls (>12,000), few genes have been
identified and results are difficult to reproduce
 Conclusions?

6. Two Unique Families
Family - 1
I-2-1
Schizophrenia
I-2-2
Bipolar
Disorder
I-1-1
Compulsive
Personality
Disorder
I-1-2
Family - 2
II-2-1
Schizophrenia
II-2-2
II-1-1 II-1-2

7. Copy Number Variation
• A candidate for disease associated
variation in humans
• Variable copies of DNA segments
• DNA deletions, insertions, duplications
• > 1kb and up to several mb
• 77% of CNVs are currently predicted to
include genes
• Covering about 12% of the genome in
healthy individuals

8. Affymetrix Genome Wide
Human SNP Array 6.0
• Median intermarker distance of less than 700 bp
• Provides breakpoint identification
• 1.8 Million Genetic Markers
> 906, 000 SNP Probes
> 946, 000 CNV Probes
Detection of Copy Number Variations

9. Chromosome CNV Architecture
Lee, Charles. 2007. Nature Genetics S39.

10. Copy Number Variation (CNV)

11. Distribution of CNV among family
members according to size
CNVs Size
Family 1 Family 2
I-1-1 I-1-2 I-2-1 I-2-2 Total II-1-1 II-1-2 II-2-1 II-2-2 Total
<=100 kb 0 0 0 0 0 2 0 0 1 3
>100 to 200 kb 17 18 15 20 70 119 50 24 24 217
>200 to 300 kb 11 6 4 10 31 25 6 13 9 53
>300 to 400 kb 5 5 6 5 21 11 3 1 4 19
>400 to 500 kb 2 0 2 2 6 6 1 1 2 10
>500 to 1000 kb 6 2 4 7 19 7 2 5 2 16
>1 to 10 Mb 9 4 5 3 21 5 2 4 5 16
>10 to 20 Mb 5 0 0 0 5 0 0 0 0 0
>20 Mb 3 0 0 0 3 2 0 2 2 6
Total 58 35 36 47 176 177 64 50 49 340

12. Distribution of CNVs within
family members

13. Chromosome Wide CNV Distribution
Chr No.
Family 1 Family 2
I.1 I.2 II.1 II.2 Total I.1 I.2 II.1 II.2 Total
1 4 2 2 2 10 11 2 6 6 25
2 4 2 5 5 16 11 2 2 3 18
3 1 4 2 3 10 7 4 4 2 17
4 4 3 2 4 13 8 1 3 2 14
5 0 0 0 0 0 12 0 2 1 15
6 0 0 0 0 0 10 2 0 0 12
7 2 6 3 4 15 10 5 3 4 22
8 1 0 3 3 7 7 3 3 3 16
9 1 1 2 3 7 4 4 3 4 15
10 2 1 1 1 5 3 5 1 1 10
11 3 1 2 1 7 5 1 2 2 10
12 0 1 0 1 2 4 3 0 1 8
13 0 0 0 0 0 40 1 1 0 42
14 4 6 3 5 18 4 6 5 3 18
15 4 3 1 3 11 2 6 6 8 22
16 2 1 2 3 8 9 1 1 1 12
17 4 1 2 3 10 8 2 2 1 13
18 0 0 0 0 0 1 0 0 1 2
19 0 1 0 0 1 7 3 2 1 13
20 0 0 0 0 0 0 0 0 1 1
21 1 2 2 3 8 2 3 2 1 8
22 3 0 3 2 8 3 1 1 1 6
X 18 0 1 1 20 9 9 1 2 21
Total 58 35 36 47 176 177 64 50 49 340

14. Gain/Loss Profiles

15. Gain/Loss Profiles

16. Gene and Pathway Analysis
Family 1: affected patient (schizophrenia) had
unique CNVs that overlapped 8 genes
Family 2: affected patient (schizophrenia) had
unique CNVs that overlapped 3 genes
Genes in the affected individual of family 1
harboured genes involved in starch and
sucrose metabolism networks (2.2 E-06)

17. Repeat Elements at de novo CNV
Breakpoints

18. de novo CNVs
• Meiotic de novo (in both twins, N=12)
• Mitotic de novo (in one twin only, N=28)
• Three de novo regions that were novel,
harbouring three genes
– PSMC1: 26S protease regulatory subunit 4
– C14orf102: highly conserved gene, no known
function
– KIAA0146: function unknown, expressed in brain
among other tissues

19. Twin Based Approach
• 6 pairs of MZ twins discordant for
schizophrenia
– Average number of CNVs per individual = 37.25
– Gains more frequent than losses
– 31 novel CNVs across 12 samples
– The majority (211 CNVs) were within 100 and 200
kb in size

20. Ingenuity Pathway Analysis (IPA)
Physiological System or Disease P-Value # Genes
Genetic Disorder 2.16 E-03 - 4.64 E-02 10
Neurological Disease 2.16 E-03 - 4.64 E-02 14
Nervous System Development and Function 9.16 E-03 3

21. In Summary
Copy Number Variants were found to:
– be frequent,
– harbour repeats at their breakpoints,
– overlap genes associated with
neurological networks,
– be both meiotic and mitotic in origin
– vary in location across patients
CNV differences can be detected
in MZ twins and are patient specific

22. Acknowledgements
We would like to acknowledge the following groups for their
funding and support:
- Canadian Institutes for Health Research (CIHR)
- Ontario Mental Health Foundation (OMHF)
- Schizophrenia Society of Ontario (SSO)
- The University of Western Ontario
A special thanks to David Carter (London Regional Genomics
Center) and the individuals who contributed samples for
use in this study.