Costain, Lionel, et al.

Copy number variation in community schizophrenia 1

SUPPLEMENTAL MATERIAL

This file includes the following:

Supplemental data Page

Table of Contents 1

Supplemental Tables:
Table S1: Summary of Affymetrix 6.0 microarray CNV data for 420 schizophrenia cases of
2
European ancestry
Table S2: Summary of Affymetrix 6.0 microarray CNV data for 416 OPGP control individuals
3
of European ancestry
Table S3: Frequency of typical large gains/losses at chromosome 2q13 in 23,838 population-
4
based controls
See Excel
Table S4: All stringent rare CNVs in schizophrenia cases and OPGP control individuals
attachment
Table S5: Gene-set association results for all gene-sets tested, involving very rare CNVs See Excel
restricted to exonic losses attachment
Table S6: Additional gene-set information for the 70 significant gene-sets showing significant See Excel
enrichment for schizophrenia attachment
Table S7: Gene-set association results for 25 neurological gene-sets tested, involving very rare See Excel
CNVs restricted to exonic losses attachment
Supplemental Figures:

Figure S1: Overview of study design and CNV analysis workflow 5

Figure S2: Large rare pathogenic CNVs (see Table 1) and smaller rare CNVs overlapping
6
putative candidate genes for schizophrenia
Figure S3: Large rare CNV at 7q22.3-q31.2 overlapping FOXP2 in an adult with
7
schizophrenia
Figure S4: Overlapping large rare CNVs at three novel loci for schizophrenia 8

Figure S5: Detailed gene-set association results and clusters 9

Figure S6: Detailed gene-set association results, clusters and genes 10

Figure S7: Overlap of gene-set association results with ASD genes 11

Supplemental References 12
 Costain, Lionel, et al. Copy number variation in community schizophrenia 2

Table S1. Summary of Affymetrix 6.0 microarray CNV data for 420 schizophrenia cases of European ancestry

All (n=420) Caucasian probands

Non-genic Genic All1
Gain Loss Mixed Gain Loss Mixed
Total number of stringent CNVs for all
samples with results 2,485 5,400 19 3,759 5,088 173 16,924
% of total stringent CNVs 14.69 31.91 0.11 16.30 30.06 1.02 100.00
Average number of CNVs per genome2
5.92 12.86 0.05 8.59 12.11 0.41 40.30
(N=420)
Median size (range) 31,810 (10,086- 24,086 (10,022- 111,225 (45,159- 83,941 (10,072- 52,393 (10,033- 83,941 (26,147- 39,394 (10,022-
1,620,721) 1,156,392) 251,551) 6,498,447) 3,687,431) 900,917) 6,498,447)
Median size (range) for rare3 CNVs 45,840 (11,231- 37,363.5 (10,115- 98,494 (10,904- 45,417 (10,033- 49657.5 (10,033-
0 0
1,073,381) 626,127) 6,498,447) 3,687,431) 6,498,447)
Number of >100kb CNVs 339 649 15 1,805 1,632 83 4,523
% of total CNVs, of same type, that are
>100kb 13.64 12.02 78.95 65.42 32.08 47.98 26.73
Number of rare3 CNVs 188 318 0 316 299 0 1121
% of total CNVs, of same type, that are
rare3 7.57 5.89 0.00 11.45 5.88 0.00 6.62

Average number of rare3 CNVs per

0.45 0.76 0.00 0.75 0.71 0.00 2.67
genome4
Average number of rare3 CNVs per
genome5 0.49 0.83 0.00 0.83 0.78 0.00 2.94
Number of subjects with one or more
144 213 0 211 214 0 382
rare3 CNVs
% of subjects with one or more rare3
CNVs 34.29 50.71 0.00 50.24 50.95 0.00 90.95
Number of subjects with one or more
131 205 0 199 210 0 376
rare3 CNVs6
% of subjects with one or more rare3
31.19 48.81 0.00 47.38 50.00 0.00 89.52
CNVs6
This table accounts for stringent CNVs 10kb-6.5Mb; no restriction on chromosome (i.e., includes X chromosome except where indicated)
1
“All” category comprises genic and non-genic CNVs
2
Average number of CNVs per genome= total number of CNVs in each column divided by total number of subjects
3
Rare CNVs defined as CNVs present in <0.1% of population controls
4
Average number of rare CNVs per genome= total number of rare CNVs in each column divided by the total number of subjects (include subjects with no rare CNV)
5
Average number of rare CNVs per genome = total number of rare CNVs in each column divided by the total number of subjects (only include subjects with 1 or more rare
CNVs)
6
Excluded CNVs on X chromosome 
Costain, Lionel, et al. Copy number variation in community schizophrenia 3

Table S2. Summary of Affymetrix 6.0 microarray CNV data for 416 OPGP control individuals of European ancestry*
All (n=416) Caucasian OPGP controls
Non-genic Genic All1
Gain Loss Mixed Gain Loss Mixed
Total number of stringent CNVs
for all samples with results 2,129 5,774 64 3,472 5,056 225 16,720
% of total stringent CNVs 12.73 34.53 0.38 20.77 30.24 1.35 100.00
Average number of CNVs per
genome2 (N=416) 5.117788462 13.87980769 0.153846154 8.346153846 12.15384615 0.540865385 40.19230769
Median size (range) 29,851 (10,103- 22,754 (10,022- 58,168 (12,803- 76,846 (10,022- 46,286 (10,016- 83,936 (26,147- 39,394 (10,016-
1,654,909) 2,041,019) 409,887) 2,605,726) 1,855,636) 1,354,407) 2,605,726)
Median size (range) for rare3 39,821.5 (10,178- 37,586 (10,134- 92,828 (10,037- 39,536 (10,016- 47,466.5 (10,016-
CNVs 672,304) 2,041,019) 0 2,605,726) 1,430,916) 0 2,605,726)
Number of >100kb CNVs 366 646 25 1,633 1,481 106 4,254
% of total CNVs, of same type,
that are >100kb 17.19 11.19 39.06 47.03 29.29 47.11 25.44
Number of rare3 CNVs 168 325 0 273 256 0 1022
% of total CNVs, of same type,
that are rare3 7.89 5.63 0 7.86 5.06 0 6.11
Average number of rare3 CNVs
per genome3 0.40 0.78 0 0.66 0.62 0 2.46
Average number of rare3 CNVs
per genome4 0.44 0.85 0 0.71 0.67 0 2.68
Number of subjects with one or
more rare3 CNVs 138 220 0 186 205 0 382
% of subjects with one or more
rare3 CNVs 33.17 52.88 0 44.71 49.28 0 91.83
Number of subjects with one or
more rare3 CNVs6 118 211 0 181 203 0 372
% of subjects with one or more
rare3 CNVs6 28.37 50.72 0 43.51 48.80 0 89.42
This table accounts for stringent CNVs 10kb-6.5Mb; no restriction on chromosome (i.e., includes X chromosome except where indicated)
1
“All” category comprises genic and non-genic CNVs
2
Average number of CNVs per genome= total number of CNVs in each column divided by total number of subjects in each category
3
Rare CNVs defined as CNVs present in <0.1% of population controls
4
Average number of rare CNVs per genome= total number of rare CNVs in each column divided by the total number of subjects (include subjects with no rare CNV)
5
Average number of rare CNVs per genome = total number of rare CNVs in each column divided by the total number of subjects (only include subjects with 1 or more rare
CNVs)
6
Excluded CNVs on X chromosome
Costain, Lionel, et al. Copy number variation in community schizophrenia 4

Table S3. Frequency of typical large gains/losses at chromosome 2q13 in 23,838 population-based controls.
Typical large gains/losses at chromosome 2q13
Dataset N Array type Geographic origin Reference
(chr2:111,105,101-112,832,463)

POPGEN controls 1,123 Affymetrix 6.0 Germany (1) 0

Ottawa Heart Institute controls 1,234 Affymetrix 6.0 Ontario, Canada (2) 0

HapMap
HapMap (Phase 3) controls 1,056 Affymetrix 6.0 populations across (3) 0
the world

Wellcome Trust Case Control

4,783 Affymetrix 6.0 UK (4) 0
Consortium (WTCCC) controls

Ontario Population Genomics

416 Affymetrix 6.0 Ontario, Canada (5) 0
Platform (OPGP) controls

Starr County Diabetes cases &

1,794 Affymetrix 6.0 USA (6) 2 (gains; chr2:111,105,101-112,832,463)
controls

Geneva NHS/HPFS Diabetes cases

5,966 Affymetrix 6.0 USA (7) 0
& controls

SAGE consortium controls 1,287 Illumina 1M USA (8) 1 (loss; chr2:111,078,231-112,816,485)

Health, Aging, and Body

Composition (Health ABC) Study 2,566 Illumina 1M-Duo USA (9) 1 (gain; chr2:111,078,231-112,816,485)
controls

Ontario ARCTIC controls 1,120 Affymetrix 500k Ontario, Canada (10) 0

Illumina Hap550,
Itsara et al. controls 2,493 Hap650Y and Various (11) 0
Hap300

Total 23,838 - - - 4
Costain, Lionel, et al. Copy number variation in community schizophrenia 5

Figure S1. Overview of study design and CNV analysis workflow

459 adult cases with schizophrenia (SZ)

5 cases with 22q11.2 deletions

454 discovery sample SZ cases 416 OPGP controls

Genotyping on
Affymetrix 6.0 SNP array

CNV detection
Single algorithm only
< 5 consecutive probes
< 10 kb in size
Stringent CNVs (SZ cases, OPGP controls)
Global CNV burden

CNV frequency (rarity) assignment using data from 2,357 independent controls2
CNVs present in > 0.1 % controls2
(<50% unique sequence)
Stringent rare CNVs (SZ cases, OPGP controls)
Stringent rare CNV burden analysis1
CNVs present in any control individual2 (SZ vs. OPGP and syndromic SZ vs. non-syndromic SZ)
(<50% unique sequence)
Stringent very rare CNVs (SZ cases, OPGP controls)
Functional gene enrichment mapping1
Rare CNVs present in both
SZ and OPGP control datasets
Stringent very rare CNVs in SZ cases only3
• Comprehensive examination of genes for evidence of relevant expression in human and
model animal (mouse, zebrafish) systems
• Overlap with previous genetic findings in SZ
• Recurrent and overlapping rare CNVs identifying familiar and novel SZ risk genes

• Experimental validation of CNVs (quantitative PCR or clinical microarray)

1
CNV burden analysis and functional gene enrichment mapping focused on comparing the
subset of unrelated SZ cases of European ancestry (n = 420) with ancestry-matched unrelated
adult OPGP controls (n=416).
2
Population-based adult controls of European ancestry (n=2,357), used in previous studies of
autism and attention deficit disorder and independent to OPGP controls, were genotyped on
the Affymetrix 6.0 platform and analyzed for CNVs in an identical manner to the SZ cases
and OPGP controls.
3
Included CNVs 4–10 kb in size (n=7) that overlapped CNVs > 10kb in size overlapping SZ
candidate genes
Costain, Lionel, et al. Copy number variation in community schizophrenia 6

Figure S2. Large rare pathogenic CNVs (see Table 1) and smaller rare CNVs overlapping putative
candidate genes for schizophrenia.
Costain, Lionel, et al. Copy number variation in community schizophrenia 7

Figure S3. Large rare CNV at 7q22.3-q31.2 overlapping FOXP2 in an adult with
schizophrenia.
Costain, Lionel, et al. Copy number variation in community schizophrenia 8

Figure S4. Overlapping large rare CNVs at three novel loci for schizophrenia.
Costain, Lionel, et al. Copy number variation in community schizophrenia 9

Figure S5. Detailed gene-set association results and clusters.

Supplementary Figure 5  Negative Reg.
Node: Gene‐set 
Proportional to the number 
Signal Transduction Chromatin of genes harboring exonic
Chromosome loss CNVs
Organization Link: Gene‐set Overlap
Proportional to the number of 
Transcription 
shared genes harboring loss
Cofactor
Chromatin 
Modification
Synapse

Transcription  Secretion
Ion Transport
Modulation
Negative Reg. 
Transcription
CH2H2 Zinc  Ion Homeostasis
Fingers Nervous System 
Development

Kinase Cascade
Development

Positive Reg.  Signal Transduction
Transcription
Positive Reg. 
Negative Reg. 
Cell proliferation
Cell proliferation
Regulation of 
Phosphorylation

Axonogenesis Cell Motility

Cell Projection
Costain, Lionel, et al. Copy number variation in community schizophrenia 10

Figure S6. Detailed gene-set association results, clusters and genes.

Nervous System Development [11] Chromatin [13] but not [1‐4] or [8‐11] Synapse [1]

ATN1 Supplementary Figure 6 BUB1
DOT1L
CHAT 10q11.22‐q11.23
CHRNA7 15q13.2‐q13.3
DISC1
DRD3 3q13.31 HIRA 22q11.21 COMT 22q11.21
FGF2 HIST3H3 S DOC2A 16p11.2
GABRA5 15q11‐q13 OBFC1 DRD3 3q13.31
IL1RAPL1 Xp21.3‐p21.2 PAX5 9p13.3‐p13.2 FGF2
NDN 15q11‐q13 PDS5B 13q13.1‐q13.2 GABRA5 15q11‐q13
NEUROG2 4q25‐q26 RFC3 GABRB3 15q11‐q13
NR0B1 SMG6 GABRG3 15q11‐q13
NRP1 10p11.22 SUPT3H GABRR1
OTP 5q13.3‐q14.1 (note: Chromatin also includes the more  KCND2 7q31.31
POU3F2 6q16.2‐q16.3 general Chromosome Organization) LIN7A 12q21.31
PRKCA S MTNR1B
RELN PI4KA 22q11.21
RTN4R 22q11.21 PRKCA S
S100B SEPT5 22q11.21
SOX5 S SLC1A1
UBE3A 15q11‐q13  SLC18A3 10q11.22‐q11.23

Development [10] not [1, 8,9,11] Secretion [2] but not [1, 8‐11]
AP3D1 ATP6V0A4
KL IL33
KLF13 PDE8B 5q13.3‐q14.1
MAPK8 10q11.22‐q11.23  PIK3C3
RUNX2 PTGER3
ZC3H8 SNAP29 22q11.21

Ion Transport [3] but not [1‐2, 8‐11]
Axonogenesis [8] C16orf7
ABLIM1 PDZK1 1q21.1
ANK2 4q25‐q26 TRPM1 15q13.2‐q13.3
CLTA 9p13.3‐p13.2
IL1RAPL1 Xp21.3‐p21.2 Ion Homeostasis [4] but not [1‐3, 8‐11]
JAK2 S COMMD1 S
MAPK3 16p11.2 RYR2 1q43
NDN 15q11‐q13
NEUROG2 4q25‐q26
NRP1 10p11.22 Legend
POU3F2 6q16.2‐q16.3
Cluster Name [Cluster Number]
PRKCA S
PTPRM Gene from functional  gene enrichment mapping 
RELN (exonic loss CNV)
RHOG CHRNA7
RTN4R 22q11.21
S100B Gene and locus from Table S3 (CNV >500 kb)
PAX5 9p13.3‐p13.2
Cell projection [9] but not [8]
Gene from Table S9 (very rare CNV <500 kb) 
DNM3 S
HIST3H3 S
Cell Motility [7] but not [1, 8‐9, 11]
Gene from locus 22q11.21 (typical loss CNV 3 Mb)
BMPER
HIRA 22q11.21
GDF2 10q11.22‐q11.23
MERTK 2q13 Gene present in more than one of clusters 1, 8, 11
WNT5B RELN
Costain, Lionel, et al. Copy number variation in community schizophrenia 11

Figure S7. Overlap of gene-set association results with ASD genes. Functional map of schizophrenia (see Figure 2 for details),
highlighting the clusters of the gene-sets significantly associated to schizophrenia for which at least half the gene-sets were also
significantly over-represented in known ASD genes.(12) Over-representation was tested using Fisher's Exact Test (FET) and Benjamini-
Hochberg FDR for multiple test correction, with a significance threshold of 5% FDR.

Supplementary Figure 7
Negative Reg.
Signal Transduction Chromatin
Chromosome
Organization

Transcription 
Cofactor
Negative Reg. 
Transcription
Synapse
Chromatin 
Modification
Transcription  Secretion Ion Transport
Modulation

Ion Homeostasis
CH2H2 Zinc  Nervous System 
Fingers
Development

Development
Kinase Cascade
Signal Transduction
Positive Reg. 
Transcription Positive Reg. 
Cell proliferation
Negative Reg. Cell 
proliferation Regulation of 
Phosphorylation

Axonogenesis Cell Motility
Cluster overlapping at least in part 
Cell Projection with gene‐sets over‐represented in 
ASD gene list (FET FDR < 5%)

 
Costain, Lionel, et al. Copy number variation in community schizophrenia 12

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