www.sciencetranslationalmedicine.org/cgi/content/full/3/95/95ra75/DC1

Supplementary Materials for

Rare Copy Number Variation Discovery and Cross-Disorder Comparisons Identify Risk Genes for ADHD

Anath C. Lionel, Jennifer Crosbie, Nicole Barbosa, Tara Goodale, Bhooma

Thiruvahindrapuram, Jessica Rickaby, Matthew Gazzellone, Andrew R. Carson, Jennifer L. Howe, Zhuozhi Wang, John Wei, Alexandre F. R. Stewart, Robert Roberts, Ruth McPherson, Andreas Fiebig, Andre Franke, Stefan Schreiber, Lonnie Zwaigenbaum, Bridget A. Fernandez, Wendy Roberts, Paul D. Arnold,Peter Szatmari, Christian R.

Marshall, Russell Schachar,* Stephen W. Scherer*

*To whom correspondence should be addressed. E-mail: russell.schachar@sickkids.ca (R.S.); stephen.scherer@sickkids.ca (S.W.S.)

Published 10 August 2011, Sci. Transl. Med. 3, 95ra75 (2011)

DOI: 10.1126/scitranslmed.3002464

The PDF file includes:

Fig. S1. Examples of loci with overlapping rare CNVs in this study and in previous ADHD studies. Fig. S2. Examples of CNV validation. Table S1. Summary statistics of stringent CNVs found in ADHD and control data sets. Table S2. List of rare stringent CNVs specific to ADHD data set. Table S3. Phenotypes of families with rare CNVs at ADHD candidate loci. Table S4. Loci with overlapping rare CNVs in this study and in previous ADHD studies. Table S5. Rare CNVs in ASD probands at loci also implicated in ADHD probands. Table S6. Summary of newly described ASTN2 and TRIM32 sequence variants. Table S7. Newly described ASTN2 sequence variants in ADHD probands. Table S8. Newly described ASTN2 sequence variants in ASD probands. Table S9. Newly described ASTN2 sequence variants in controls. Table S10. Newly described TRIM32 sequence variants in ADHD probands. Table S11. Newly described TRIM32 sequence variants in ASD probands. Table S12. Newly described TRIM32 sequence variants in controls. References

1

SUPPLEMENTARY MATERIAL

Fig. S1. Examples of loci with overlapping rare CNVs in this study and in previous

ADHD studies.

Blue and red bars represent deletions and duplications respectively: A) CHCHD3 locus at

7q32 with overlapping duplications in an ADHD proband and an ASD proband in this

study and in an ADHD proband from a previous study (S1); B) CPLX2 locus at 5q35.2

with a duplication in this study and a deletion in a previous study (S1); C) ZBBX locus at

chr3q26.1 with deletions in two ADHD probands in this study, a de novo deletion in (S2);

and a duplication in (S1); and D) 11q13.4 locus with overlapping duplications in this

study and in (S1).

2

Fig. S2. Examples of CNV validation.

(A) FISH validation of the de novo duplications at the 10q25.1 SORCS1/SORCS3 locus in

family 30600. Interphase FISH results are shown for the mother (left), father (center) and

proband (right). FISH was performed using two BAC probes (hg18 co-ordinates):

(chr10:106,689,236-106,827,525, SpectrumGreen) within SORCS3 and RP11-1007O4

(chr10:108,456,374-108,644,757, SpectrumOrange) within SORCS1. Signal patterns

indicate the presence of two copies in parental samples and three copies of the locus in

the proband. (B) Quantitative PCR intensity ratios of the 4p12 GABRG1 locus in family

27048 versus a control region of known copy number 2, confirm the presence of a

heterozygous deletion in the mother and proband and its absence in other family

members and controls.

A

B

Validation of maternally inherited loss at 4p12 by quantitative PCR

Control

Control

Father

Mother Proband

Unaffected Sibling

0.00

0.20

0.40

0.60

0.80

1.00

1.20

1.40

1.60

Sample

Rati

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Co

pie

s o

f 4p

12 l

ocu

s v

s.

co

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ol

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3

1 We did not observe a significant difference in average number of CNVs per sample in the ADHD

probands compared to the controls (Unpaired two-tailed t-test p-value is 0.251 for all ADHD probands vs.

controls and 0.522 for ADHD probands of European ancestry vs. controls).

2

controls and 0.708 for ADHD probands of European ancestry vs. controls).

ADHD probands

(All)

ADHD probands

(European ancestry) Controls

# Samples 248 218 2,357

# Males / # Females 175 / 73 157 / 61 1,209 / 1, 148

# Stringent CNVs 6,081 5,310 56,882

Mean # CNVs / sample ± Std Dev1 24.52 ± 5.16 24.36 ± 5.07 24.13 ± 5.08

Median # CNVs / sample 25 25 24

Mean CNV size (kb) ± Std Dev2 115.37 ± 175.66 115.88 ± 172.1 116.85 ± 181.05

Median CNV size (kb) 55 55 54

% Gain / % Loss 40 / 60 40 / 60 39 / 61

# CNVs of size > 1 Mb (%) 38 (0.62%) 35 (0.66%) 418 (0.73%)

# CNVs of size from 100 Kb – 1 Mb (%) 2,031 (33.4 %) 1,782 (33.56%) 18,416 (32.38%)

# CNVs of size from 20 Kb – 100 Kb (%) 4,012 (65.98%) 3,493 (65.78%) 38,048 (66.89%)

Table S1. Summary statistics of stringent CNVs found in ADHD and control data sets.

We did not observe a significant difference in mean CNV sizes between the ADHD proband data set

compared to the control data set (Unpaired two-tailed t-test p-value is 0.543 for all ADHD probands vs.

4

Loci in red indicate CNVs presented in Table 1.

Sample Sex Chr. Start

(Build 36/hg18)

End

(Build 36/hg18) Size (bp) CNV Genes

19887.3 M 1 6,726,334 6,749,939 23,606 Gain -

19719.3 M 1 15,103,757 15,132,694 28,938 Loss KAZ

133500.3 M 1 20,166,123 20,202,332 36,210 Loss PLA2G2A

19671.3 M 1 27,213,139 27,428,831 215,693 Gain SLC9A1

20061.3 M 1 30,066,051 30,187,613 121,563 Loss -

20115.3 F 1 34,947,115 35,015,480 68,366 Gain GJB5,GJB4

126300.3 F 1 40,620,062 40,643,132 23,071 Loss SMAP2

19743.3 M 1 74,931,827 74,961,806 29,980 Gain CRYZ

19812.3 M 1 79,076,338 79,118,659 42,322 Loss -

19875.4 F 1 102,133,210 102,200,932 67,723 Loss OLFM3

111000.3 M 1 102,193,167 102,226,187 33,021 Loss OLFM3

126300.3 F 1 110,720,424 110,896,938 176,515 Gain KCNA10,PROK1,CYMP,HBXIP,SLC16A4

19953.3 F 1 143,580,441 143,681,581 101,141 Loss PDE4DIP

27054.3 M 1 144,093,481 144,503,421 409,941 Loss 17 genes

27300.3 M 1 187,802,307 187,873,921 71,615 Loss -

19701.3 M 1 206,157,392 206,180,354 22,963 Loss -

19737.3 M 1 218,154,326 218,179,823 25,498 Gain SLC30A10

26100.3 M 1 223,725,840 223,750,819 24,980 Gain ENAH

27045.3 M 2 677,775 797,576 119,802 Gain LOC339822

27147.3 M 2 8,523,659 8,561,883 38,225 Gain -

135000.3 M 2 18,441,578 18,463,108 21,531 Gain -

19686.3 M 2 19,043,235 19,114,625 71,391 Gain -

22455.3 M 2 34,671,199 34,760,471 89,273 Loss -

99000.5 F 2 49,246,886 49,275,075 28,190 Loss -

84300.3 M 2 52,075,257 52,108,739 33,483 Loss -

19743.3 M 2 71,435,816 71,580,025 144,210 Gain ZNF638,DYSF

93072.3 M 2 81,211,134 81,295,549 84,416 Loss -

135000.3 M 2 81,580,749 81,846,267 265,519 Loss -

19464.3 M 2 111,105,101 112,832,463 1,727,363 Loss 10 genes

19776.3 M 2 114,797,905 114,861,770 63,866 Loss -

114900.3 F 2 117,855,258 117,879,411 24,154 Gain -

27300.3 M 2 137,761,562 137,782,241 20,680 Loss THSD7B

104400.3 F 2 168,352,744 168,541,327 188,584 Gain STK39,B3GALT1

108900.3 M 2 183,853,658 183,945,292 91,635 Loss -

19713.3 M 2 195,484,469 195,536,005 51,537 Loss -

86700.3 M 2 197,412,293 197,477,302 65,010 Gain PGAP1

110100.3 M 3 62,187 354,484 292,298 Gain CHL1

20139.3 M 3 30,355,090 30,380,940 25,851 Gain -

39300.3 M 3 41,380,748 41,402,673 21,926 Loss ULK4

70800.3 M 3 45,218,934 45,267,453 48,520 Gain TMEM158

66000.3 M 3 60,284,581 60,392,379 107,799 Loss FHIT

137100.3 M 3 65,671,420 65,838,213 166,794 Gain MAGI1

127200.3 M 3 84,788,974 84,857,452 68,479 Gain LOC440970

93270.3 M 3 85,201,744 85,303,749 102,006 Loss CADM2

19764.3 F 3 98,239,193 98,351,525 112,333 Loss EPHA6

84300.3 M 3 100,281,128 100,331,180 50,053 Loss -

49800.3 F 3 109,208,157 109,239,869 31,713 Loss -

127200.3 M 3 117,495,083 117,561,080 65,998 Gain LSAMP

106800.3 M 3 139,825,527 140,104,748 279,222 Gain FAIM,PIK3CB

54000.3 F 3 144,251,569 144,289,980 38,412 Gain SR140

111300.3 F 3 146,356,376 146,452,889 96,514 Gain -

35100.3 F 3 147,865,684 148,275,297 409,614 Gain -

125700.3 M 3 159,758,284 159,794,365 36,082 Gain MLF1

35100.3 F 3 164,902,109 164,983,137 81,029 Loss -

91200.3 M 3 167,048,623 167,144,734 96,112 Loss -

22512.3 F 3 168,346,915 168,511,454 164,540 Loss ZBBX

19365.3 F 3 168,547,242 168,569,695 22,454 Loss ZBBX

Table S2. List of rare stringent CNVs specific to ADHD data set.

5

19707.3 F 3 189,967,770 190,015,503 47,734 Loss LPP

19767.3 M 3 189,967,770 190,015,503 47,734 Loss LPP

139200.4 M 3 199,113,288 199,161,746 48,459 Gain IQCG,RPL35A

19752.3 F 4 1,401,559 1,788,392 386,834 Gain SLBP,LETM1,TACC3,TMEM129,FGFR3,FAM53A

87600.3 M 4 5,116,316 5,213,162 96,847 Loss STK32B

27027.3 M 4 9,337,161 9,819,488 482,328 Gain MIR3138,DRD5,WDR1,SLC2A9

27027.3 M 4 9,845,240 10,512,445 667,206 Gain ZNF518B,CLNK

136200.3 F 4 14,238,846 14,271,316 32,471 Gain -

19788.3 M 4 24,022,488 24,049,192 26,705 Gain -

19788.3 M 4 24,185,257 24,299,153 113,897 Gain DHX15

55800.3 M 4 28,649,954 28,705,007 55,054 Gain -

134400.3 M 4 32,823,302 32,870,320 47,019 Gain -

22449.3 M 4 34,534,306 34,554,927 20,622 Loss -

27048.3 M 4 45,705,844 45,769,554 63,711 Loss GABRG1

86700.3 M 4 48,245,039 48,788,543 543,505 Gain OCIAD2,OCIAD1,FRYL,CWH43

19356.3 F 4 57,215,132 57,243,040 27,909 Loss HOPX

106800.3 M 4 59,888,910 61,452,073 1,563,164 Gain -

19773.3 M 4 77,181,395 77,224,152 42,758 Loss ART3

19992.3 M 4 80,876,908 80,907,420 30,513 Loss -

19710.3 M 4 89,393,217 89,448,853 55,637 Gain PPM1K

20118.3 M 4 101,610,128 101,667,917 57,790 Loss EMCN

122100.3 M 4 103,050,308 103,256,273 205,966 Loss BANK1

22437.3 M 4 120,775,039 120,832,466 57,428 Gain -

137100.3 M 4 125,185,975 125,335,052 149,078 Loss -

20130.3 F 4 126,957,261 127,054,564 97,304 Loss -

87600.3 M 4 128,064,755 128,159,463 94,709 Loss -

27696.3 M 4 151,308,871 151,342,002 33,132 Loss DCLK2

104400.3 F 4 158,840,964 158,862,019 21,056 Loss -

39300.3 M 4 164,880,889 164,909,603 28,715 Gain MARCH1

20046.3 M 4 183,686,910 183,793,993 107,084 Loss ODZ3

63600.3 M 4 189,022,067 189,106,355 84,289 Gain -

20076.3 M 5 12,168,805 12,200,367 31,563 Gain -

132000.3 M 5 16,812,470 16,838,622 26,153 Loss MYO10

80400.3 M 5 18,674,429 18,732,704 58,276 Loss -

122400.3 M 5 35,129,799 35,187,359 57,561 Gain PRLR

27045.3 M 5 40,950,187 40,979,607 29,421 Loss C7

19743.3 M 5 42,009,967 42,413,583 403,617 Loss -

129600.4 M 5 78,344,487 78,552,741 208,255 Gain BHMT2,DMGDH,BHMT

27270.3 F 5 79,979,470 80,009,301 29,832 Loss DHFR,MTRNR2L2,MSH3

19713.3 M 5 101,647,978 101,803,797 155,820 Loss SLCO4C1,SLCO6A1

96600.3 M 5 101,988,066 102,017,641 29,576 Loss -

19929.3 F 5 115,560,964 115,581,167 20,204 Loss COMMD10

80400.3 M 5 119,902,205 120,027,398 125,194 Loss PRR16

133200.5 M 5 122,184,982 122,469,076 284,095 Gain SNX2,PRDM6,PPIC,SNX24

19992.3 M 5 128,465,795 128,924,927 459,133 Gain ADAMTS19,ISOC1

19734.3 M 5 143,367,586 143,402,961 35,376 Gain -

27060.3 M 5 175,090,559 175,221,327 130,769 Gain CPLX2

123300.3 M 5 177,187,571 177,372,169 184,599 Gain FAM153C,PROP1,LOC728554

57300.3 M 6 10,384,323 10,646,232 261,910 Gain TFAP2A,LOC100130275,GCNT2,C6orf218

19698.4 F 6 10,656,503 10,748,220 91,718 Loss GCNT2

80400.3 M 6 33,604,179 33,629,523 25,345 Loss -

19710.3 M 6 38,808,721 38,833,354 24,634 Loss DNAH8

47400.3 M 6 57,416,954 57,565,044 148,091 Gain PRIM2

20130.3 F 6 117,615,877 117,669,245 53,369 Loss -

20079.3 F 6 118,788,984 118,839,763 50,780 Loss -

84900.3 F 6 128,678,096 128,787,283 109,188 Loss PTPRK

20118.3 M 6 151,775,590 151,895,575 119,986 Gain C6orf97,C6orf211,RMND1

27174.3 M 6 156,046,355 156,073,043 26,689 Loss -

99000.5 F 6 167,533,253 167,572,885 39,633 Gain -

99000.5 F 6 167,600,547 167,692,835 92,289 Loss TTLL2,UNC93A

19365.3 F 7 2,844,359 2,864,678 20,320 Loss GNA12

19875.4 F 7 3,115,426 3,150,697 35,272 Loss -

27237.3 F 7 3,148,349 3,192,655 44,307 Loss -

103200.3 M 7 3,487,526 3,526,927 39,402 Loss SDK1

27072.3 F 7 5,897,071 5,922,785 25,715 Loss CCZ1

122100.3 M 7 7,836,572 7,892,813 56,242 Loss LOC729852

6

71400.3 F 7 8,635,877 8,664,219 28,343 Gain NXPH1

19809.3 F 7 9,705,277 9,762,670 57,394 Gain -

19761.3 M 7 15,469,392 15,521,937 52,546 Loss TMEM195

27288.3 M 7 17,354,703 17,596,179 241,477 Gain -

27204.3 M 7 84,916,633 84,937,706 21,074 Loss -

89700.3 M 7 102,625,183 102,664,964 39,782 Loss DPY19L2P2

27084.3 F 7 109,016,489 109,057,993 41,505 Gain -

73800.4 M 7 109,495,636 109,536,977 41,342 Gain -

27039.3 F 7 125,443,958 125,464,638 20,681 Loss -

63900.3 F 7 132,307,121 132,466,121 159,001 Gain CHCHD3

63900.3 F 7 132,471,776 132,845,360 373,585 Gain EXOC4

123300.3 M 7 132,612,228 132,637,335 25,108 Loss EXOC4

136200.3 F 7 139,856,282 139,880,181 23,900 Gain DENND2A

20049.3 M 7 145,687,353 145,710,951 23,599 Gain CNTNAP2

19896.3 M 7 157,474,064 158,486,774 1,012,710 Gain PTPRN2,MIR595,WDR60,NCAPG2,ESYT2

19764.3 F 7 157,888,587 157,959,207 70,621 Gain PTPRN2

19662.3 F 8 4,583,157 4,697,836 114,680 Loss CSMD1

93300.3 M 8 8,363,730 8,385,745 22,016 Gain -

106800.3 M 8 10,968,130 11,087,819 119,690 Gain XKR6

19713.3 M 8 13,900,422 13,974,271 73,850 Loss -

19716.3 F 8 14,225,151 14,520,808 295,658 Loss SGCZ

27603.3 M 8 25,574,066 25,595,747 21,682 Loss -

104400.3 F 8 38,326,280 38,354,650 28,371 Loss WHSC1L1

135300.3 M 8 46,982,700 47,862,427 879,728 Loss -

19698.4 F 8 54,030,334 54,081,042 50,709 Gain -

103200.3 M 8 56,729,997 56,823,849 93,853 Gain TMEM68

283800.3 M 8 71,043,645 71,143,292 99,648 Gain PRDM14

27942.4 M 8 78,544,800 78,579,180 34,381 Gain -

20115.3 F 8 84,182,673 84,295,735 113,063 Loss -

18780.4 F 8 84,861,734 84,900,500 38,767 Gain -

84300.3 M 8 88,410,466 88,458,293 47,828 Loss CNBD1

136200.3 F 8 106,992,645 107,028,263 35,619 Loss -

19737.3 M 8 121,912,646 121,998,812 86,167 Gain -

22749.3 M 8 127,553,100 129,032,780 1,479,681 Gain MIR1204,LOC727677,PVT1,FAM84B,POU5F1B,MYC

55200.3 M 8 127,553,100 129,031,946 1,478,847 Gain MIR1204,LOC727677,PVT1,FAM84B,POU5F1B,MYC

19869.3 M 8 141,535,164 141,616,408 81,245 Gain TRAPPC9,CHRAC1,EIF2C2

63600.3 M 9 2,565,021 2,598,538 33,518 Loss FLJ35024

19794.3 F 9 7,254,558 7,287,075 32,518 Loss -

27003.3 F 9 11,474,182 11,577,106 102,925 Loss -

20010.3 F 9 11,691,596 11,780,990 89,395 Loss -

20031.3 M 9 18,279,918 18,998,759 718,842 Gain FAM154A,MIR3152,ADAMTSL1

88800.3 M 9 18,937,109 19,009,505 72,397 Loss FAM154A

89700.3 M 9 22,311,178 22,339,183 28,006 Loss -

137100.3 M 9 26,401,166 26,491,479 90,314 Loss -

27015.3 F 9 29,455,446 29,760,176 304,731 Gain -

73800.4 M 9 30,227,599 30,270,020 42,422 Gain -

73800.4 M 9 30,327,953 30,453,766 125,814 Gain -

19869.3 M 9 80,542,086 80,572,641 30,556 Gain -

19869.3 M 9 86,428,967 86,466,027 37,061 Gain -

19899.3 M 9 96,289,175 96,340,805 51,631 Loss -

103200.3 M 9 103,938,179 104,015,174 76,996 Loss -

27207.3 M 9 104,625,715 104,686,262 60,548 Loss -

27207.3 M 9 104,783,671 104,812,909 29,239 Loss CYLC2

27006.3 F 9 106,497,096 106,524,677 27,582 Loss OR13D1

19812.3 M 9 118,479,893 118,627,637 147,745 Loss ASTN2,TRIM32

19761.3 M 9 118,493,276 118,670,608 177,333 Loss ASTN2,TRIM32

20082.3 M 10 253,778 550,264 296,487 Gain DIP2C,ZMYND11

73800.4 M 10 2,410,981 2,532,839 121,859 Loss -

27624.3 M 10 6,117,851 6,447,743 329,893 Gain IL2RA,PFKFB3,RBM17,MIR3155

27942.4 M 10 16,311,822 16,451,689 139,868 Gain -

27276.3 F 10 28,182,844 28,207,441 24,598 Loss ARMC4

30600.3 M 10 106,610,088 106,851,842 241,755 Gain SORCS3

30600.3 M 10 108,341,799 108,659,882 318,084 Gain SORCS1

27024.3 F 10 110,430,754 110,536,878 106,125 Gain -

19356.3 F 10 121,502,565 121,528,426 25,862 Gain INPP5F

18780.4 F 11 22,879,419 22,918,282 38,864 Loss -

7

103200.3 M 11 24,138,688 24,188,693 50,006 Loss -

19812.3 M 11 35,609,762 35,696,678 86,917 Gain TRIM44

19950.3 M 11 47,747,867 48,331,189 583,323 Gain OR4C45,NUP160,OR4S1,PTPRJ,OR4C3,OR4X1,OR4X2,

OR4B1

49500.3 M 11 61,734,168 61,761,521 27,354 Gain SCGB2A1

19929.3 11 73,219,073 73,366,164 147,092 Gain DNAJB13,CHCHD8,MRPL48,PAAF1,UCP2

120600.3 M 11 81,950,592 81,999,742 49,151 Gain -

55200.3 M 11 84,271,204 84,898,421 627,218 Gain DLG2

26100.3 M 11 88,876,277 89,044,786 168,510 Gain FOLH1B,NOX4

125700.3 M 11 98,563,840 98,612,652 48,813 Loss CNTN5

49800.3 F 11 111,546,830 111,588,790 41,961 Loss BCO2,TEX12

19899.3 M 11 116,704,813 116,730,541 25,729 Gain CEP164

84300.3 M 11 134,036,846 134,071,470 34,625 Loss -

73500.3 M 12 28,053,577 28,122,183 68,607 Loss -

84900.3 F 12 46,988,069 47,019,351 31,283 Loss H1FNT

19869.3 M 12 81,492,172 81,589,490 97,319 Gain -

54000.3 F 12 86,280,288 86,347,841 67,554 Loss -

19956.3 M 12 112,748,145 113,040,821 292,677 Gain RBM19

19896.3 M 12 121,166,750 121,231,275 64,526 Gain LRRC43,MLXIP,IL31

20151.3 F 12 130,254,437 130,289,268 34,832 Gain LOC116437

20151.3 F 12 130,466,075 130,524,700 58,626 Loss -

89700.3 M 12 131,692,481 131,903,396 210,916 Gain ANKLE2,LOC645277,GOLGA3,POLE,PGAM5,PXMP2,

P2RX2

87900.3 M 13 42,372,228 42,648,425 276,198 Gain DNAJC15,EPSTI1

27069.3 M 13 49,933,277 49,974,896 41,620 Loss -

84300.3 M 13 65,997,219 66,064,074 66,856 Loss PCDH9

20049.3 M 13 65,997,219 66,064,074 66,856 Loss PCDH9

19779.3 M 13 66,968,574 66,996,502 27,929 Loss -

22437.3 M 13 75,625,861 75,964,448 338,588 Gain -

84300.3 M 13 95,986,410 96,237,290 250,881 Loss HS6ST3

67200.3 M 13 101,239,021 101,290,488 51,468 Loss FGF14

20025.3 M 14 24,331,680 24,353,845 22,166 Gain STXBP6

20130.3 F 14 26,174,875 26,212,221 37,347 Loss -

27210.3 F 14 37,226,520 37,285,907 59,388 Loss -

19812.3 M 14 39,012,296 39,099,090 86,795 Gain -

19929.3 F 14 40,139,744 40,375,578 235,835 Loss -

67500.3 F 14 42,651,618 42,675,572 23,955 Loss -

27027.3 M 14 55,255,589 55,333,856 78,268 Gain RPL13AP3,C14orf34

22749.3 M 14 61,694,202 61,810,571 116,370 Loss -

55200.3 M 14 61,694,433 61,810,571 116,139 Loss -

111000.3 M 14 62,573,415 62,866,072 292,658 Gain KCNH5,RHOJ,GPHB5

27168.3 F 14 62,573,415 62,866,072 292,658 Gain KCNH5,RHOJ,GPHB5

111000.3 M 14 65,068,547 65,479,081 410,535 Gain FUT8

27168.3 F 14 65,068,547 65,479,081 410,535 Gain FUT8

19953.3 F 14 70,054,704 70,077,790 23,087 Gain ADAM20

27288.3 M 14 73,405,361 73,429,247 23,887 Gain PTGR2,ZNF410

27030.3 M 14 86,025,183 86,120,442 95,260 Loss -

19947.3 F 14 101,459,334 101,598,096 138,763 Gain DYNC1H1,PPP2R5C

19752.3 F 15 26,752,537 30,419,013 3,666,477 Gain 20 genes

27072.3 F 15 30,935,499 31,337,153 401,655 Gain FMN1

42600.3 M 16 5,762,457 5,792,957 30,501 Gain -

19764.3 F 16 6,808,722 6,868,435 59,714 Loss RBFOX1

27237.3 F 16 23,601,271 23,644,982 43,712 Gain PLK1,ERN2

19839.3 M 16 29,425,212 30,214,469 789,258 Gain 40 genes

19737.3 M 16 61,768,217 61,814,170 45,954 Gain -

102300.3 M 16 68,926,410 68,962,003 35,594 Gain DDX19A

127500.3 M 16 71,185,295 71,216,243 30,949 Loss -

27288.3 M 16 76,970,948 76,997,116 26,169 Loss WWOX

19689.3 F 16 79,686,811 79,714,886 28,076 Gain PKD1L2,LOC100329108,GCSH

66000.3 M 16 81,671,755 81,693,979 22,225 Loss CDH13

20076.3 M 16 82,957,174 82,977,842 20,669 Loss ATP2C2

19956.3 M 16 84,837,516 84,867,945 30,430 Loss -

129300.3 M 17 1,435,016 1,541,967 106,952 Gain PRPF8,SLC43A2,SCARF1,RILP

19974.3 M 17 6,716,227 6,778,429 62,203 Gain ALOX12P2

27030.3 M 17 10,518,971 10,544,962 25,992 Loss C17orf48,SCO1

19710.3 M 17 46,854,723 46,876,167 21,445 Gain -

8

19905.3 F 17 63,254,993 63,313,543 58,551 Gain BPTF

102300.3 M 17 77,676,845 77,802,538 125,694 Gain SLC16A3,CSNK1D,CCDC57

123000.3 M 18 1,970,034 2,013,813 43,780 Loss -

64500.3 M 18 2,258,254 2,845,023 586,770 Gain LOC645158,NDC80,METTL4,EMILIN2,SMCHD1

20082.3 M 18 7,069,997 7,562,725 492,729 Gain LRRC30,LAMA1,PTPRM

19713.3 M 18 9,152,268 9,520,408 368,141 Gain ANKRD12,RALBP1,TWSG1

27138.3 M 18 35,834,118 35,999,434 165,317 Loss -

127200.3 M 18 52,879,592 53,041,561 161,970 Gain BOD1P

115200.3 M 18 61,284,844 61,330,292 45,449 Loss -

30600.3 M 18 66,797,768 66,860,522 62,755 Gain -

20115.3 F 18 68,368,375 68,390,765 22,391 Loss -

27210.3 F 18 73,987,742 74,034,537 46,796 Gain -

57900.3 M 19 24,000,237 24,028,354 28,118 Loss -

27003.3 F 19 34,185,400 34,826,521 641,122 Loss UQCRFS1,VSTM2B,POP4

114600.3 M 19 53,049,172 53,078,612 29,441 Loss SULT2A1

123000.3 M 19 54,037,948 54,065,293 27,346 Loss PLEKHA4

133500.3 M 20 9,685,413 9,831,947 146,535 Gain PAK7

19737.3 M 20 12,479,180 12,609,633 130,454 Loss -

108300.3 M 20 14,005,434 14,547,435 542,002 Loss FLRT3,MACROD2

113400.3 M 20 14,363,228 14,472,741 109,514 Loss MACROD2

19695.3 M 20 19,018,152 19,046,511 28,360 Loss -

122100.3 M 20 31,983,664 32,008,175 24,512 Loss -

134700.3 M 20 51,115,548 51,326,664 211,117 Loss TSHZ2

27039.3 F 21 19,038,404 19,138,205 99,802 Loss -

64500.3 M 21 26,734,668 26,767,571 32,904 Gain CYYR1

94500.3 F 21 40,446,032 40,575,224 129,193 Gain DSCAM

283800.3 M 22 32,165,319 32,290,714 125,396 Loss LARGE

120300.3 M 22 35,078,939 35,301,903 222,965 Gain TXN2,FOXRED2,CACNG2,MYH9,EIF3D

19356.3 F 22 42,403,791 42,455,564 51,774 Gain EFCAB6

121200.3 M 22 46,651,134 46,687,888 36,755 Gain -

27030.3 M 22 48,865,544 48,910,194 44,651 Gain MLC1,MOV10L1

84300.3 M X 8,955,187 8,992,358 37,172 Gain FAM9B

20115.3 F X 15,901,467 16,103,986 202,520 Gain GRPR

93300.3 M X 21,809,482 21,853,905 44,424 Gain MBTPS2

27075.3 M X 22,678,814 23,066,819 388,006 Loss DDX53

131700.3 F X 35,766,511 35,786,584 20,074 Loss -

87600.3 M X 36,517,014 36,539,868 22,855 Loss -

70800.3 M X 36,517,014 36,539,868 22,855 Loss -

27603.3 M X 36,517,014 36,539,868 22,855 Loss -

116100.3 M X 36,517,014 36,539,868 22,855 Loss -

27168.3 F X 36,517,014 36,539,868 22,855 Loss -

129600.4 M X 46,256,745 46,294,513 37,769 Gain ZNF674,LOC401588

19704.3 F X 46,260,583 46,293,576 32,994 Gain ZNF674,LOC401588

27027.3 M X 65,853,157 65,877,861 24,705 Gain -

127500.3 M X 69,377,325 69,560,736 183,412 Gain KIF4A,GDPD2,ARR3,PDZD11,RAB41,P2RY4

56700.4 F X 71,776,705 71,873,400 96,696 Gain PHKA1

22455.3 M X 98,600,791 98,746,817 146,027 Loss LOC442459

86700.3 M X 100,637,234 100,739,175 101,942 Gain ARMCX4,ARMCX1

94500.3 F X 118,367,952 118,398,867 30,916 Loss -

71400.3 F X 125,804,054 127,242,190 1,438,137 Loss ACTRT1

84300.3 M X 137,202,047 137,273,761 71,715 Loss -

108300.3 M X 139,908,341 140,157,773 249,433 Gain SPANXB1,SPANXB2,SPANXF1,LDOC1

19764.3 F X 143,615,723 143,724,582 108,860 Loss -

9

Table S3. Phenotypes of families with rare CNVs at ADHD candidate loci.

Abbreviations: ADHD-C: (ADHD combined type), ADHD-I (ADHD inattentive type), ADHD-HI (ADHD

hyperactive/impulsive type), BPD: Bipolar disorder, CD: Conduct disorder, GAD: Generalized anxiety

disorder, LD: Learning disability, OCD: Obsessive-compulsive disorder, ODD: Oppositional defiant

disorder; SAD: Separation anxiety disorder. “neg.” indicates individuals who did not have a diagnosis for, or

any symptoms/traits of, any neuropsychiatric disorder, “CNV present” and “No CNV” indicate presence and

absence of CNV respectively as determined by qPCR or FISH testing, “No DNA” indicates samples which

could not be tested for CNV status due to unavailability of DNA.”Unknown” indicates individuals whose

phenotype information is not known.

Family Proband phenotype Maternal phenotype Paternal phenotype Sibling phenotype

27696 ADHD-I;

possible seizure disorder (No CNV)

neg. (No CNV)

neg.

(No CNV)

sister: LD,ODD

brother: mild tics

30600 ADHD-C

BPD (@ age 15) (No CNV)

neg. (No CNV)

ADHD (No CNV)

brother: ADHD, OCD traits

113400 ADHD-I; LD (No CNV)

depression, inattention (No CNV)

neg. (No DNA)

2 brothers: Unknown

27027 ADHD-C, SAD

(No CNV)

anxiety, depression, post-traumatic stress disorder

(CNV present)

ADHD

(No CNV)

Sister: neg.

27060 ADHD-I, transient tic

disorder, LD

(CNV present)

Depression

(No CNV)

neg.

(No DNA)

Brother: ODD traits, OCD traits

63900 ADHD-I; ODD (CNV present)

unknown

(No CNV)

unknown

(No DNA)

2 brothers: Unknown

19896 ADHD-HI; ODD (CNV present)

depression

(No CNV)

neg.

(CNV present)

Brother:

ADHD, anxiety, ODD, query Asperger’s, learning problems

19929 ADHD-I, LD

(No CNV)

anxiety, depression, learning problems

(No DNA) ADHD traits, learning

problems, CD, problems

with law, alcohol and drugs

No siblings

19752

ADHD, LD, GAD Major

depressive episode @ age 15

(CNV present)

depression, learning problems

(No CNV)

query learning problems, query ADHD, query ODD

(No DNA)

sister and brother: neg. for both

19839 ADHD-C; LD (No CNV)

Anxiety (CNV present)

neg.

(No DNA)

brother: LD. (No CNV)

brother: LD

22512 ADHD-C, LD (No CNV)

neg.

(CNV present)

query ADHD;

anxiety/depressive traits

(No DNA)

sister: ADHD traits, anxiety

trait

19365 ADHD-I, ODD, sleep

disorder

(No DNA)

neg.

(No CNV)

neg.

(No DNA)

2 brothers: eldest brother -

ADHD, language delay

57300 ADHD-I, dysthymia, LD,

Crohn's disease

(CNV present)

depression

(No CNV)

learning problems, ADHD No siblings

19698 ADHD-I, SAD, LD (CNV present)

neg.

(No DNA)

depression, learning

problems, problems with law, alcohol abuse, drug

abuse

(CNV present)

brother: LD, depressive traits

19761 ADHD-C, LD (No CNV)

neg.

(CNV present)

anxiety (as a teen)

(No DNA)

sister: unknown

19812 ADHD-C (No CNV)

neg. (No DNA)

neg. (CNV present) brother: neg.

10

108300 ADHD-C; LD; depressive

disorder-NOS

(CNV present)

anxiety, depression

(No CNV)

Anxiety, depression, ADHD

traits

(CNV present)

Sister: ADHD traits

87600 ADHD-C, ODD (CNV present)

anxiety; depression; inattentive traits

(No CNV) ADHD, ODD, learning

problems

No siblings

27048 ADHD-C, ODD, sleep

disorder

(CNV present)

anxiety, query learning problems

(No CNV)

ADHD

(No CNV)

sister: Neg.

125700 ADHD, LD (No CNV)

neg.

(CNV present)

ADHD traits

(No DNA) brother: LD, query ODD.

(No CNV)

sister: LD

89700 ADHD- C; LD (No CNV)

anxiety; traits of hyperactivity

(CNV present)

query ADHD and LD, traits of ODD and OCD

(No DNA)

brother: language delay; learning problems, ADHD traits

27075 ADHD, LD (CNV present)

anxiety, depression (No CNV)

neg. (No DNA)

2 sisters: anxious traits in eldest

11

Table S4. Loci with overlapping rare CNVs in this study and in previous ADHD

studies.

Dup: Duplication, Del: Deletion

Variants in table are exonic unless indicated otherwise

Cytoband Gene(s) Rare CNVs

in this study

Rare CNVs in

Elia et al.

(ref. S1)

Rare CNVs

in Lesch et

al. (ref. S2)

Rare CNVs

in Williams

et al.

(ref. S3)

3p26.3 CHL1 1 dup 1 dup* - -

3q11.2 EPHA6 1 del

(intronic) - - 1 dup*

3q26.1 ZBBX 2 dels 1 dup* 1 del* -

4p15.2 DHX15 1 dup - - 1 dup*

4q22.1 PPM1K 1 dup - - 1 del*

5q35.2 CPLX2 1 dup 1 del - -

6q22.33 PTPRK 1 del - - 1 dup*

7p22.2 SDK1 1 del

(intronic)

2 dels (intronic)

& 1 dup - -

7q32.3 CHCHD3 1 dup 1 dup - -

7q35 CNTNAP2 1 dup

(intronic) 1 del (intronic) - -

8p23.2 CSMD1 1 del

(intronic) 1 del (intronic) - -

8p22 SGCZ 1 del - - 1 dup*

8q21.3 CNBD1 1 del 1 del*

11q13.4

DNAJB13,

CHCHD8,

MRPL48,PAAF1,

UCP2

1 dup* - 1 dup* -

15q13.3 FMN1 1 dup - - 2 dups*

16p11.2 16p11.2 locus

(40 genes) 1 dup* - -

2 dels* & 2

dups*

16q23.3 CDH13 1 del

(intronic) - - 1 del*

16q24.1 ATP2C2 1 del 1 del - -

20p12.2 PAK7 1 dup 1 dup - -

20p12.1 MACROD2 2 dels 2 dels (intronic) - 1 del and 1

dup*

* These variants overlap multiple genes.

12

Table S5. Rare CNVs in ASD probands at loci also implicated in ADHD probands.

All variants in table were validated by qPCR

Inh (Inheritance) –M: Maternal; D: De Novo. Ancestry – EA: European; MIX:

Admixture.

Genes – Rare CNVs were found at the loci in bold in both the ADHD and the ASD

1 Maternally inherited 16p11.2 deletion is also present in autistic brother of the proband. 2 Proband was brought in for ASD testing and was found to be dysmorphic with speech apraxia and motor delay. Deletion is absent in

autistic brother.

Sample Sex Chr Start

(Build36/hg18)

End

(Build36/hg18) Size(bp) CNV Inh Ancestry Genes

88032 M 7 132,116,272 132,230,166 113,895 Gain M MIX CHCHD3

136929 M 9 118,263,609 118,308,641 45,033 Gain M EA ASTN2

128963 M 9 118,407,129 118,523,510 116,382 Loss M EA ASTN2, TRIM32

64119 M 9 118,480,042 118,570,447 90,406 Loss M EA ASTN2, TRIM32

84657 M 9 118,568,208 118,605,377 37,170 Loss M EA ASTN2 (intronic)

124498 M 12 131,714,545 131,822,519 107,975 Loss D EA POLE,PGAM5,PXMP2,ANKLE2

1218511 M 16 29,474,810 30,085,308 610,499 Loss M EA 16p11.2 locus (28 genes)

1099092 M 20 14,887,620 15,537,065 649,446 Loss M EA MACROD2

91548 M X 22,891,502 23,015,874 124,373 Loss M EA DDX53, upstream of PTCHD1

data sets.

13

Table S6. Summary of newly described ASTN2 and TRIM32 sequence variants.

Gene Data set

Individuals with

rare missense

variants

Individuals without

rare missense

variants

Total

Fisher’s Exact

Test p-value

(vs. controls)

ASTN2

ADHD 8 268 276 0.2130

ASD 9 337 346 0.3432

ADHD & ASD 17 605 622 0.272

Controls 2 186 188 -

TRIM32

ADHD 4 253 257 1

ASD 6 351 357 1

ADHD & ASD 10 604 614 1

Controls 2 155 157 -

14

Table S7. Newly described ASTN2 sequence variants in ADHD probands.

All exons of ASTN2 were sequenced in 276 ADHD cases and 188 controls. TaqMan assays were

performed in 190 additional control samples for two of the variants: c870T>A (het) and c2187G>A

(het).

Sample Sex Change Variant (DNA) Variant

(Protein)

Amino Acid

change Exon Inheritance

Freq in ADHD

cases

Freq in

controls

112353 M Missense c160C>A (het) p20P>Q (het) Proline to

Glutamine Exon 1 Paternal 1 in 276 0 in 188

115361 M Missense c870T>A (het) p257S>T (het) Serine to

Threonine Exon 3 Paternal 3 in 276 0 in 378

121771 M Missense c870T>A (het) p257S>T (het) Serine to

Threonine Exon 3 Paternal 3 in 276 0 in 378

121768 F Missense c2187G>A (het) p696D>N (het) Aspartate to

Asparagine

Exon

12

Present in

both parents 1 in 276 0 in 378

186-3 M Missense c2121G>A (het) p674V>M (het) Valine to

Methionine

Exon

11 Maternal 1 in 276 0 in 188

141667 M Missense c870T>A (het) p257S>T (het) Serine to

Threonine Exon 3 Paternal 3 in 276 0 in 378

139948 M Missense c3664C>T(het) p1188T>M

(het)

Threonine to

Methionine

Exon

22 Maternal 1 in 276 0 in 188

133153 M Missense c2990G>A(het) p963M>I (het) Methionine to

Isoleucine Exon

18 Maternal 1 in 276 0 in 188

15

Table S8. Newly described ASTN2 sequence variants in ASD probands.

All exons of ASTN2 were sequenced in 346 ASD cases and 188 control samples. TaqMan assays were

performed in 190 additional control samples for two variants: c1963T>G (het) and c870T>A (het).

Sample Sex Change Variant (DNA) Variant (Protein) Amino Acid

change Exon Inheritance

Freq. in

ASD cases

Freq. in

controls

60504L M Missense c1963T>G (het) p.621L>R (het) Leucine to Arginine

Exon 10 Paternal 1 in 346 0 in 378

82359L M Missense c2452G>A (het) p.784R>Q (het) Arginine to

Glutamine Exon 13 Paternal 1 in 346 0 in 188

109003 M Missense c1179C>T (het) p.360R>C (het) Arginine to

Cysteine Exon 4 Not maternal 1 in 346 0 in 188

97132L M Missense c3084A>G (het) p.995K>E (het) Lysine to

Glutamate Exon 18 Maternal 1 in 346 0 in 188

104049L M Missense c1629G>T (het) p.510V>L (het) Valine to Leucine

Exon 7 Maternal 1 in 346 0 in 188

139374L M Missense c3501A>C (het) p.1134T>P (het) Threonine to

Proline Exon 21 Maternal 1 in 346 0 in 188

93613 M Missense c3502C>T (het) p.1134T>I (het) Threonine to

Isoleucine Exon 21 Paternal 1 in 346 0 in 188

122687L F Missense c870T>A (het) p.257S>T (het) Serine to

Threonine Exon 3 N/A 1 in 346 0 in 378

96279L M Missense c2633G>T (het) p.844R>S (het) Arginine to

Serine Exon 15 N/A 1 in 346 0 in 188

16

Table S9. Newly described ASTN2 sequence variants in controls.

Sample Sex Change Variant (DNA) Variant (Protein) Amino Acid

change Exon Inh. Freq in cases

Freq in

controls

88919 M Missense c807C>T (het) p236R>C (het) Arginine to

Cysteine Exon 3 N/A

0 in 346 ASD 0 in 276 ADHD

1 in 188

89967 F Missense c3312C>T(het) p1071R>W(het) Arginine to

Tryptophan Exon 20 N/A

0 in 346 ASD

0 in 276 ADHD 1 in 188

17

Table S10. Newly described TRIM32 sequence variants in ADHD probands.

Sample Sex Change Variant (DNA) Variant (Protein) Amino Acid

change Exon Inheritance

Freq in

ADHD

cases

Freq in

controls

131275 M Missense c1902A>C (het) p581M>L (het) Methionine to

Leucine Exon 2

Probably

maternal 1 in 257 0 in 157

87-3 M Missense c1975G>A (het) p605G>D (het) Glycine to Aspartate

Exon 2 Maternal 1 in 257 0 in 157

138761 F Missense c1140A>G (het) p327M>L (het) Methionine to

Leucine Exon 2 N/A 1 in 257 0 in 157

146248 M Missense c933G>A (het) p258A>T (het) Alanine to Threonine

Exon 2 N/A 1 in 257 0 in 157

18

Table S11. Newly described TRIM32 sequence variants in ASD probands.

Sample Sex Change Variant (DNA) Variant (Protein) Amino Acid

change Exon Inheritance

Freq in

ASD cases

Freq in

controls

60504L M Missense c.1099 C>T (het) p.313 A>V (het) Alanine to

Valine Exon 2 Maternal 1 in 357 0 in 157

58568 M Missense c.1366 G>A (het) p.402 G>D (het) Glycine to

Aspartate Exon 2 Maternal 2 in 357 0 in 157

96277L M Missense c.1366 G>A (het) p.402 G>D (het) Glycine to Aspartate

Exon 2 Maternal 2 in 357 0 in 157

105532 M Missense c.1173 G>A (het) p.338 A>T (het) Alanine to

Threonine Exon 2

Probably

maternal 1 in 357 0 in 157

77447 M Missense c.2115A>G (het) p.652T>A (het) Threonine to

Alanine Exon 2 Maternal 1 in 357 0 in 157

117482 M Missense c.1140A>G(het) p.327M>V (het) Methionine to

Valine Exon 2 Paternal 1 in 357 0 in 157

19

Table S12. Newly described TRIM32 sequence variants in controls.

Sample Sex Change Variant (DNA) Variant (Protein) Amino Acid

change Exon Inh. Freq in cases

Freq in

controls

87451 M Missense c.595 G>A (het) p. 145R>Q (het) Arginine to Glutamine

Exon 2 N/A 0 in 357 ASD

0 in 257 ADHD 1 in 157

88874 M Missense c719G>C (het) p186Q>H (het) Glutamine to

Histidine Exon 2 N/A

0 in 357 ASD

0 in 257 ADHD 1 in 157

20

Supplementary References:

S1. J. Elia, X. Gai, H. M. Xie, J. C. Perin, E. Geiger, J. T. Glessner, M. D'Arcy, R.

deBerardinis, E. Frackelton, C. Kim, F. Lantieri, B. M. Muganga, L. Wang, T. Takeda,

E. F. Rappaport, S. F. Grant, W. Berrettini, M. Devoto, T. H. Shaikh, H. Hakonarson,

P. S. White, Rare structural variants found in attention-deficit hyperactivity disorder

are preferentially associated with neurodevelopmental genes. Mol. Psychiatry 15, 637-

646 (2010).

S2. K. P. Lesch, S. Selch, T. J. Renner, C. Jacob, T. T. Nguyen, T. Hahn, M. Romanos, S.

Walitza, S. Shoichet, A. Dempfle, M. Heine, A. Boreatti-Hummer, J. Romanos, S.

Gross-Lesch, H. Zerlaut, T. Wultsch, S. Heinzel, M. Fassnacht, A. Fallgatter, B.

Allolio, H. Schafer, A. Warnke, A. Reif, H. H. Ropers, R. Ullmann, Genome-wide

copy number variation analysis in attention-deficit/hyperactivity disorder: association

with neuropeptide Y gene dosage in an extended pedigree. Mol. Psychiatry 16, 491-

503 (2011).

S3. N. M. Williams, I. Zaharieva, A. Martin, K. Langley, K. Mantripragada, R. Fossdal,

H. Stefansson, K. Stefansson, P. Magnusson, O. O. Gudmundsson, O. Gustafsson, P.

Holmans, M. J. Owen, M. O'Donovan, A. Thapar, Rare chromosomal deletions and

duplications in attention-deficit hyperactivity disorder: a genome-wide analysis.

Lancet 376, 1401-1408 (2010).