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1 Supplemental Tables and Figures Post-zygotic de novo changes in glutamate and dopamine pathways may explain discordance of monozygotic twins for schizophrenia Castellani, CA., Melka, MG., Gui, JL., Gallo, AJ., O Reilly, RL., Singh, SM The University of Western Ontario
2 Figure S1-A. Circos plot of high confidence unique mutations in the affected member of Family 1. These variations were unshared between twins and not found in either parent. Blue represents a gain and red represents a loss. Outside track=snvs, Indels, Subs, Middle track=cnvs and Inside track= SVs. The arrow represents an inter chromosomal event.
3 Figure S1-B. Circos plot of high confidence unique mutations in the affected member of Family 2. These variations were unshared between twins. Blue represents a gain and red represents a loss. Outside track=snvs, Indels, Subs, Middle track=cnvs and Inside track= SVs.
4 Figure S2. Call Quality of raw variant calls.
5 Figure S3. Read Depth Density of raw variant calls. Outliers (above 250) were not included
6 Figure S4. Venn diagram of shared top 20 canonical pathways found to be overrepresented by variants in the sequencing dataset of affected and unaffected twins. The pathways from the unaffected twin in Family 1 and Family 2 have been merged to represent 36 unique pathways (4 shared). The 18 pathways unique to unaffected twins are broken down into 11 from Family 1 and 7 in Family 2.
7 Table S1. Structural Variants unique to the affected member of Family 1 (I-2-1). Shared identity is based on a 50% reciprocal overlap rule. Chr Start End Size (bp) SV Type Gene(s) Father Mother Inheritance Deletion 0 Present Absent Inherited Deletion 0 Present Present Inherited Deletion 0 Present Absent Inherited Deletion C1orf168 Present Present Inherited Deletion 0 Present Absent Inherited Deletion 0 Present Absent Inherited Deletion 0 Present Present Inherited Deletion PDE4DIP Present Present Inherited Deletion PDE4DIP Present Present Inherited Deletion 0 Present Present Inherited Deletion 0 Present Absent Inherited Deletion 0 Present Present Inherited Deletion MYT1L Present Absent Inherited Deletion 0 Present Present Inherited Deletion LOC Present Present Inherited Deletion 0 Present Absent Inherited Deletion 0 Present Present Inherited Deletion 0 Present Present Inherited Deletion 0 Present Absent Inherited Deletion GALNTL2 Present Absent Inherited Deletion 0 Present Present Inherited Deletion 0 Present Absent Inherited Deletion 0 Present Absent Inherited Deletion 0 Present Absent Inherited
8 Deletion 0 Present Absent Inherited Deletion 0 Present Absent Inherited Deletion 0 Present Present Inherited Deletion ANTXR2 Present Present Inherited Deletion 0 Present Absent Inherited Deletion 0 Present Absent Inherited Deletion LOC ;TPPP Present Present Inherited Deletion 0 Present Absent Inherited Deletion GHR Present Absent Inherited Deletion 0 Present Present Inherited Deletion REEP5 Present Absent Inherited Deletion LMNB1 Present Absent Inherited Deletion LOC Present Present Inherited Deletion UIMC1 Present Absent Inherited Deletion 0 Present Present Inherited Deletion 0 Present Absent Inherited Deletion PKHD1 Present Absent Inherited Deletion 0 Present Present Inherited Deletion 0 Present Absent Inherited Deletion 0 Present Absent Inherited Deletion 0 Present Absent Inherited Deletion 0 Present Present Inherited Deletion ANLN Present Absent Inherited
9 Deletion ABHD11;AUTS2;BAZ1B;BCL7B;C7orf42;CALN1;CLDN3;CLD N4;DNAJC30;FKBP6;FZD9;GTF2IRD2P;LOC ;LOC ;LOC ;LOC ;LOC ;LOC ;LOC442572;LOC644794;LOC729156;ML XIPL;NCF1B;NSUN5;NSUN5C;PMS2L4;POM121;RABGEF1;S BDS;SBDSP;SPDYE7P;SPDYE8P;STAG3L3;STAG3L4;STX1A;T BL2;TRIM50;TRIM74;TYW1;TYW1B;VPS37D;WBSCR17;WB SCR22;WBSCR26;WBSCR27;WBSCR28 Present Present Inherited Deletion 0 Present Present Inherited Deletion MUC12 Present Absent Inherited Deletion 0 Present Absent Inherited Deletion 0 Present Absent Inherited Deletion 0 Present Absent Inherited Deletion 0 Present Absent Inherited Deletion 0 Present Present Inherited Deletion 0 Present Absent Inherited Deletion 0 Present Present Inherited Deletion 0 Present Present Inherited Deletion 0 Present Absent Inherited Deletion DAB2IP Present Absent Inherited Deletion 0 Present Absent Inherited Deletion C9orf98 Present Absent Inherited Deletion DNAJC1 Present Absent Inherited Deletion 0 Present Absent Inherited Deletion KCNMA1 Present Absent Inherited Deletion 0 Present Absent Inherited Deletion OR52N1;OR52N5 Present Absent Inherited Deletion MICAL2 Present Present Inherited Deletion 0 Present Present Inherited
10 Deletion 0 Present Present Inherited Deletion LOC Present Absent Inherited Deletion A2ML1 Present Present Inherited Deletion 0 Present Absent Inherited Deletion ANKS1B Absent Absent De novo Deletion MAPKAPK5 Present Absent Inherited Deletion 0 Present Absent Inherited Deletion 0 Absent Present Inherited Deletion ZDHHC20 Present Absent Inherited Deletion 0 Absent Absent De novo Deletion 0 Present Absent Inherited Deletion FUT8 Present Absent Inherited Deletion 0 Absent Absent De novo Deletion 0 Present Absent Inherited Deletion 0 Absent Present Inherited Deletion 0 Present Present Inherited Deletion 0 Absent Absent De novo Deletion LASS3 Present Present Inherited Deletion 0 Present Absent Inherited Deletion 0 Present Present Inherited Deletion NXN Absent Present Inherited Deletion 0 Absent Absent De novo Deletion LOC ;XYLT2 Present Present Inherited Deletion 0 Absent Absent De novo Deletion 0 Present Absent Inherited Deletion 0 Present Present Inherited Deletion 0 Absent Absent De novo
11 Deletion 0 Absent Absent De novo Deletion EMR3 Present Present Inherited Deletion 0 Present Absent Inherited Deletion 0 Absent Absent De novo Deletion PLTP Absent Present Inherited Deletion 0 Absent Present Inherited Deletion A4GALT Present Absent Inherited Deletion FAM19A5 Present Present Inherited Deletion 0 Absent Absent De novo X Deletion 0 Present Absent Inherited X Deletion 0 Absent Present Inherited X Deletion CLCN5 Absent Absent De novo Tandem Dup ACAP3;ACTRT2;AGRN;AJAP1;ARHGEF16;ATAD3A;ATAD3B; ATAD3C;AURKAIP1;B3GALT6;C1orf159;C1orf170;C1orf174 ;C1orf222;C1orf70;C1orf86;C1orf93;CALML6;CCDC27;CCN L2;CDC2L1;CDC2L2;CPSF3L;DFFB;DVL1;FAM132A;FLJ1410 0;FLJ39609;FLJ42875;GABRD;GLTPD1;GNB1;HES4;HES5;IS G15;KIAA0495;KIAA0562;KIAA1751;KLHL17;LOC ;LOC ;LOC ;LOC ;LOC ;LOC ;LOC ;LOC ;LO C ;LOC ;LOC ;LOC ;LOC ;LOC ;LOC ;LOC10 Absent Absent De novo ;LOC115110;LOC148413;LOC284661;LOC388588; LOC401934;LOC441869;LOC643988;LOC728661;LOC ;LRRC47;MEGF6;MIB2;MMEL1;MMP23A;MMP23B;MO RN1;MRPL20;MXRA8;NADK;NOC2L;PANK4;PEX10;PLCH2; PLEKHN1;PRDM16;PRKCZ;PUSL1;RER1;SAMD11;SCNN1D; SDF4;SKI;SLC35E2;SSU72;TAS1R3;TMEM52;TMEM88B;TN FRSF14;TNFRSF18;TNFRSF4;TP73;TPRG1L;TTLL10;UBE2J2; VWA1;WDR Tandem Dup 0 Absent Absent De novo
12 Tandem Dup TPO Absent Present Inherited Tandem Dup 0 Present Absent Inherited Tandem Dup 0 Present Absent Inherited Tandem Dup 0 Absent Absent De novo Tandem Dup COL23A1 Absent Present Inherited Tandem Dup LOC Absent Absent De novo Tandem Dup PRKAR1B Present Present Inherited Tandem Dup 0 Present Present Inherited Tandem Dup 0 Absent Absent De novo Tandem Dup 0 Absent Absent De novo Tandem Dup NTM Absent Absent De novo Tandem Dup 0 Absent Absent De novo Tandem Dup 0 Present Present Inherited Tandem Dup SNORD Absent Absent De novo Tandem Dup 0 Absent Present Inherited Tandem Dup GZMM Absent Absent De novo Tandem Dup 0 Present Absent Inherited Tandem Dup C20orf39 Present Absent Inherited / / Distal Dup 0 Absent Present Inherited / / Distal Dup LOC Present Absent Inherited / / Distal Dup LOH12CR1 Present Present Inherited / / Distal Dup MGAT4C Present Absent Inherited / / Distal Dup 0 Present Absent Inherited / / Distal Dup 0 Absent Present Inherited
13 / / Distal Dup 0 Absent Present Inherited / / Distal Dup DHRSX;LOC ;LOC Present Absent Inherited / / Distal Dup XAGE-4;XAGE3 Absent Present Inherited Interchrom CDC27 Absent Absent De novo
14 Table S2. Structural Variants unique to the affected member of Family 2 (II-2-1). Shared identity is based on a 50% reciprocal overlap rule. Chr Start End Size (bp) SV Type Gene(s) Deletion Deletion Deletion INADL Deletion Deletion Deletion C4BPA Deletion Deletion Deletion Deletion Deletion DHX Deletion Deletion Deletion Deletion Deletion Deletion ATP2B Deletion Deletion Deletion Deletion Deletion Deletion Deletion 0
15 Deletion Deletion KIAA Deletion Deletion Deletion Deletion Deletion Deletion Deletion Deletion MARVELD Deletion C5orf Deletion LOC Deletion COL23A Deletion Deletion Deletion TMEM170B Deletion Deletion Deletion Deletion Deletion PRIM Deletion AIM Deletion FAM184A Deletion Deletion Deletion OPRM Deletion 0
16 Deletion Deletion PTPRN Deletion Deletion Deletion Deletion Deletion Deletion CCNY Deletion Deletion Deletion ACSL Deletion OVCH Deletion Deletion Deletion Deletion Deletion CASP Deletion ZNF Deletion TMEM132D Deletion Deletion Deletion GPC Deletion Deletion Deletion Deletion Deletion 0
17 Deletion WDR Deletion LOC Deletion Deletion TYRO Deletion MGA Deletion TRPM Deletion Deletion Deletion CRTC Deletion Deletion CHD Deletion GSPT Deletion PRKCB Deletion Deletion RPH3AL Deletion RPH3AL Deletion Deletion LOC Deletion Deletion B4GALNT Deletion Deletion Deletion TFG/GPR Deletion Deletion ZNF Deletion Deletion LOC647946
18 Deletion SLC14A Deletion Deletion DCC Deletion Deletion AP3D Deletion CLPTM Deletion Deletion PIGU Deletion Deletion Deletion CLIC Deletion Deletion SYN Deletion 0 X Deletion DMD X Deletion DACH2 X Deletion Tandem Dup Tandem Dup Tandem Dup CLSTN Tandem Dup Tandem Dup LOC ;LPA;LPAL Tandem Dup PRKAR1B Tandem Dup Tandem Dup LOC Tandem Dup Tandem Dup C10orf51
19 Tandem Dup Tandem Dup CRIP Tandem Dup CLEC17A X Tandem Dup / / / / / XAGE4;ALAS2;APEX2;FAM104B;FAM120C;FAM156A;FAM156B;FGD1 ;FOXR2;GNL3L;GPR173;HSD17B10;HUWE1;IQSEC2;ITIH5L;KDM5C;LO C ;LOC ;LOC ;LOC ;LOC ;LOC644893;MAGED2;MAGEH1;PAGE2;PAGE2B;PAGE3;PAGE 5;PFKFB1;PHF8;RIBC1;SMC1A;SNORA11;TRO;TSPYL2;TSR2;USP51;W NK3;XAGE / Distal Dup / Distal Dup / Distal Dup MUC3A / Distal Dup / Distal Dup REPS2
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