Supplementary Table 2: Full list of high stringency genic CNV calls (2 or more algorithms), with no overlapping calls in 2,357 POPGEN and OHI controls, and 50% overlap in DGV. Coordinates refer to Human Genome Build36/hg18. Algorithms used include iPattern (IPN), Genotyping Console (GTC) and BirdSuite (BS). CNVs validated by qPCR are indicated by bold type. Ancestry is European unless otherwise stated in the footnotes. A list of all calls, including lower stringency calls is available from the corresponding author.
ID / Cytoband / Start / Stop / Size / CNV / Algorithms / # of Probes / # of Genes / # of Exons / Genes / MIM #; Associated pathologyA217# / 1q24.3 / 170,174,111 / 170,226,179 / 52,069 / gain / BS,IPN|GTC / 41 / 1 / 2 / DNM3
A217# / 1q31.3 / 195,206,342 / 195,222,522 / 16,181 / Loss / BS,IPN|GTC / 19 / 1 / 3 / CFHR5 / 61480;nephropathy
A86 / 1q41 / 218,154,670 / 218,179,823 / 25,154 / Gain / BS,IPN / 18 / 1 / 4 / SLC30A10 / 613280; hypermangan- esemia with dystonia, polycythemia & cirrhosis
A62 / 2p25.1 / 10,208,865 / 10,474,077 / 265,213 / Loss / BS,IPN|GTC / 213 / 3 / 5 / HPCAL1,C2orf48
A187 / 2p23.3 / 25,717,735 / 25,777,692 / 59,958 / gain / BS,IPN|GTC / 33 / 1 / 2 / DTNB
A156 / 2q21.2 / 133,600,528 / 133,728,969 / 128,442 / Loss / BS,IPN|GTC / 90 / 1 / 2 / NCKAP5
A116* / 3p25.3 / 11,451,728 / 11,466,305 / 14,578 / Loss / BS,IPN|GTC / 17 / 1 / 0 / ATG7
A200 / 3p24.3 / 17,655,221 / 17,758,388 / 103,168 / Loss / BS,IPN|GTC / 45 / 1 / 3 / TBC1D5
A204 / 3q21.1 / 124,907,330 / 124,956,275 / 48,946 / Loss / BS,IPN|GTC / 28 / 1 / 12 / MYLK / 613780; familial thoracic aortic aneuysm 7
A27 / 3q25.32 / 158,558,282 / 158,639,900 / 81,619 / Gain / BS,IPN|GTC / 57 / 2 / 7 / VEPH1,PTX3
A184 / 3q28 / 192,624,900 / 192,672,766 / 47,867 / Loss / BS,IPN|GTC / 37 / 1 / 1 / PYDC2
A217 / 3q28 / 193,415,193 / 193,427,820 / 12,628 / Gain / BS,IPN|GTC / 35 / 1 / 0 / FGF12
A217 / 3q28 / 193,430,546 / 193,452,431 / 21,886 / Loss / BS,IPN|GTC / 16 / 1 / 0 / FGF12
A6 / 4p12 / 47,881,699 / 47,910,404 / 28,706 / Loss / BS,IPN|GTC / 86 / 1 / 0 / TEC
A213 / 5q12.3 / 63,974,156 / 64,240,025 / 265,870 / Gain / BS,IPN|GTC / 143 / 3 / 19 / FAM159B,CWC27,SREK1IP1
A23 / 6p25.1 / 5,170,870 / 5,308,007 / 137,138 / Loss / BS,IPN|GTC / 95 / 2 / 2 / FARS2,LYRM4 / 614946 (FARS2) ; Combined oxidative phosphorylation deficiency 14
A44 / 6p24.1,6p24.2 / 11,192,623 / 11,233,071 / 40,449 / Loss / BS,IPN|GTC / 23 / 2 / 3 / LOC221710,HERV-FRD
A196 / 6p22.3 / 17,763,624 / 17,862,652 / 99,029 / Gain / BS,IPN|GTC / 54 / 1 / 11 / NUP153
A83 / 6q15 / 88,234,016 / 88,350,126 / 116,111 / Gain / BS,IPN|GTC / 62 / 2 / 27 / SLC35A1,RARS2 / 603585 (SLC35A1); Congenital disorder of glycosylation, type IIf
A50 / 7q11.22 / 68,391,493 / 68,846,056 / 454,564 / Gain / BS,IPN|GTC / 235 / 1 / 1 / AUTS2 / 607373; autism susceptibility 8
A103 / 7q35 / 145,687,353 / 145,707,079 / 19,727 / Loss / BS,IPN|GTC / 19 / 1 / 0 / CNTNAP2 / 610042; cortical dysplasia-focal epilepsy syndrome; Pitt-Hopkins Like syndrome1;
612100; autism susceptibility 15
A210 / 7q36.2 / 152,909,758 / 153,711,379 / 801,622 / Gain / BS,IPN|GTC / 571 / 1 / 3 / DPP6 / 612956; Ventricular fibrillation, paroxysmal familial, 2
A35$ / 7q36.2 / 153,462,809 / 153,529,856 / 67,048 / Loss / BS,IPN|GTC / 38 / 1 / 0 / DPP6
A41 / 8p23.1 / 9,948,345 / 9,980,334 / 31,990 / Loss / BS,IPN|GTC / 28 / 1 / 1 / MSRA
A196 / 9p11.2-q12 / 45,506,516 / 65,370,766 / 19.9Mb / Loss / BS|GTC / 55 / 6 / 19 / FAM75A5,FAM75A7,FAM74A4,FAM74A2,FAM27A,KGFLP1
A32 / 10p14 / 8,021,446 / 8,034,890 / 13,445 / Loss / BS,IPN / 14 / 1 / 0 / TAF3
A67% / 10p11.21 / 35,393,771 / 35,496,363 / 102,593 / Loss / BS,IPN|GTC / 45 / 2 / 6 / CREM,CUL2
A67 / 10q22.1 / 74,184,905 / 74,230,349 / 45,445 / Loss / BS,IPN|GTC / 26 / 1 / 0 / CCDC109A
A210 / 11p14.1 / 28,105,472 / 28,135,299 / 29,828 / Loss / BS,IPN|GTC / 17 / 1 / 0 / METTL15
A196 / 11q13.4 / 73,617,083 / 73,947,977 / 330,895 / Gain / BS,IPN|GTC / 230 / 5 / 41 / P4HA3,PPME1,KCNE3,LIPT2,PGM2L1
A21 / 11q14.1 / 83,108,466 / 83,378,706 / 270,241 / Gain / BS,IPN|GTC / 208 / 1 / 7 / DLG2
A16 / 12q24.11 / 108,087,877 / 108,127,535 / 39,659 / Loss / BS,IPN|GTC / 28 / 1 / 17 / ACACB
A136 / 12q24.22 / 115,655,372 / 115,797,029 / 141,658 / Gain / BS,IPN|GTC / 89 / 3 / 14 / C12orf49,RNFT2,HRK
A213 / 12q24.33 / 130,105,794 / 130,333,801 / 228,008 / Gain / BS,IPN|GTC / 187 / 2 / 17 / LOC116437,GPR133
A94 / 13q21.33 / 69,452,461 / 69,471,066 / 18,606 / Loss / BS,IPN|GTC / 11 / 1 / 0 / KLHL1
A182 / 14q23.3 / 66,274,499 / 66,631,750 / 357,252 / loss / BS,IPN|GTC / 142 / 1 / 10 / GPHN / 252150; Molybdenum cofactor deficiency, type C
A83 / 14q31.1 / 78,548,117 / 78,587,995 / 39,879 / Loss / BS,IPN|GTC / 35 / 1 / 0 / NRXN3
A187 / 14q32.33 / 103,116,875 / 103,151,310 / 34,436 / loss / BS,IPN|GTC / 16 / 1 / 2 / C14orf153 (APOPT1)
A23 / 15q21.3 / 52,531,915 / 52,555,069 / 23,155 / Loss / BS,IPN|GTC / 16 / 1 / 0 / UNC13C
A136 / 16p11.2 / 28,660,952 / 28,951,376 / 290,425 / Loss / BS,IPN|GTC / 77 / 9 / 125 / ATXN2L,ATP2A1,NFATC2IP,SPNS1,RABEP2,SH2B1,LAT,TUFM,CD19 / 613444; 16p11.2 deletion syndrome (220Kb);
601003 (ATP2A1); Brody myopathy;
610678 (TUFM); Combined oxidative phosphorylation deficiency 4;
613493 (CD19); Immunodeficiency, common variable, 3
A67 / 16q12.1 / 47,911,712 / 48,519,007 / 607,296 / Gain / BS,IPN|GTC / 456 / 2 / 14 / C16orf78,ZNF423 / 614844 (ZNF423); Joubert syndrome 19, Nephronophthisis 14
A217# / 17p12 / 12,238,673 / 12,985,028 / 746,356 / gain / BS,IPN|GTC / 563 / 4 / 64 / ARHGAP44,MYOCD,FLJ34690,ELAC2 / 614731 (ELAC2); susceptibility to hereditary prostate cancer 2
A44 / 17q21.31 / 39,578,594 / 39,756,006 / 177,413 / Gain / BS,IPN|GTC / 77 / 9 / 96 / C17orf65,ASB16,TMUB2,SLC25A39,UBTF,RUNDC3A,SLC4A1,C17orf53,ATXN7L3 / 179800 (SLC4A1); Renal tubular acidosis, distal, AD
A162 / 17q23.3 / 58,985,825 / 58,999,732 / 13,908 / loss / BS,IPN|GTC / 11 / 1 / 0 / DCAF7
A196 / 17q24.3 / 68,081,137 / 68,107,879 / 26,743 / gain / IPN|GTC / 18 / 2 / 2 / FLJ26484,LOC100499467
A196 / 17q24.3 / 68,143,014 / 68,212,703 / 69,690 / gain / BS,IPN|GTC / 69 / 2 / 5 / FLJ26484,SLC39A11
A79 / 17q25.3 / 74,912,218 / 75,225,624 / 313,407 / Gain / BS,IPN|GTC / 81 / 1 / 1 / hCG_1776007
A144 / 18q23 / 75,895,798 / 75,956,745 / 60,948 / Gain / BS,IPN|GTC / 43 / 1 / 6 / C18orf22
A153 / 18q23 / 75,895,798 / 75,956,745 / 60,948 / Gain / BS,IPN|GTC / 43 / 1 / 6 / C18orf22
A161 / 19p13.2 / 11,891,258 / 11,922,384 / 31,127 / Gain / BS,IPN / 24 / 1 / 4 / ZNF700
A62 / 21q22.11 / 31,680,657 / 31,991,168 / 310,512 / Gain / BS,IPN|GTC / 201 / 3 / 20 / TIAM1,SFRS15,SOD1 / 105400 (SOD1); Amyotrophic lateral sclerosis 1
A150a / Xp22.11,Xp21.3 / 24,513,979 / 27,864,451 / 3,350,473 / Gain / BS,IPN|GTC / 2105 / 10 / 60 / MAGEB18,POLA1,PCYT1B,ARX,VENTXP1,SMEK3P,MAGEB10,MAGEB6,SCARNA23,DCAF8L2 / 310465 (POL1); N syndrome;
300419 (ARX); Mental retardation, X-linked 29 and others
A38b& / Xq13.1 / 68,811,631 / 68,873,651 / 62,021 / Gain / BS,IPN|GTC / 39 / 1 / 0 / EDA / 313500; Tooth agenesis, selective, X-linked 1
305100; Ectodermal dysplasia 1, hypohidrotic, X-linked
A67b / Xq23 / 111,485,534 / 112,035,904 / 550,371 / Gain / BS,IPN|GTC / 329 / 4 / 18 / AMOT,ZCCHC16,LHFPL1
aproband is male
bproband is female
%:qPCR was attempted but was unable to validate this CNV
#:father from Pakistan, mother from Austria
*: Ugandan
$:Egyptian
&: Turkish