Supplementary Table 1. Number of Unique CNV in HLHS Alone Vs. HLHS with Additional Birth Defect

Supplementary Table 1. Number of unique CNV in HLHS alone vs. HLHS with additional birth defect

Unique CNV / Isolated (n=33) / Anomalies (n=10) / P value
60,000 / 1 (0.03 ± 0.17) / 0 (0.00 ± 0.00) / 0.5881
60,001-120,000 / 5 (0.15 ± 0.36) / 2 (0.20 ± 0.63) / 0.7603
120,001-480,000 / 6 (0.18 ± 0.39) / 1 (0.10 ± 0.32) / 0.5504
>480,000 / 8 (0.24 ± 0.44) / 1 (0.10 ± 0.32) / 0.3439
Total / 20 (0.61 ± 0.61) / 4 (0.40 ± 0.70) / 0.3703

Total number of CNV is listed. Mean CNV per person with standard deviation are shown in parentheses.

Supplementary Table 2. All CNV identified in HLHS and control populations (as totaled in Table 2)

Control (47)
Chromosome / Start / End / Value / Del/Dup / Gene / Unique
1p12 / 120,449,999 / 120,569,999 / 0.44077 / Dup / *
1p36.13 / 16,769,999 / 17,009,999 / 0.30041 / Dup / *
1q25.1 / 173,729,999 / 174,089,999 / -0.40627 / Del / *
2p11.2 / 86,969,999 / 87,449,999 / -0.355 / Del / *
2p11.2 / 86,969,999 / 87,989,999 / -0.31764 / Del / *
2p11.2-p11.1 / 89,669,999 / 91,049,999 / -0.43933 / Del / *
2q13 / 113,909,999 / 114,089,999 / -0.46154 / Del / * / *
2q21.1 / 130,529,999 / 130,649,999 / -0.36105 / Del
3p12.3 / 75,509,999 / 75,749,999 / -0.34093 / Del / *
3p21.31 / 46,169,999 / 46,469,999 / -0.36467 / Del / *
3p21.31 / 46,289,999 / 46,469,999 / -0.31575 / Del / *
3q21.3 / 131,249,999 / 131,309,999 / -0.62637 / Del / *
4p16.1 / 9,749,999 / 9,809,999 / -0.34657 / Del
6p12.3 / 49,949,999 / 50,009,999 / 0.35409 / Dup / * / *
6p21.32 / 32,609,999 / 32,729,999 / -0.3547 / Del / *
6p21.32 / 32,609,999 / 32,729,999 / -0.40162 / Del / *
6p21.32 / 32,609,999 / 32,729,999 / -0.33234 / Del / *
6p21.32 / 32,609,999 / 32,729,999 / -0.48304 / Del / *
6p21.32 / 32,609,999 / 32,849,999 / -0.30345 / Del / *
7p11.2 / 56,789,999 / 57,209,999 / 0.32567 / Dup / *
7q11.21 / 64,109,999 / 64,229,999 / -0.31115 / Del / *
7q22.1 / 101,789,999 / 101,909,999 / 0.3131 / Dup / * / *
8p11.23 / 39,389,999 / 39,449,999 / -0.44567 / Del / *
8p23.1 / 12,269,999 / 12,449,999 / -0.54807 / Del / *
8p23.1 / 7,229,999 / 7,769,999 / 0.44604 / Dup / *
9p11.2 / 44,669,999 / 44,789,999 / 0.59112 / Dup
9p24.3 / 89,999 / 209,999 / -0.3267 / Del / *
9p24.3 / 89,999 / 209,999 / -0.38881 / Del / *
9p24.3 / 89,999 / 209,999 / -0.43149 / Del / *
9p24.3 / 89,999 / 209,999 / -0.37911 / Del / *
10p11.21 / 38,549,999 / 38,609,999 / -0.38312 / Del / *
10q11.22 / 46,349,999 / 46,529,999 / -0.46331 / Del
10q11.22 / 47,189,999 / 47,909,999 / -0.55275 / Del / *
11p11.2-p11.12 / 48,689,999 / 48,809,999 / 0.50033 / Dup
11p11.2-p11.12 / 48,629,999 / 48,809,999 / 0.30017 / Dup
11p15.4 / 3,149,999 / 3,269,999 / -0.40524 / Del / *
12p13.31 / 7,889,999 / 8,069,999 / 0.32173 / Dup / *
12p13.33 / 29,999 / 149,999 / 0.43456 / Dup / * / *
14q11.1-q11.2 / 19,049,999 / 19,289,999 / -0.63087 / Del
14q11.2 / 19,289,999 / 19,469,999 / -0.33933 / Del / *
16p11.2 / 34,349,999 / 34,589,999 / 0.35967 / Dup / *
16p11.2 / 31,949,999 / 33,509,999 / 0.47245 / Dup / *
16q23.2 / 79,469,999 / 80,189,999 / 0.30186 / Dup / * / *
18p11.21 / 14,429,999 / 14,489,999 / -0.51731 / Del / *
21q11.1 / 13,949,999 / 14,129,999 / -0.38828 / Del / *
21q11.2 / 13,889,999 / 13,949,999 / -0.42406 / Del / *
22q11.21 / 18,749,999 / 18,989,999 / -0.67724 / Del / *
HLHS (198)
Chromosome / Start / End / Value / Del/Dup / Gene / Unique
1p12 / 120,450,000 / 120,570,000 / 0.4737 / Dup / *
1p21.1 / 103,830,000 / 103,950,000 / -0.4551 / Del / *
1p21.1 / 103,890,000 / 104,010,000 / -0.4508 / Del
1p21.1 / 104,010,000 / 104,130,000 / -0.751 / Del / *
1p36.13 / 16,770,000 / 16,890,000 / 0.3798 / Dup / *
1p36.13 / 16,770,000 / 16,890,000 / 0.4577 / Dup / *
1p36.13 / 16,830,000 / 16,950,000 / 0.4125 / Dup / *
1p36.13 / 16,890,000 / 16,950,000 / 0.6201 / Dup / *
1p36.13 / 16,890,000 / 17,070,000 / -0.3336 / Del / *
1p36.13 / 16,950,000 / 17,010,000 / -0.474 / Del / *
1p36.13 / 16,950,000 / 17,010,000 / 0.63803 / Dup / *
1p36.21 / 12,810,000 / 12,870,000 / -0.60501 / Del / *
1p36.21 / 12,810,000 / 13,650,000 / -0.30638 / Del / *
1p36.21 / 12,870,000 / 13,110,000 / 0.41133 / Dup / *
1p36.32 / 2,610,000 / 2,670,000 / 0.8855 / Dup / *
1p36.32 / 2,610,000 / 2,670,000 / 0.604 / Dup / *
1q21.1 / 147,450,000 / 147,510,000 / -0.7922 / Del / *
1q23.2 / 159,750,000 / 159,870,000 / 0.3726 / Dup / * / *
1q23.3 / 159,810,000 / 159,870,000 / 0.3972 / Dup / *
1q31.3 / 193,470,000 / 193,530,000 / -0.5755 / Del
1q31.3 / 194,970,000 / 195,150,000 / -0.3812 / Del / *
1q43 / 240,030,000 / 240,810,000 / 0.3893 / Dup / *
2p11.1 / 90,990,000 / 91,530,000 / -0.46539 / Del
2p11.2 / 87,450,000 / 87,990,000 / 0.4652 / Dup / *
2p11.2 / 87,450,000 / 87,990,000 / 0.5296 / Dup / *
2p11.2 / 89,010,000 / 89,190,000 / -1.00451 / Del / *
2p11.2-p11.1 / 89,250,000 / 91,050,000 / -0.31251 / Del / *
2p11.2-p11.1 / 89,670,000 / 91,050,000 / -0.7029 / Del / *
2q21.2 / 132,510,000 / 132,630,000 / -0.38573 / Del / *
3q21.3 / 131,250,000 / 131,310,000 / -0.4174 / Del / *
3q26.1 / 164,010,000 / 164,070,000 / -0.4531 / Del / *
3q29 / 199,230,000 / 199,322,570 / 0.3328 / Dup / *
4p11 / 48,810,000 / 49,230,000 / -0.53098 / Del / *
4p11 / 49,230,000 / 49,290,000 / 0.3838 / Dup / *
4p16.1 / 8,970,000 / 9,270,000 / -0.41379 / Del / *
4q13.2 / 69,030,000 / 69,090,000 / 0.46433 / Dup / *
4q13.2 / 69,030,000 / 69,150,000 / -0.50584 / Del / *
4q13.2 / 69,030,000 / 69,150,000 / -0.50746 / Del / *
4q13.2 / 69,030,000 / 69,150,000 / -0.50326 / Del / *
4q13.2 / 69,030,000 / 69,150,000 / -0.363 / Del / *
4q13.2 / 69,030,000 / 69,510,000 / -0.586 / Del / *
4q13.2 / 69,090,000 / 69,150,000 / 0.38275 / Dup / *
4q13.2 / 69,090,000 / 69,150,000 / 0.4726 / Dup / *
4q26 / 119,610,000 / 119,670,000 / 0.3015 / Dup / *
5p15.33 / 750,000 / 810,000 / 0.52868 / Dup / *
5q13.2 / 70,290,000 / 70,470,000 / -0.343 / Del / *
5q21.1 / 99,690,000 / 99,750,000 / -0.3426 / Del / *
6p21.32 / 32,550,000 / 32,610,000 / -0.3004 / Del / *
6p21.32 / 32,610,000 / 32,730,000 / -0.3292 / Del / *
6p21.32 / 32,610,000 / 32,730,000 / 0.3257 / Dup / *
6p22.1 / 26,790,000 / 26,850,000 / 0.4562 / Dup / *
6p22.1 / 26,970,000 / 27,030,000 / -0.55269 / Del / *
6p22.1 / 26,970,000 / 27,030,000 / -0.6637 / Del / *
6p22.2-p22.1 / 26,970,000 / 27,090,000 / -0.5073 / Del / *
6p22.2-p22.1 / 26,970,000 / 27,090,000 / -0.3608 / Del / *
6p22.2-p22.1 / 26,970,000 / 27,090,000 / -0.4355 / Del / *
6q12 / 68,250,000 / 68,490,000 / -0.3936 / Del
6q27 / 168,090,000 / 168,330,000 / 0.3962 / Dup / *
6q27 / 170,730,000 / 170,761,340 / -0.37403 / Del / *
6q27 / 170,730,000 / 170,761,340 / -0.35997 / Del / *
7p11.2 / 56,850,000 / 57,570,000 / 0.3197 / Dup / *
7p13 / 44,010,000 / 44,070,000 / 0.3312 / Dup / *
7q11.1-q11.21 / 61,590,000 / 61,950,000 / 0.34578 / Dup
7q11.21 / 64,230,000 / 64,290,000 / -0.47013 / Del / *
7q11.21 / 64,650,000 / 64,710,000 / 0.4772 / Dup / *
7q11.23 / 74,130,000 / 74,910,000 / 0.3448 / Dup / *
8p11.22 / 39,390,000 / 39,510,000 / -0.51946 / Del / *
8p11.23 / 39,390,000 / 39,450,000 / -0.75835 / Del / *
8p11.23 / 39,390,000 / 39,450,000 / -0.76906 / Del / *
8p11.23 / 39,390,000 / 39,450,000 / -0.7324 / Del / *
8p11.23 / 39,390,000 / 39,450,000 / -0.77199 / Del / *
8p11.23 / 39,390,000 / 39,450,000 / -0.5538 / Del / *
8p11.23 / 39,390,000 / 39,450,000 / -0.5794 / Del / *
8p11.23 / 39,390,000 / 39,450,000 / -0.836 / Del / *
8p11.23 / 39,390,000 / 39,450,000 / -1.0613 / Del / *
8p23.1 / 6,930,000 / 7,770,000 / 0.5227 / Dup / *
8p23.1 / 11,910,000 / 12,450,000 / 0.5206 / Dup / *
8p23.1 / 11,910,000 / 12,570,000 / 0.3212 / Dup / *
8p23.1 / 12,030,000 / 12,270,000 / 0.41974 / Dup / *
8p23.1 / 12,270,000 / 12,450,000 / 0.3453 / Dup / *
8p23.1 / 12,450,000 / 12,510,000 / -0.5272 / Del / *
8p23.1 / 12,510,000 / 12,570,000 / -0.3238 / Del / *
8q24.23 / 137,790,000 / 137,910,000 / -0.4279 / Del
9p11.2 / 44,190,000 / 45,570,000 / 0.4694 / Dup / *
9p11.2 / 44,670,000 / 44,850,000 / -0.31553 / Del
9p11.2 / 44,850,000 / 45,570,000 / -0.41062 / Del / *
9p12 / 41,910,000 / 43,530,000 / 0.36 / Dup / *
9p12 / 43,230,000 / 43,590,000 / -0.4918 / Del
9p22.2 / 16,890,000 / 16,950,000 / 0.3918 / Dup
9p23 / 11,310,000 / 12,270,000 / -0.3461 / Del
9p23 / 11,490,000 / 11,610,000 / -0.45879 / Del
9q13 / 66,630,000 / 66,750,000 / 0.723 / Dup / *
9q13 / 66,810,000 / 67,710,000 / -0.5437 / Del / *
9q13 / 67,650,000 / 67,830,000 / 0.41739 / Dup / *
9q13 / 67,710,000 / 68,310,000 / 0.404 / Dup / *
9q22.31 / 96,090,000 / 96,210,000 / 0.56098 / Dup / *
9q34.3 / 137,970,000 / 139,290,000 / 0.3999 / Dup / *
10p11.1 / 38,790,000 / 38,910,000 / -0.52568 / Del
10p11.1 / 38,790,000 / 38,910,000 / -0.48567 / Del
10p11.1 / 38,790,000 / 39,210,000 / -0.30113 / Del
10p11.1 / 39,090,000 / 39,210,000 / -0.30412 / Del
10p11.21-p11.1 / 38,790,000 / 38,850,000 / 0.3312 / Dup / *
10q11.1 / 41,970,000 / 42,150,000 / -0.33092 / Del / *
10q11.21 / 44,550,000 / 44,670,000 / 0.3342 / Dup / *
10q11.21-q11.22 / 45,570,000 / 46,590,000 / -0.5643 / Del / *
10q11.22 / 46,350,000 / 46,590,000 / -0.39768 / Del / *
10q11.23 / 51,450,000 / 51,630,000 / 0.39664 / Dup / *
10q11.23 / 52,110,000 / 52,170,000 / 0.33907 / Dup / *
11p15.4 / 3,390,000 / 3,450,000 / 0.35533 / Dup / *
11q11 / 55,110,000 / 55,170,000 / -0.8908 / Del
11q13.2 / 67,290,000 / 67,410,000 / -0.37622 / Del / *
11q14.1 / 85,350,000 / 85,470,000 / -0.32888 / Del / *
12p11.21 / 31,230,000 / 31,290,000 / 0.42232 / Dup / *
12p13.31 / 7,890,000 / 8,010,000 / 0.4412 / Dup / *
12p13.31 / 8,190,000 / 8,430,000 / 0.31741 / Dup / *
12p13.31 / 9,510,000 / 9,810,000 / -0.37269 / Del / *
12q11 / 36,210,000 / 36,270,000 / -0.64861 / Del / *
12q11 / 36,330,000 / 36,690,000 / 0.32222 / Dup / *
12q13.11 / 46,230,000 / 46,290,000 / 0.61599 / Dup / *
13q12.11 / 19,710,000 / 19,950,000 / -0.50219 / Del / * / *
13q14.3 / 51,990,000 / 52,050,000 / 0.39178 / Dup / *
13q31.1 / 83,010,000 / 83,070,000 / -0.4615 / Del
14q11.1-q11.2 / 18,270,000 / 19,470,000 / 0.3039 / Dup
14q11.1-q11.2 / 18,330,000 / 19,470,000 / -0.41372 / Del
14q11.1-q11.2 / 18,450,000 / 19,470,000 / -0.3067 / Del
14q11.1-q11.2 / 18,510,000 / 19,470,000 / -0.39 / Del
14q11.1-q11.2 / 18,870,000 / 19,350,000 / 0.36017 / Dup
14q11.1-q11.2 / 18,870,000 / 19,470,000 / -0.52342 / Del
14q11.1-q11.2 / 18,870,000 / 19,470,000 / -0.46299 / Del
14q11.1-q11.2 / 18,870,000 / 19,470,000 / -0.37227 / Del
14q11.1-q11.2 / 18,870,000 / 19,470,000 / -0.3256 / Del
14q11.1-q11.2 / 19,050,000 / 19,170,000 / 0.92148 / Dup
14q11.1-q11.2 / 19,050,000 / 19,290,000 / 0.5801 / Dup
14q11.2 / 19,290,000 / 19,470,000 / -0.56002 / Del / *
14q11.2 / 19,290,000 / 19,470,000 / -0.39873 / Del / *
14q11.2 / 19,290,000 / 19,470,000 / -0.54538 / Del / *
14q11.2 / 19,290,000 / 19,470,000 / -0.5823 / Del / *
14q11.2 / 19,350,000 / 19,470,000 / -0.445 / Del / *
14q11.2 / 19,350,000 / 19,470,000 / -0.4669 / Del / *
14q23.3 / 65,790,000 / 65,910,000 / -0.37287 / Del / * / *
14q32.33 / 105,270,000 / 105,810,000 / -0.45347 / Del / *
14q32.33 / 105,150,000 / 105,270,000 / 0.4014 / Dup / *
14q32.33 / 105,510,000 / 105,630,000 / -0.3226 / Del / *
14q32.33 / 105,510,000 / 105,630,000 / -0.4452 / Del / *
14q32.33 / 105,690,000 / 105,810,000 / 0.3721 / Dup / *
15q11.1 / 19,110,000 / 20,070,000 / 0.3167 / Dup / *
15q11.1 / 19,890,000 / 20,010,000 / 0.4213 / Dup / *
15q11.2 / 20,970,000 / 21,090,000 / 0.4029 / Dup / *
15q11.2 / 22,110,000 / 22,350,000 / 0.3679 / Dup / *
15q12 / 26,250,000 / 26,730,000 / 0.494 / Dup / *
15q12 / 26,730,000 / 26,910,000 / 0.46836 / Dup / * / *
15q13.2 / 30,330,000 / 30,450,000 / -0.3663 / Del / *
15q25.2 / 82,710,000 / 82,770,000 / 0.6122 / Dup / *
16p11.2 / 31,890,000 / 33,390,000 / 0.4104 / Dup / *
16p11.2 / 32,070,000 / 32,190,000 / 0.7112 / Dup / *
16p11.2 / 32,070,000 / 32,190,000 / 0.43912 / Dup / *
16p11.2 / 32,070,000 / 32,190,000 / 0.66393 / Dup / *
16p11.2 / 32,070,000 / 32,370,000 / 0.45 / Dup / *
16p11.2 / 32,070,000 / 32,550,000 / 0.30864 / Dup / *
16p11.2 / 32,070,000 / 33,510,000 / 0.4991 / Dup / *
16p11.2 / 32,550,000 / 33,150,000 / -0.3475 / Del / *
16p11.2 / 33,270,000 / 33,390,000 / -0.3468 / Del / *
16p11.2 / 33,330,000 / 33,510,000 / -0.46742 / Del
16p12.2 / 22,350,000 / 22,590,000 / -0.3103 / Del / *
16p12.3 / 18,090,000 / 18,150,000 / -0.39706 / Del / *
16p13.11 / 16,230,000 / 16,650,000 / 0.3426 / Dup / *
16q23.1 / 75,090,000 / 75,210,000 / -0.4889 / Del / *
17p11.2 / 18,270,000 / 18,330,000 / 0.55294 / Dup / *
17p11.2 / 18,270,000 / 18,390,000 / 0.50251 / Dup / *
17p11.2 / 20,190,000 / 20,310,000 / 0.51452 / Dup / *
17p11.2 / 21,450,000 / 21,510,000 / -0.41369 / Del / *
17q12 / 31,470,000 / 31,530,000 / 0.8056 / Dup / *
17q21.31 / 41,490,000 / 41,910,000 / -0.30823 / Del / *
17q21.31 / 41,550,000 / 41,610,000 / -0.4328 / Del / *
17q21.31 / 41,550,000 / 41,730,000 / -0.42409 / Del / *
17q21.31 / 41,550,000 / 41,730,000 / -0.39886 / Del / *
17q21.31 / 41,550,000 / 41,730,000 / -0.3469 / Del / *
17q21.31 / 41,550,000 / 41,910,000 / -0.33907 / Del / *
17q21.31 / 41,730,000 / 41,910,000 / 0.6332 / Dup / * / *
17q25.3 / 77,430,000 / 77,490,000 / -0.56729 / Del / *
18p11.21 / 14,490,000 / 14,550,000 / -0.46767 / Del / *
18p11.21 / 14,490,000 / 14,610,000 / -0.33055 / Del / *
18p11.21 / 14,490,000 / 14,670,000 / -0.4282 / Del / *
18p11.21 / 14,610,000 / 14,670,000 / -0.35943 / Del / *
18p11.32 / 30,000 / 150,000 / -0.31336 / Del / *
19q13.33 / 48,210,000 / 48,450,000 / -0.358 / Del / *
20q11.1 / 28,230,000 / 28,290,000 / -0.4866 / Del / *
20q11.2 / 34,950,000 / 35,010,000 / 0.5037 / Dup / *
21p11.2 / 9,750,000 / 9,870,000 / -0.30318 / Del / * / *
21q11.1 / 13,530,000 / 13,650,000 / -0.33313 / Del / *
21q11.2 / 13,830,000 / 13,890,000 / -0.5356 / Del / *
21q21.3 / 28,170,000 / 28,230,000 / -0.3215 / Del / * / *
21q22.3 / 46,890,000 / 46,922,620 / -0.5676 / Del / *
22q11.21 / 18,090,000 / 18,750,000 / 0.4232 / Dup / *
22q11.21 / 18,090,000 / 18,750,000 / 0.3174 / Dup / *
22q11.21 / 19,890,000 / 19,950,000 / -0.392 / Del / *
22q11.21 / 19,890,000 / 19,950,000 / -0.392 / Del / *
22q11.21 / 19,890,000 / 19,950,000 / 0.65094 / Dup / *

11