NG-LE33774R1 Shen Supplemetal Information · 3 Bio-X Institutes, Key Laboratory for the Genetics of...

1 / 21

SUPPLEMENTAL INFORMATION

A genome-wide association study identifies two risk loci for congenital heart malformations in Han Chinese populations Zhibin Hu 1, 2, 14, Yongyong Shi 3, 14, Xuming Mo 4, 14, Jing Xu5, 14, Bijun Zhao 6, 14, Yuan Lin 1, 2,14, Shiwei Yang 7, Zhengfeng Xu8, Juncheng Dai 2, Shandong Pan 2, Min Da 4, Xiaowei Wang 5, Bo Qian4, Yang Wen 1, 2, Juan Wen 1, 2, Jinliang Xing 9, Xuejiang Guo1,10, Yankai Xia 1, 11,12, Hongxia Ma 2, Guangfu Jin 2, Shiqiang Yu 6, Jiayin Liu 13, Zuomin Zhou 1,10, Xinru Wang 1, 11,12, Yijiang Chen 5, Jiahao Sha1,10, Hongbing Shen1,

2,12

1 State Key Laboratory of Reproductive Medicine, School of Public Health, Nanjing Medical University, Nanjing, China; 2 Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China; 3 Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai genomePilot Institutes for Genomics and Human Health, Shanghai Jiao Tong University, Shanghai, China; 4 Department of Cardiothoracic Surgery, Nanjing Children's Hospital, Nanjing Medical University, Nanjing, China; 5 Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China; 6 Department of Cardiovascular Surgery, Xijing hospital, The Fourth Military Medical University, Xi’an, China; 7 Department of Cardiology, Nanjing Children's Hospital, Nanjing Medical University, Nanjing, China; 8 Center of Prenatal Diagnosis, The Affiliated Nanjing Maternity and Child Health Hospital of Nanjing Medical University, Nanjing, China; 9 State Key Laboratory of Cancer Biology, Department of Cell Biology, Cell Engineering Research Center, The Fourth Military Medical University, Xi’an, China; 10 Department of Histology and Embryology, Nanjing Medical University, Nanjing, China; 11 Department of Toxicology, School of Public Health, Nanjing Medical University, Nanjing, China; 12Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China; 13 Center of Clinical Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Nanjing, China; 14 These authors contributed equally to this work. Correspondence should be addressed to H.S. ([email protected]), Z.Z. ([email protected]), Y.C. ([email protected]) and Z.H. ([email protected])

Nature Genetics: doi: 10.1038/ng.2636

2 / 21

Supplementary Fig. 1: Plot of the first two components derived from a principal component analysis implemented in the software package EIGENSTRAT. (A) Our samples & HapMap Phase-II data; (B) Our samples. (A) (B)


3 / 21

Supplementary Fig. 2: Expressions of TBX15, MAML3 and SPAG17 in cardiac tissues, liver tumor and adjacent tissues and lung tumor and adjacent tissues


4 / 21

Supplementary Fig. 3: Functinal annotation at 1p12 in a linkage disequilibrium (LD) region containing the identified SNP rs2474937 using UCSC genome browser. LD plot was generated using haploview in a window of 800 kb aroud the rs2474937 based on HapMap III CHB population (release 2; accessed on Nov 08, 2012).


5 / 21

Supplementary Fig. 4: Functinal annotation at 4q31.1 in a linkage disequilibrium (LD) region containing the identified SNP rs1531070 using UCSC genome browser. LD plot was generated using haploview in a window of 800 kb aroud the rs1531070 based on HapMap III CHB population (release 2; accessed on Nov 08, 2012).


6 / 21

Supplementary Table 1: Characteristics of CHD cases and controls among GWAS and validation stages

Variables GWAS Validation I Validation II Validation IIIa a Validation IIIb a

Case (N=945)

Control (N=1,246)

Case (N=1,578)

Control (N=2,301)

Case (N=582)

Control (N=1,565)

Case (N=864)

Control (N=2,301) Case (N=256) Control

(N=1,565) Age (mean±SD) 1.30±1.72 41.75±16.34 2.15±2.26 47.26±21.21 9.33±14.41 25.49±26.39 1.11±1.28 47.26±21.21 16.35± 18.56 25.49±26.39 Sex

Male 471 822 762 1503 270 1085 383 1503 151 1085 Female 474 424 816 798 312 480 481 798 105 480

Phenotype ASD 334 482 157 0 0 VSD 534 959 390 0 0

ASD/VSD 77 137 35 0 0 Other 0 0 0 864 256

Call rate (%) rs2474937 99.58 99.92 99.81 99.83 99.66 99.42 99.77 99.83 99.22 99.42 rs1531070 99.37 99.76 99.84 100 100 99.36 100 100 99.61 99.36

a Validation IIIa was for CHM cases with phenotypes different from isolated ASD, isolated VSD or ASD/VSD recruited from the First Affiliated Hospital of Nanjing Medical University and controls shared with Validation I; Validation IIIb was for CHM cases with phenotypes different from isolated ASD, isolated VSD or ASD/VSD recruited from the Xijing hospital and controls shared with Validation II.


7 / 21

Supplementary Table 2: Associations of 13 SNPs with CHM at P ≤ 10-5 in the GWA scan stage

Chr. SNP Position Associated Gene Major/MinorAllele

MAF a ORadd (95% CI)b Padd

b

Case Control1p12 rs2474942 118889621 SPAG17-TBX15 C/T 0.12 0.08 1.61(1.31-1.99) 8.27×10-6 1p12 rs2474937 118902978 SPAG17-TBX15 T/C 0.12 0.07 1.63(1.32-2.01) 6.07×10-6

2p22.2 rs17019472 36927283 CRIM1-STRN T/C 0.42 0.49 0.74(0.65-0.84) 2.12×10-6 2p22.2 rs10182004 36934887 CRIM1-STRN G/A 0.52 0.46 1.33(1.17-1.50) 6.68×10-6 4q31.1 rs1531070 140795327 MAML3 G/A 0.16 0.11 1.63(1.36-1.96) 1.68×10-7 4q31.1 rs2320536 140801676 MAML3 C/T 0.17 0.12 1.59(1.34-1.90) 1.69×10-7 6p21.31 rs9461938 33954192 GRM4 T/C 0.10 0.06 1.77(1.40-2.23) 1.31×10-6 9q33.3 rs72759270 126972424 NEK6 C/T 0.15 0.20 0.69(0.59-0.81) 8.15×10-6

13q14.11 rs9533839 44961158 SERP2-TSC22D1 T/C 0.39 0.30 1.49(1.31-1.70) 9.66×10-10 13q14.11 rs12868519 44972629 SERP2-TSC22D1 C/T 0.38 0.30 1.48(1.30-1.69) 2.15×10-9 13q14.11 rs1886441 44980528 SERP2-TSC22D1 T/C 0.30 0.24 1.36(1.19-1.56) 7.66×10-6 13q14.11 rs1325324 44981909 SERP2-TSC22D1 T/C 0.36 0.28 1.48(1.30-1.69) 3.32×10-9 13q14.11 rs717319 44986675 SERP2-TSC22D1 T/G 0.30 0.24 1.37(1.19-1.56) 7.37×10-6

a Minor allele frequency; b OR (95% CI) and P value derived from logistic regression analysis in the additive model with adjustment for the top eigenvector.


8 / 21

Supplementary Table 3: Associations of 8 SNPs with CHM in GWAS and validations

SNPs Chr. Study b Cases c Controls c MAF d ORadd

(95% CI)e Padd e Padd

f P g

Cases Controlsrs2474937 1p12 GWAS 14/191/736 2/182/1061 0.12 0.07 1.63(1.32-2.01) 6.07×10-6 9.46×10-6 2.54×10-6

T/C a Validation I 25/287/1263 23/323/1951 0.11 0.08 1.35(1.16-1.57) 9.97×10-5 4.00×10-4 6.23×10-5

Validation II 8/104/468 10/239/1307 0.10 0.08 1.27(1.01-1.59) 3.99×10-2 2.46×10-2 3.87×10-2

Validation IIIa 11/161/690 23/323/1951 0.11 0.08 1.34(1.12-1.61) 1.56×10-3 4.95×10-3 1.20×10-3

Validation IIIb 0/51/203 10/239/1307 0.10 0.08 1.24(0.90-1.70) 1.95×10-1 1.83×10-1 2.00×10-1

Validation III 1.32(1.12-1.54) 1.00×10-3 2.00×10-3

rs17019472 2p22.2 GWAS 158/482/299 303/619/318 0.42 0.49 0.74(0.65-0.84) 2.12×10-6 8.25×10-6 6.04×10-6

T/C a Validation I 307/778/486 460/1155/675 0.44 0.45 0.96(0.88-1.05) 3.81×10-1 4.24×10-1 3.84×10-1

rs10182004 2p22.2 GWAS Scan 244/501/200 263/613/369 0.48 0.46 1.33(1.17-1.50) 6.68×10-6 2.79×10-5 1.57×10-5

A/G a Validation I 393/783/395 588/1171/538 0.50 0.49 1.05(0.96-1.15) 3.17×10-1 2.69×10-1 3.20×10-1

rs1531070 4q31.1 GWAS 22/252/665 9/243/991 0.16 0.11 1.63(1.36-1.96) 1.68×10-7 5.07×10-7 2.49×10-7

G/A a Validation I 35/357/1184 30/436/1835 0.14 0.11 1.29(1.13-1.48) 2.70×10-4 5.80×10-4 2.17×10-4

Validation II 6/151/425 27/276/1252 0.14 0.11 1.36(1.12-1.67) 2.32×10-3 2.23×10-3 2.00×10-3

Validation IIIa 21/176/667 30/436/1835 0.13 0.11 1.19(1.01-1.40) 4.31×10-2 5.08×10-2 3.95×10-2

Validation IIIb 2/61/192 27/276/1252 0.13 0.11 1.22(0.92-1.61) 1.61×10-1 1.52×10-1 1.52×10-1

Validation III 1.20(1.04-1.38) 1.20×10-2 1.40×10-2

rs9461938 6p21.31 GWAS 9/163/764 6/128/1102 0.10 0.06 1.77(1.40-2.23) 1.31×10-6 1.71×10-6 5.81×10-7

T/C a Validation I 10/206/1349 14/338/1944 0.07 0.08 0.90(0.76-1.07) 2.25×10-1 1.25×10-1 2.24×10-1

rs72759270 9q33.3 GWAS 23/244/678 51/404/790 0.15 0.20 0.69(0.59-0.81) 8.15×10-6 1.44×10-5 2.33×10-5

C/T a Validation I 66/445/1049 77/668/1532 0.18 0.18 1.03(0.92-1.16) 6.26×10-1 8.83×10-1 6.21×10-1

rs9533839 13q14.11 GWAS 140/452/353 117/510/619 0.39 0.30 1.49(1.31-1.70) 9.66×10-10 6.45×10-10 7.46×10-10

T/C a Validation I 221/726/629 288/1045/967 0.37 0.35 1.08(0.98-1.19) 1.03×10-1 1.41×10-1 1.02×10-1

rs1325324 13q14.11 GWAS 122/439/384 104/480/662 0.36 0.28 1.48(1.30-1.69) 3.32×10-9 3.25×10-9 1.63×10-9


9 / 21

a Major/minor alleles; b Validation IIIa was for CHM cases with phenotypes different from isolated ASD, isolated VSD or ASD/VSD recruited from the First Affiliated Hospital of Nanjing Medical University and controls shared with Validation I; Validation IIIb was for CHM cases with phenotypes different from isolated ASD, isolated VSD or ASD/VSD recruited from the Xijing hospital and controls shared with Validation II; ORs, 95%CIs and P values in Validation III are derived from meta-analysis of Validation IIIa and Validation IIIb; c Minor homozygote/Heterozygote/Major homozygote; d Minor allele frequency; e OR (95% CI) and P value derived from logistic regression analysis in additive model with adjustment for the top eigenvector; f OR (95% CI) and P value derived from logistic regression analysis in additive model with adjustment for sex, age and top eigenvector; g P value derived from chi-square analysis.

T/C Validation I 185/693/686 255/1010/1033 0.34 0.33 1.04(0.95-1.15) 4.07×10-1 4.55×10-1 4.05×10-1


10 / 21

Supplementary Table 4: SNPs reached the validation criteria but in strong linkage disequilibrium (r2 ≥ 0.8) with selected SNPs Chr. Position SNP Position SNP r2

1 118889621 rs2474942 118902978 rs2474937 1.004 140795327 rs1531070 140801676 rs2320536 0.8313 44961158 rs9533839 44972629 rs12868519 0.9513 44980528 rs1886441 44981909 rs1325324 0.8013 44980528 rs1886441 44986675 rs717319 0.9913 44981909 rs1325324 44986675 rs717319 0.80


11 / 21

Supplementary Table 5: Stratified analysis by major subtypes of CHM for the two identified SNPs

SNP Subtypes Cases a Controls a MAF b OR (95% CI)c P c Padjust d P e Cases Controls 1p12: rs2474937 ASD 11/176/783 35/744/4319 0.10 0.08 1.30(1.11-1.53) 1.54×10-3 6.16×10-3

0.546 VSD 33/361/1483 35/744/4319 0.11 0.08 1.46(1.29-1.65) 1.86×10-9 7.44×10-9

ASD/VSD 3/45/201 35/744/4319 0.10 0.08 1.31(0.97-1.76) 7.56×10-2 3.02×10-1

PDA 3/51/181 35/744/4319 0.12 0.08 1.58(1.19-2.11) 1.60×10-3 6.40×10-3

4q31.1: rs1531070 ASD 28/247/694 66/955/4078 0.16 0.11 1.54(1.34-1.77) 6.08×10-10 2.43×10-9

0.428 VSD 29/455/1395 66/955/4078 0.14 0.11 1.33(1.19-1.49) 7.17×10-7 2.87×10-6

ASD/VSD 6/58/185 66/955/4078 0.14 0.11 1.37(1.06-1.77) 1.68×10-2 6.72×10-2

PDA 7/51/179 66/955/4078 0.14 0.11 1.33(1.02-1.73) 3.77×10-2 1.51×10-1 a Minor homozygote/Heterozygote/Major homozygote; b Minor allele frequency (MAF); c ORs, 95% CIs and P values were derived from additive model; d P adjust were from Bonferroni correction for multiple testing. e P for heterogeneity test between groups. ASD: septal defect; VSD: ventricular septal defect; ASD/VSD: atrial septal defect combined ventricular septal defect; PDA: patent ductus arteriosus.


12 / 21

Supplementary Table 6: Summary results of SNPs at 1p12 and 4q31.1 that were associated with CHM at P < 1.0 × 10-5

Chr. SNP Major Allele

Minor Allele

MAF a ORadd

b Paddb Identification LD c

Cases Controls1 rs2474945 A C 0.12 0.08 1.65 4.01×10-6 Imputed 0.99 1 rs2474943 T C 0.12 0.08 1.63 3.18×10-6 Imputed 0.99 1 rs2474942 C T 0.12 0.07 1.61 8.27×10-6 Genotyped 0.99 1 rs9428110 G A 0.12 0.07 1.64 3.18×10-6 Imputed 1.00 1 rs10923553 G T 0.12 0.07 1.64 3.18×10-6 Imputed 1.00 1 rs9428111 T C 0.12 0.07 1.64 3.18×10-6 Imputed 1.00 1 rs2474941 T C 0.12 0.07 1.64 3.18×10-6 Imputed 1.00 1 rs9428113 C T 0.12 0.07 1.64 3.18×10-6 Imputed 1.00 1 rs9428114 C A 0.12 0.07 1.64 3.18×10-6 Imputed 1.00 1 rs2493798 G A 0.12 0.07 1.64 3.18×10-6 Imputed 1.00 1 rs2493799 G A 0.12 0.07 1.64 3.18×10-6 Imputed 1.00 1 rs2493800 G C 0.12 0.07 1.64 3.18×10-6 Imputed 1.00 1 rs2490199 C T 0.12 0.07 1.64 3.18×10-6 Imputed 1.00 1 rs2474939 G A 0.12 0.07 1.64 3.18×10-6 Imputed 1.00 1 rs2474937 T C 0.12 0.07 1.63 6.07×10-6 Genotyped -- 1 rs2493807 T C 0.12 0.07 1.64 3.18×10-6 Imputed 1.00 1 rs2493809 C G 0.12 0.07 1.64 3.18×10-6 Imputed 1.00 1 rs2493810 T C 0.12 0.07 1.64 3.18×10-6 Imputed 1.00 1 rs77887247 T A 0.06 0.03 2.07 4.98×10-6 Imputed 0.40 1 rs2224405 G A 0.12 0.07 1.64 3.18×10-6 Imputed 1.00 1 rs2493814 A G 0.12 0.07 1.64 3.18×10-6 Imputed 1.00 1 rs2224404 T G 0.12 0.07 1.64 3.18×10-6 Imputed 1.00 1 rs2493816 A T 0.12 0.07 1.64 3.18×10-6 Imputed 1.00


13 / 21

1 rs2474936 C T 0.12 0.07 1.64 3.18×10-6 Imputed 1.00 1 rs2474935 T C 0.12 0.07 1.64 3.18×10-6 Imputed 1.00 1 rs7515407 G A 0.12 0.07 1.64 3.18×10-6 Imputed 1.00 1 rs2493819 A G 0.12 0.07 1.64 3.18×10-6 Imputed 1.00 4 rs11721536 T C 0.15 0.10 1.58 1.39×10-6 Imputed 0.95 4 rs7683979 G T 0.17 0.12 1.58 2.56×10-7 Imputed 0.89 4 rs4863698 G C 0.17 0.12 1.58 2.56×10-7 Imputed 0.89 4 rs1840540 A G 0.17 0.12 1.58 2.56×10-7 Imputed 0.89 4 rs1531070 G A 0.16 0.11 1.63 1.68×10-7 Genotyped -- 4 rs6834463 G A 0.17 0.12 1.57 2.81×10-7 Imputed 0.87 4 rs11100326 A G 0.17 0.12 1.57 2.81×10-7 Imputed 0.87 4 rs1455480 G C 0.18 0.12 1.56 4.06×10-7 Imputed 0.86 4 rs4863518 C T 0.17 0.11 1.62 1.05×10-7 Imputed 0.95 4 rs4863519 C T 0.18 0.12 1.56 4.06×10-7 Imputed 0.86 4 rs4863699 T C 0.18 0.12 1.56 4.06×10-7 Imputed 0.86 4 rs17290188 G A 0.16 0.10 1.62 1.57×10-7 Imputed 0.99 4 rs17368602 C T 0.18 0.12 1.56 4.06×10-7 Imputed 0.86 4 rs795979 C T 0.45 0.39 1.37 7.92×10-6 Imputed 0.28 4 rs795980 G A 0.45 0.39 1.37 9.25×10-6 Imputed 0.28 4 rs2320536 C T 0.17 0.12 1.59 1.69×10-7 Genotyped 0.86 4 rs1473056 G C 0.15 0.10 1.56 1.36×10-6 Imputed 0.80 4 rs12508981 G A 0.17 0.12 1.48 6.33×10-6 Imputed 0.68 4 rs13121182 A G 0.15 0.10 1.56 1.49×10-6 Imputed 0.77 4 rs11729794 C T 0.15 0.11 1.54 2.23×10-6 Imputed 0.74

a Minor allele frequency (MAF); b ORs, 95% CIs and P values were derived from additive model adjusted by the top eigenvector; c Linkage disequilibrium (LD) value (r2) of the lead SNP (rs2474937 or rs1531070) with other SNPs for each locus in Chinese population.


14 / 21

Supplementary Table 7: Summary of SNPs that were associated with CHM in previous studies. Chr. Gene SNPs Associated Type Case Control Country Year Ref. 1p36.22 MTHFR rs1801131(A1298C) CHD 230 251 Netherlands 2008 1 1p36.22 MTHFR rs2274976(1793G>A) CHD 1033 1067 China 2010 2 1p36.32 MTHFR rs1801133(C677T) CHD 114 228 German 2001 3 1p36.32 MTHFR rs1801133(C677T) CHD 26 116 America 2001 4 1p36.32 MTHFR rs1801133(C677T) Conotruncal heart defects 97 118 China 2005 5 1p36.32 HOXC5 rs2071450(A1701G) Simple CHD 108 200 China 2005 6 1p36.32 MTHFR rs1801133(C677T) ASD+PDA 56 104 China 2006 7 1p36.32 MTHFR rs1801133(C677T) Tetralogy of Fallot 38 251 Portugal 2009 8 1p36.32 MTHFR rs1801133(C677T) CHD 104 208 China 2009 9 5p15.31 MTRR rs326119 CHD 2340 2270 China 2012 10 5q11.1 ISL1 rs1017 Non-syndromic CHD 100 576 America, Canada and Netherlands 2010 11 5q35.1 NKX2.5 rs104893905(C646T) CHD 150 70 South India 2010 12 5q35.1 NKX2.5 rs118026695 VSD 213 194 China 2012 13 6p12.3 TFAP2B rs2272903 (1-34G>A) PDA 100 100 China 2011 14 6p21.1 VEGF rs2010963 (G405C) CHD 102 112 Hungary 2006 15 6p21.1 VEGF rs2010963 (G405C) VSD 222 352 China 2007 16 12q13.13 miR-196a2(HOX) rs11614913 Non-syndromic CHD 1,324 1,783 China 2009 17 12q24.21 TBX5 rs11067075 Ventricular septal defect 192 192 China 2009 18 21q22.3 RFC1 rs1051266(A80G) CHD 163 239 America 2003 19 21q22.3 CBC rs121964962 (G919A) CHD 127 129 China 2006 20


15 / 21

Supplementary Table 8: Summary results of SNPs that have been reported previously in the GWAS stage.

Chr. SNPs Major/Minor allele

Reference allele OR(95% CI)a RAF b ORadd

(95% CI)c P add c Identification

Cases Controls1p36.22 rs2274976 G/A G 0.67(0.54-0.84) 0.07 0.08 0.95(0.75-1.19) 6.40×10-1 Genotyped 1p36.22 rs1801131 A/C A 0.60(0.40-0.90) 0.16 0.17 0.98(0.83-1.15) 7.87×10-1 Genotyped 1p36.32 rs1801133 G/A G 2.20(1.20-4.30) 0.45 0.47 0.88(0.77-0.99) 3.16×10-2 Genotyped 1p36.32 rs2071450 T/C T 1.46(1.03-2.07) 0.34 0.37 0.87(0.76-0.98) 2.50×10-2 Imputed 5p15.31 rs326119 A/C A 1.36(1.25-1.48) 0.43 0.41 1.06(0.94-1.20) 3.43×10-1 Imputed 5q11.1 rs1017 A/T A 1.27(1.05-1.54) 0.13 0.13 1.01(0.85-1.21) 8.99×10-1 Imputed 6p21.1 rs2010963 G/C G 0.76(0.59-0.97) 0.41 0.41 0.97(0.86-1.10) 6.70×10-1 Imputed 6p12.3 rs2272903 G/A G 2.06(1.24-3.41) 0.20 0.20 1.02(0.87-1.19) 8.17×10-1 Genotyped 21q22.3 rs1051266 G/A A 2.30(1.30-3.90) 0.48 0.49 0.97(0.85-1.09) 5.78×10-1 Genotyped

a Association results in reported studies: study with the largest sample size was shown if multiple studies reported the same SNP; b Reference allele frequency (RAF) for cases and controls in GWAS stage; c OR, 95% CI and P value were derived from additive model.


16 / 21

Supplementary Table 9: CHM types CHM types GWAS Validation I Validation II Validation IIIa Validation IIIb Total % Isolated ventricular septal defect 534 959 390 0 0 1883 44.57 Trilogy of Fallot 0 0 0 55 11 66 1.56 Tetralogy of Fallot 0 0 0 186 72 258 6.11 Tetralogy of Fallot combined Patent ductus arteriosus 0 0 0 0 3 3 0.07 Pentalogy of Fallot 0 0 0 25 3 28 0.66 Isolated ostium secundum atrial septal defect 334 482 157 0 0 973 23.03 Patent ductus arteriosus 0 0 0 224 13 237 5.61 Patent ductus arteriosus combined Coarctation of Aorta 0 0 0 0 1 1 0.02 Double outlet right ventricular combined Pulmonary stenosis and ventricular septal defect 0 0 0 0 2 2 0.05

Double-chambered right ventricle combined ventricular septal defect 0 0 0 16 2 18 0.43

Double-chambered right ventricle combined ventricular septal defect and Ostium secundum atrial septal defect 0 0 0 3 0 3 0.07

Double outlet right ventricle combined ventricular septal defect 0 0 0 20 0 20 0.47 Double outlet right ventricle combined ventricular septal defect and Ostium secundum atrial septal defect 0 0 0 3 0 3 0.07

Pulmonary stenosis 0 0 0 46 20 66 1.56 Ventricular septal defect combined Ostium secundum atrial septal defect 77 137 35 0 0 249 5.89

Ventricular septal defect combined Patent ductus arteriosus 0 0 0 31 0 31 0.73 Ventricular septal defect combined Pulmonary stenosis 0 0 0 43 0 43 1.02 Ventricular septal defect combined Aortic stenosis 0 0 0 11 0 11 0.26 Patent ductus arteriosus combined Ostium secundum atrial septal defect 0 0 0 16 0 16 0.38

Patent ductus arteriosus combined Ostium secundum atrial septal defect and ventricular septal defect 0 0 0 16 0 16 0.38


17 / 21

Patent ductus arteriosus combined Pulmonary stenosis 0 0 0 2 0 2 0.05 Patent ductus arteriosus combined Aortic stenosis 0 0 0 6 1 7 0.17 Ventricular septal defect combined Ostium secundum atrial septal defect and Pulmonary stenosis 0 0 0 8 0 8 0.19

Ostium secundum atrial septal defect combined Pulmonary stenosis and Patent ductus arteriosus 0 0 0 4 0 4 0.09

Patent ductus arteriosus combined ventricular septal defect combined Pulmonary stenosis 0 0 0 2 0 2 0.05

Coronary Artery Malformation 0 0 0 3 0 3 0.07 Anonalous pulmonary venous connection 0 0 0 0 5 5 0.12 Aortic Aneurysm 0 0 0 0 1 1 0.02 Aortic Insufficlency 0 0 0 0 17 17 0.40 Aortic stenosis 0 0 0 11 4 15 0.36 Aortic stenosis combined Coarctation of Aorta 0 0 0 0 1 1 0.02 Aortic stenosis combined Ostium secundum atrial septal defect 0 0 0 1 0 1 0.02 Aortic stenosis combined Ostium secundum atrial septal defect and ventricular septal defect 0 0 0 3 0 3 0.07

Mitral Insufficiency 0 0 0 0 12 12 0.28 Mitral Stenosis 0 0 0 0 3 3 0.07 Tricuspid Insufficiency 0 0 0 0 1 1 0.02 Rupture of Valsalva Sinus Aneurysm 0 0 0 15 14 29 0.69 Coarctation of Aorta 0 0 0 0 4 4 0.09 Ebstein Anomaly 0 0 0 30 23 53 1.25 Ebstein Anomaly combined Ostium secundum atrial septal defect 0 0 0 9 0 9 0.21 Pulmonary Atresia combined Ostium secundum atrial septal defect and Patent ductus arteriosus 0 0 0 29 0 29 0.69

Persistent truncus arteriosus combined ventricular septal defect 0 0 0 5 0 5 0.12 Persistent truncus arteriosus combined ventricular septal defect and Ostium secundum atrial septal defect 0 0 0 3 0 3 0.07


18 / 21

Transposition of the Great Arteries combined Ostium secundum atrial septal defect 0 0 0 4 2 6 0.14

Transposition of the Great Arteries combined ventricular septal defect 0 0 0 8 0 8 0.19

Transposition of the Great Arteries combined ventricular septal defect and Ostium secundum atrial septal defect 0 0 0 4 0 4 0.09

Bicuspid Aortic Valve 0 0 0 19 37 56 1.33 Coronary Artery Fistula 0 0 0 1 0 1 0.02 Main Pulmonary Artery Fistula 0 0 0 0 1 1 0.02 Cor Triatriatum 0 0 0 1 1 2 0.05 Single Atrium 0 0 0 0 1 1 0.02 Cor Triatriatum combined Total anomalous pulmonary venous connection 0 0 0 0 1 1 0.02

Congenital Pulmonary Vascular Ring Condole Belt 0 0 0 1 0 1 0.02 Total 945 1578 582 864 256 4225 100.00


19 / 21

Reference:

1. Van Driel, L.M. et al. Two MTHFR polymorphisms, maternal B-vitamin intake, and CHDs. Birth Defects Res. A. Clin. Mol. Teratol. 82,

474-481 (2008).

2. Xu, J. et al. MTHFR c.1793G>A polymorphism is associated with congenital cardiac disease in a Chinese population. Cardiol. Young. 20,

318-326 (2010).

3. Junker, R. et al. Infant methylenetetrahydrofolate reductase 677TT genotype is a risk factor for congenital heart disease. Cardiovasc. Res. 51,

251-254 (2001).

4. Wenstrom, K.D., Johanning, G.L., Johnston, K.E. & DuBard, M. Association of the C677T methylenetetrahydrofolate reductase mutation and

elevated homocysteine levels with congenital cardiac malformations. Am. J. Obstet. Gynecol. 184, 806-812; discussion 812-817 (2001).

5．Liu, F., Bai, P., Chen, S.B., Qiu, W.J., Qiu, X.P. & Zhang, Y.F. Association between 5,10-Methylenetetrahydrofolate Reductase C677T

Polymorphisms and conotruncal heart defects in Chinese children. Chinese J. Contemp. Pediatr. 7, 99–102 (2005).

6. Gong, L.G., Qiu, G.R., Jiang, H., Xu, X.Y., Zhu, H.Y. & Sun, K.L. Analysis of single nucleotide polymorphisms and haplotypes in HOXC

gene cluster within susceptible region 12q13 of simple congenital heart disease. Zhonghua Yi Xue Yi Chuan Xue Za Zhi. 22, 497-501 (2005).

7. Zhu, W.L., Li, Y., Yan, L., Dao, J. & Li, S. Maternal and offspring MTHFR gene C677T polymorphism as predictors of congenital atrial septal

defect and patent ductus arteriosus. Mol. Hum. Reprod. 12, 51-54 (2006).

8. Marinho, C., Alho, I., Guerra, A., Rego, C., Areias, J. & Bicho, M. The methylenetetrahydrofolate reductase gene variant (C677T) as a


20 / 21

susceptibility gene for tetralogy of Fallot. Rev. Port. Cardiol. 28, 809-812 (2009).

9. Li, D., Jing, X.A., Wang, H.Y., Ye, W.J. & Fan, H. [Study of correlationship between congenital heart disease and 5, 10-methylenetetra

hydrofolate reductase gene's polymorphism or folacin intakes]. Zhonghua Yu Fang Yi Xue Za Zhi. 43, 700-704 (2009).

10.Zhao, J.Y. et al. Functional variant in methionine synthase reductase intron-1 significantly increases the risk of congenital heart disease in the

Han Chinese population. Circulation. 125, 482-490 (2012).

11.Stevens, K.N. et al. Common variation in ISL1 confers genetic susceptibility for human congenital heart disease. PLoS. One. 26, e10855

(2010).

12.Dinesh, S.M. et al. Single-nucleotide polymorphisms of NKX2.5 found in congenital heart disease patients of Mysore, South India. Genet.

Test Mol. Biomarkers. 14, 873-879 (2010).

13. Pang, S. et al. Genetic and Functional Analysis of the NKX2-5 Gene Promoter in Patients with Ventricular Septal Defects. Pediatr. Cardiol.

2012 [Epub ahead of print].

14. Chen, Y.W. et al. Familial nonsyndromic patent ductus arteriosus caused by mutations in TFAP2B. Pediatr. Cardiol. 32, 958-965 (2011).

15. Vannay, A. et al. Single-nucleotide polymorphisms of VEGF gene are associated with risk of congenital valvuloseptal heart defects. Am.

Heart J. 151, 878-881 (2006).

16. Xie, J. et al. VEGF C-634G polymorphism is associated with protection from isolated ventricular septal defect: case-control and TDT studies.


21 / 21

Eur. J. Hum. Genet. 15, 1246-1251 (2007).

17. Xu, J. et al. Functional variant in microRNA-196a2 contributes to the susceptibility of congenital heart disease in a Chinese population. Hum.

Mutat. 30, 1231-1236 (2009).

18. Liu, C.X. et al. Association of TBX5 gene polymorphism with ventricular septal defect in the Chinese Han population. Chin Med J (Engl).

122, 30-34 (2009).

19. Shaw, G.M., Zhu, H., Lammer, E.J., Yang, W. & Finnell, R.H. Genetic variation of infant reduced folate carrier (A80G) and risk of orofacial

and conotruncal heart defects. Am. J. Epidemiol. 158, 747-752 (2003).

20. Song, X.M., Zheng, X.Y., Zhu, W.L., Huang, L. & Li, Y. Relationship between polymorphism of cystathionine beta synthase gene and

congenital heart disease in Chinese nuclear families. Biomed. Environ. Sci. 19, 452-456 (2006).


NG-LE33774R1 Shen Supplemetal Information · 3 Bio-X Institutes, Key Laboratory for the Genetics of...

Documents

Transcript of NG-LE33774R1 Shen Supplemetal Information · 3 Bio-X Institutes, Key Laboratory for the Genetics of...