MM Parker, JB Hetmanski, P Balakrishnan, MA Mansilla, E Mangold, KU Ludwig

Supplemental Material for “Confirming genes influencing risk to cleft lip with/without cleft palate in a case-parent trio study” HUMAN GENETICS

TH Beaty, MA Taub, AF Scott, JC Murray, ML Marazita, H Schwender,

MM Parker, JB Hetmanski, P Balakrishnan, MA Mansilla, E Mangold, KU Ludwig,

MM Noethen, M Rubini, N Elcioglu, I Ruczinski

Corresponding author: TH Beaty,

Supplemental Material

Supplemental Table 1: Genes typed in the replication study
Genes / Chromosome / Physical distance (hg18) / # SNPs genotyped (unflagged)
ABCA4 / 1p22-p23.1 / 94306578-94369455 / 72 (71)
ABCD3 / 94602357-94720243
PAX7 / 1q36.12 / 18812967-18872418 / 33 (33)
TRAF3IP3/IRF6/C1orf107 / 1q32-q32.2 / 207995922-208134740 / 45 (45)
SYT14 / 208177160-208437213
THADA / 2p21 / 43338060-43636645 / 49 (43)
COL8A1 / 3q12.3 / 100919114-100998440 / 89 (78)
FILIP1L / 3q12.3 / 101054616-101257410
EPHA3/PROSP / 3p11.2/3p21-cen / 89615458-89787083 / 51 (45)
hCG_1814486 / 8q24 / 129778467-130181350 / 55 (53)
DCAF4L2 / 8q21.3 / 88859742-89050656 / 12 (12)
VAX1 / 10q26.1 / 118817550-118824981 / 3 (2)
ZIC2 / 13q32 / 99433607-99436393 / 7 (6)
NTN1 & LOC728665 / 17p13 / 8855418-8906276 / 59 (54)
TTR / 18q12.1 / 27414750-27444172 / 4 (3)
MAFB / 20q11.2-q13.1 / 38688962-38719885 / 94 (93)
PARD6B / 20q13.13 / 48796589-48808649 / 11 (11)
HDAC4 / 2q37.3 / 239739972-239773961 / 93 (91)
ELAVL2 / 9p21 / 24717103-24723492 / 83 (80)
GADD45G / 9q22.1 / 91399407-91471223 / 52 (52)
FOXE1 / 9q22.33 / 99657300 / 10 (10)
EGR2 / 10q21.2 / 64254816-64317510 / 17 (16)
RTN1 / 14q23.1 / 59230318-59311190 / 10 (10)
JAG2 / 14q32 / 104656653-104688936 / 5 (5)
FAM98B / 15q14 / 36521518-36544415 / 12 (12)
RBFOX3 / 17q25.3 / 74813683-74822048 / 88 (84)
SLC39A9 / 14q24.1 / 21466467-26829516 / 5 (5)
GRID2 / 4q22 / 93992250-94213961 / 116 (115)
DSP / 6p24 / 7521526-7535179 / 18 (16)
NEBL / 10p12 / 20869682-21607571 / 59 (59)
CRP / 1q21-q23 / 157908973-157919563 / 18 (17)
FHIT / 3p14.2 / 59789088-60274300 / 117 (112)
ATP6V0D2 / 8q21 / 87175826-87256166 / 18 (18)

Supplemental Figure 1: Significance of genotypic TDT in 669 European & 439 Filipino CL/P case-parent trios for four genes achieving genome wide significance in Beaty et al. 2010 (note the difference in scale of Y-axis for chr. 8q24)

Supplemental Figure 2: Significance of genotypic TDT in 669 European & 439 Filipino CL/P case-parent trios for three genes achieving genome wide significance a meta-analysis between the original GWAS sample and this replication samples (notethe difference in scale of Y-axis for chr. 8q24)

Supplemental Table 2: Top 10 Pairs of SNPs in different genes showing the most significant evidence of GxG interaction using Cordell’s 4 df test
Gene1 / Chr / SNP 1 / Position1 (build 36) / Gene2 / Chr / Marker2 / Position2 (build 36) / Cordell’s Statistic / p-value
NTN1 / 17 / rs11650357 / 8904113 / IRF6 / 1 / rs2235375 / 208032210 / 29.60 / 0.000006
GADD45G / 9 / rs10992228 / 91740320 / MAFB / 20 / rs6065258 / 38689978 / 29.20 / 0.000007
chr8q24 / 8 / rs987525 / 130015336 / THADA / 2 / rs6544647 / 43431923 / 29.00 / 0.000008
ABCA4 / 1 / rs4147830 / 94316864 / NTN1 / 17 / rs7215246 / 8933522 / 27.90 / 0.000013
GADD45G / 9 / rs10992228 / 91740320 / MAFB / 20 / rs6072081 / 38694468 / 27.30 / 0.000017
NTN1 / 17 / rs11650357 / 8904113 / IRF6 / 1 / rs2013162 / 208035307 / 26.40 / 0.000027
NTN1 / 17 / rs11650357 / 8904113 / IRF6 / 1 / rs6685182 / 208034942 / 26.30 / 0.000027
ABCA4 / 1 / rs4147839 / 94281814 / THADA / 2 / rs4372955 / 43419650 / 26.10 / 0.000030
chr8q24 / 8 / rs894263 / 130072445 / NTN1 / 17 / rs7218002 / 8864443 / 25.50 / 0.000040
chr8q24 / 8 / rs987525 / 130015336 / THADA / 2 / rs3901678 / 43440955 / 25.30 / 0.000044

Supplemental Figure 3: Significance of genotypic TDT including GxSmoking interaction in two genes among 429 Filipino CL/P case-parent trios (where the exposure rate for maternal smoking was 8%).

Supplemental Figure 4: Predicted OR(CL/P|unexposed carrier) and OR(CL/P|exposed carrier) in two genes showing evidence of GxSmoking interaction among 439 Filipino CL/P trios. Open circles represent exposed infants with one risk allele (i.e. those whose mother smoked) and black dots represent unexposed carrier infants whose mother did not smoke. P-values from 1 df test for GxSmoking interaction are shown along the x-axis. A) 24 SNPs in GRID2, B) 24 SNPs in ELAVL2 (n.b. low MAF SNPs were omitted).

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Supplemental Table 3: Results of including GxSmoking interaction term into a conditional logistic model for European and Filipino CL/P trios for markers in GRID2
SNPs in GRID2 / European CL/P case-parent trios / Filipino CL/P case-parent trios
GxE OR / GxE x2 / GxE
p-value / trios / SNP OR / SNP x2 / SNP
p-value / MAF / GxE OR / GxE x2 / GxE
p-value / trios / SNP OR / SNP x2 / SNP
p-value / MAF
rs17019283 / 0.74 / 1.77 / 0.1830 / 77 / 1.17 / 2.31 / 0.1284 / 0.23 / 0.80 / 0.44 / 0.5055 / 32 / 1.02 / 0.03 / 0.8709 / 0.32
rs1319374 / 1.80 / 7.62 / 0.0058 / 89 / 0.88 / 1.82 / 0.1771 / 0.36 / 0.99 / 0.00 / 0.9789 / 18 / 0.91 / 0.28 / 0.5989 / 0.09
rs2089990 / 0.99 / 0.00 / 0.9721 / 54 / 0.87 / 1.87 / 0.1710 / 0.21 / 1.02 / 0.00 / 0.9494 / 30 / 1.03 / 0.09 / 0.7642 / 0.40
rs12710870 / 0.86 / 0.43 / 0.5097 / 74 / 0.95 / 0.27 / 0.6029 / 0.31 / 1.12 / 0.11 / 0.7363 / 30 / 0.94 / 0.37 / 0.5425 / 0.35
rs13109229 / 0.84 / 0.70 / 0.4017 / 88 / 1.15 / 2.07 / 0.1499 / 0.29 / 0.86 / 0.16 / 0.6892 / 28 / 1.03 / 0.05 / 0.8149 / 0.25
rs4374594 / 2.30 / 11.69 / 0.0006 / 77 / 0.90 / 1.00 / 0.3162 / 0.24 / 0.96 / 0.00 / 0.9466 / 15 / 0.91 / 0.29 / 0.5902 / 0.09
rs5021051 / 2.18 / 9.49 / 0.0021 / 74 / 0.95 / 0.20 / 0.6548 / 0.21 / 0.96 / 0.00 / 0.9466 / 15 / 0.91 / 0.29 / 0.5902 / 0.09
rs7668752 / 0.66 / 4.14 / 0.0419 / 94 / 1.21 / 3.82 / 0.0507 / 0.33 / 0.86 / 0.18 / 0.6752 / 28 / 1.03 / 0.09 / 0.7695 / 0.25
rs4389540 / 2.91 / 12.95 / 0.0003 / 55 / 0.77 / 4.18 / 0.0409 / 0.14 / NA / NA / NA / 0 / NA / NA / NA / 0.00
rs7659338 / 0.80 / 1.01 / 0.3148 / 84 / 0.94 / 0.49 / 0.4858 / 0.31 / 1.47 / 1.13 / 0.2872 / 28 / 0.86 / 1.67 / 0.1968 / 0.24
rs6532374 / 0.74 / 1.45 / 0.2288 / 72 / 1.25 / 4.01 / 0.0453 / 0.19 / 1.25 / 0.32 / 0.5707 / 26 / 0.98 / 0.02 / 0.9001 / 0.19
rs1450500 / 0.83 / 0.88 / 0.3492 / 90 / 0.97 / 0.13 / 0.7173 / 0.37 / 1.02 / 0.01 / 0.9423 / 36 / 1.02 / 0.04 / 0.8407 / 0.37
rs921354 / 0.74 / 2.13 / 0.1441 / 95 / 1.13 / 1.65 / 0.1987 / 0.37 / 1.02 / 0.00 / 0.9551 / 36 / 1.03 / 0.06 / 0.8019 / 0.37
rs9307120 / 0.74 / 2.16 / 0.1414 / 95 / 1.04 / 0.20 / 0.6571 / 0.30 / 0.75 / 0.52 / 0.4705 / 22 / 1.07 / 0.32 / 0.5731 / 0.19
rs921355 / 0.67 / 3.31 / 0.0687 / 87 / 0.98 / 0.04 / 0.8434 / 0.28 / 0.95 / 0.02 / 0.9011 / 24 / 1.05 / 0.15 / 0.6998 / 0.19
rs6532381 / 0.77 / 1.40 / 0.2361 / 85 / 1.04 / 0.12 / 0.7254 / 0.27 / 1.01 / 0.00 / 0.9631 / 39 / 1.06 / 0.35 / 0.5544 / 0.49
rs1369166 / 0.94 / 0.09 / 0.7639 / 83 / 1.07 / 0.44 / 0.5065 / 0.32 / 0.99 / 0.00 / 0.9654 / 37 / 0.98 / 0.06 / 0.8024 / 0.38
rs13135521 / 0.65 / 4.09 / 0.0431 / 91 / 1.08 / 0.68 / 0.4085 / 0.30 / 1.63 / 1.61 / 0.2041 / 29 / 1.07 / 0.28 / 0.5963 / 0.18
rs7671095 / 1.87 / 6.77 / 0.0093 / 73 / 0.94 / 0.37 / 0.5445 / 0.23 / 0.77 / 0.46 / 0.4963 / 25 / 1.07 / 0.29 / 0.5901 / 0.22
rs11933557 / 0.90 / 0.30 / 0.5866 / 92 / 1.08 / 0.73 / 0.3932 / 0.39 / 1.02 / 0.00 / 0.9493 / 27 / 0.88 / 1.53 / 0.2160 / 0.31
rs6532382 / 1.05 / 0.06 / 0.8073 / 84 / 0.92 / 0.84 / 0.3594 / 0.35 / 1.08 / 0.05 / 0.8167 / 29 / 0.87 / 1.54 / 0.2146 / 0.32
rs1456362 / 1.65 / 6.19 / 0.0128 / 96 / 0.96 / 0.23 / 0.6325 / 0.50 / 0.69 / 1.13 / 0.2869 / 30 / 0.89 / 1.57 / 0.2102 / 0.44
rs17261940 / 3.04 / 10.25 / 0.0014 / 41 / 0.88 / 0.98 / 0.3232 / 0.13 / 0.32 / 0.92 / 0.3385 / 4 / 1.04 / 0.02 / 0.8927 / 0.03
rs17328778 / 1.61 / 5.42 / 0.0199 / 97 / 0.96 / 0.21 / 0.6481 / 0.40 / 1.10 / 0.07 / 0.7953 / 22 / 1.03 / 0.08 / 0.7710 / 0.22
rs17263644 / 1.97 / 7.36 / 0.0067 / 67 / 0.85 / 2.34 / 0.1263 / 0.21 / 1.02 / 0.00 / 0.9796 / 6 / 0.98 / 0.01 / 0.9174 / 0.06
Supplemental Table 4: Results of including GxSmoking interaction term into a conditional logistic model for European and Filipino CL/P trios for markers in ELAVL2.
SNPs in ELAVL2 / European CL/P case-parent trios / Filipino CL/P case-parent trios
GxE OR / GxE x2 / GxE
p-value / # trios / SNP OR / SNP x2 / SNP
p-value / MAF / GxE OR / GxEx2 / GxE
p-value / # trios / SNP OR / SNP x2 / SNP
p-value / MAF
rs16908243 / 1.69 / 4.17 / 0.0412 / 67 / 0.94 / 0.33 / 0.5651 / 0.19 / 0.45 / 1.22 / 0.2696 / 9 / 0.95 / 0.08 / 0.7718 / 0.07
rs2162900 / 1.35 / 1.84 / 0.1753 / 86 / 0.89 / 1.67 / 0.1958 / 0.35 / 1.64 / 2.40 / 0.1214 / 36 / 0.91 / 0.82 / 0.3659 / 0.38
rs17699118 / 0.55 / 5.44 / 0.0197 / 64 / 1.33 / 6.10 / 0.0135 / 0.17 / NA / NA / NA / 0 / 0.00 / NA / NA / 0.00
rs10738693 / 1.43 / 2.58 / 0.1080 / 84 / 0.84 / 3.42 / 0.0642 / 0.33 / 0.63 / 0.10 / 0.7579 / 2 / 1.60 / 0.68 / 0.4097 / 0.01
rs7034759 / 0.63 / 4.24 / 0.0394 / 82 / 1.19 / 3.42 / 0.0642 / 0.30 / 2.73 / 4.02 / 0.0450 / 18 / 0.92 / 0.44 / 0.5079 / 0.17
rs4512474 / 1.28 / 1.29 / 0.2562 / 83 / 0.99 / 0.02 / 0.8919 / 0.37 / 1.92 / 3.38 / 0.0661 / 34 / 1.08 / 0.56 / 0.4544 / 0.28
rs1984582 / 1.45 / 2.63 / 0.1049 / 81 / 0.96 / 0.16 / 0.6854 / 0.25 / 0.99 / 0.00 / 0.9674 / 31 / 1.13 / 1.56 / 0.2110 / 0.43
rs1985995 / 0.62 / 2.93 / 0.0868 / 55 / 1.01 / 0.00 / 0.9558 / 0.19 / 1.46 / 0.95 / 0.3303 / 30 / 1.09 / 0.50 / 0.4811 / 0.23
rs12552851 / 0.51 / 7.32 / 0.0068 / 67 / 1.15 / 1.89 / 0.1692 / 0.25 / 0.92 / 0.04 / 0.8479 / 22 / 1.09 / 0.43 / 0.5134 / 0.17
rs10812054 / 1.06 / 0.07 / 0.7918 / 96 / 1.03 / 0.13 / 0.7232 / 0.48 / 0.97 / 0.01 / 0.9137 / 34 / 0.99 / 0.01 / 0.9146 / 0.33
rs1411216 / 0.64 / 4.30 / 0.0382 / 86 / 1.10 / 1.12 / 0.2890 / 0.39 / 1.07 / 0.02 / 0.8782 / 23 / 1.02 / 0.02 / 0.9001 / 0.19
rs2257210 / 0.46 / 12.66 / 0.0004 / 84 / 1.30 / 7.61 / 0.0058 / 0.31 / 0.94 / 0.02 / 0.8892 / 23 / 0.85 / 1.74 / 0.1873 / 0.23
rs10966331 / 1.04 / 0.03 / 0.8740 / 79 / 0.81 / 3.71 / 0.0541 / 0.22 / 1.02 / 0.00 / 0.9567 / 24 / 0.98 / 0.03 / 0.8549 / 0.21
rs6475797 / 1.37 / 2.77 / 0.0960 / 109 / 0.82 / 5.17 / 0.0229 / 0.48 / 1.20 / 0.20 / 0.6520 / 23 / 0.97 / 0.06 / 0.7995 / 0.19
rs2772578 / 0.51 / 9.20 / 0.0024 / 80 / 1.26 / 5.88 / 0.0153 / 0.31 / 1.55 / 1.16 / 0.2824 / 24 / 1.00 / 0.00 / 1.0000 / 0.21
rs2772575 / 1.89 / 10.49 / 0.0012 / 102 / 0.90 / 1.51 / 0.2188 / 0.48 / 1.53 / 0.61 / 0.4353 / 15 / 0.98 / 0.02 / 0.8846 / 0.14
rs1162608 / 1.63 / 5.01 / 0.0252 / 87 / 0.94 / 0.39 / 0.5303 / 0.29 / 1.17 / 0.15 / 0.6966 / 25 / 1.07 / 0.29 / 0.5887 / 0.23
rs10812061 / 0.56 / 8.93 / 0.0028 / 108 / 1.19 / 3.58 / 0.0586 / 0.45 / 0.74 / 0.74 / 0.3897 / 31 / 0.94 / 0.29 / 0.5901 / 0.23
rs1759041 / 0.45 / 11.52 / 0.0007 / 75 / 1.10 / 0.97 / 0.3235 / 0.26 / 0.56 / 1.45 / 0.2291 / 17 / 0.83 / 1.45 / 0.2284 / 0.13
rs1329851 / 0.94 / 0.09 / 0.7596 / 89 / 0.93 / 0.67 / 0.4124 / 0.36 / 1.01 / 0.00 / 0.9722 / 24 / 0.86 / 1.61 / 0.2044 / 0.24
rs7862580 / 0.73 / 2.80 / 0.0942 / 108 / 1.06 / 0.45 / 0.5045 / 0.45 / 0.53 / 1.59 / 0.2070 / 18 / 0.76 / 3.43 / 0.0640 / 0.13
rs7862849 / 1.55 / 5.48 / 0.0192 / 108 / 0.89 / 1.78 / 0.1817 / 0.48 / 0.54 / 1.53 / 0.2156 / 18 / 0.75 / 3.87 / 0.0491 / 0.13
rs10966381 / 0.51 / 10.47 / 0.0012 / 91 / 1.09 / 0.88 / 0.3492 / 0.44 / 0.68 / 1.33 / 0.2486 / 30 / 1.09 / 0.68 / 0.4082 / 0.36
rs1412645 / 0.50 / 9.06 / 0.0026 / 82 / 1.11 / 1.17 / 0.2787 / 0.26 / 0.67 / 0.55 / 0.4589 / 13 / 0.90 / 0.37 / 0.5410 / 0.09
rs6475808 / 0.61 / 5.98 / 0.0145 / 97 / 1.17 / 3.18 / 0.0745 / 0.42 / 0.74 / 0.83 / 0.3609 / 34 / 1.06 / 0.37 / 0.5425 / 0.40
rs16908722 / 0.59 / 5.84 / 0.0157 / 86 / 1.21 / 3.93 / 0.0475 / 0.29 / 0.85 / 0.26 / 0.6108 / 35 / 0.90 / 1.16 / 0.2810 / 0.36

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