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. 2016 Jul 1;95(11):1245–1256. doi: 10.1177/0022034516657003

Table 2.

Meta-analyses of the Case-Control Cohorts from Ghana, Ethiopia, and Nigeria.

Part A: Meta-analyses of NSCL/P and NSCPO Case-Control Cohorts from All 3 Countries
NSCL/P
 NSCPO
SNP Probable Gene/Loci Minor Allelesa African MAF P OR I P OR I
rs1801131 MTHFR C/Ab 0.15 0.32 1.08 0.00 0.19 0.79 0.00
rs1801133 MTHFR A/Gc 0.09 0.49 1.08 18.19 0.44 0.83 0.00
rs766325 PAX7 G/Ab,d,e 0.18 0.29 0.92 0.00 0.23 0.82 0.00
rs742071 PAX7 T/Gb 0.39 5.10E-03f 1.19 54.68 0.76 0.96 0.00
rs560426 ABCA4 C/Tb,g 0.49 0.10 0.90 6.15 0.16 1.18 0.00
rs481931 ABCA4 T/Gc 0.10 0.40 1.09 11.13 0.49 0.85 0.00
rs4147811 ABCA4 T/Cc 0.11 0.23 1.13 67.35 0.93 1.02 0.00
rs138751793 ARHGAP29 C/Th 0.02 0.24 1.32 0.00 0.47 1.34 27.90
rs6677101 SLC25A24 G/Tb,e,g 0.33 0.80 0.98 12.11 0.87 1.02 53.89
rs861020 IRF6 A/Gb 0.11 0.23 1.11 0.00 0.83 0.96 24.15
rs34743335 IRF6 T/A 0.02 0.59 0.90 0.00 0.84 0.89 38.34
rs642961 IRF6 A/Gb 0.09 0.32 1.11 68.47 0.57 0.88 44.17
rs7590268 THADA G/Tb 0.20 0.74 0.98 0.00 0.38 0.87 0.00
rs4332945 DYSF T/Gb,e,g 0.16 0.94 0.99 0.00 0.97 1.01 0.00
rs2303596 DYSF T/Cc,d,e 0.22 0.20 0.91 75.32 0.57 1.09 73.54
rs227782 DYSF A/Gb,g 0.42 0.33 1.06 0.00 0.35 1.12 61.90
rs115200552 MSX1 C/Gh 0.02 0.38 1.16 28.63 0.01f 1.81 0.00
rs12532 MSX1 G/Ac,e 0.44 0.49 0.96 0.00 0.37 0.90 0.43
rs2674394 Gene desert A/Cb 0.17 0.62 1.04 0.00 0.68 1.07 0.00
rs651333 TULP4 C/Tb,d,g 0.34 0.97 1.00 0.00 0.04f 1.29 0.00
rs6558002 EPHX2 C/Tb,g 0.24 0.39 1.06 0.00 0.87 1.02 0.00
rs987525 8q24 A/Cb,g 0.38 1.22E-03f 0.81 40.55 0.22 0.86 0.00
rs894673 FOXE1 A/Tc 0.33 0.42 0.95 0.00 0.93 1.01 0.00
rs3758249 FOXE1 T/Cc 0.33 0.56 0.96 0.00 0.90 1.02 0.00
rs7078160 VAX1 A/Gb 0.25 0.04f 1.16 0.00 0.88 1.02 0.00
rs4752028 VAX1 C/Tb,g 0.45 0.51 0.96 0.00 0.80 0.97 0.00
rs10785430 ADAMTS20 G/Ab 0.32 0.90 0.99 0.00 0.49 1.09 0.00
rs9574565 SPRY2 T/Cc,g 0.35 0.75 1.02 0.00 0.45 1.10 0.00
rs8001641 SPRY2 G/Ac,d,e,g 0.10 0.35 1.08 0.00 0.37 0.85 0.00
rs17563 BMP4 T/Cb,d,e,g 0.18 0.95 0.99 0.00 0.77 1.04 0.00
rs1258763 GREM1 C/Tc,d,e,g 0.49 0.11 1.11 0.00 0.50 0.92 0.00
rs8049367 ADCY9 C/Tc,d,e 0.30 0.20 1.09 0.00 0.10 0.81 0.00
rs16260 CDH1 A/Cb 0.13 0.59 1.05 0.00 0.39 0.85 0.00
rs11642413 CDH1 G/Ab,e,g 0.28 0.83 1.02 0.00 0.21 0.83 0.00
rs1546124 CRISPLD2 G/Cb,e 0.25 0.60 0.96 0.00 0.89 0.98 0.00
rs4783099 CRISPLD2 T/Cb 0.33 0.59 1.04 0.00 0.02f 0.74 0.00
rs8069536 NTN1 T/Gb 0.32 0.13 1.11 0.97 0.88 0.98 0.00
rs8081823 NTN1 A/Gc 0.24 0.08 0.88 0.00 0.63 0.94 32.54
rs17760296 NOG1 G/Tb 0.02 0.92 0.99 0.00 0.04f 1.74 0.00
rs227731 NOG1 G/Tb,g 0.22 0.86 0.99 0.00 0.26 1.17 0.00
rs7224837 AXIN2 G/Ab 0.11 0.75 1.04 0.00 0.81 0.95 0.00
rs3923086 AXIN2 A/Cb,d,e,g 0.02 0.25 1.15 0.00 NA NA NA
rs17820943 MAFB T/Cc 0.25 0.33 0.93 15.15 0.68 1.06 22.99
rs13041247 MAFB C/Tc 0.25 0.37 0.94 34.01 0.42 1.12 0.00
rs11696257 MAFB T/Cc 0.25 0.30 0.93 32.24 0.61 1.07 0.00
Part B: Meta-analyses of Subphenotypes of NSCL/P Cohorts from the 3 Countries
NSCL
 NSCLP
rs1801131 MTHFR C/Ab 0.15 0.78 1.03 0.00 0.22 1.13 0.00
rs1801133 MTHFR A/Gc 0.09 0.71 1.06 8.24 0.30 0.30 0.00
rs766325 PAX7 G/Ab,d,e 0.18 0.91 0.99 0.00 0.17 0.86 0.00
rs742071 PAX7 T/Gb 0.39 0.02f 1.23 68.74 0.03f 1.19 0.00
rs560426 ABCA4 C/Tb 0.49 0.73 1.03 0.00 0.03f 1.20 10.33
rs481931 ABCA4 T/Gc 0.10 0.81 0.97 0.00 0.08 1.27 63.75
rs4147811 ABCA4 T/Cc 0.11 0.50 1.10 65.82 0.15 1.21 15.35
rs138751793 ARHGAP29 C/Th 0.02 0.19 1.53 66.38 0.41 1.29 0.00
rs6677101 SLC25A24 G/Tb,e,g 0.33 0.92 0.99 0.00 0.98 1.00 58.97
rs861020 IRF6 A/Gb 0.11 0.18 1.17 17.72 0.57 1.07 0.00
rs34743335 IRF6 T/A 0.02 0.87 0.96 0.00 0.50 0.85 23.72
rs642961 IRF6 A/Gb 0.09 0.96 0.99 15.60 0.15 1.21 62.97
rs7590268 THADA G/Tb 0.20 0.45 0.92 0.00 0.50 1.07 0.00
rs4332945 DYSF T/Gb,e,g 0.16 0.54 0.94 10.40 0.71 1.04 0.00
rs2303596 DYSF T/Cc,d,e 0.22 0.29 0.89 63.58 0.44 0.93 75.54
rs227782 DYSF A/Gb,g 0.42 0.85 0.98 0.00 0.13 1.14 0.00
rs115200552 MSX1 C/Gh 0.02 0.18 1.37 61.30 0.68 1.10 0.00
rs12532 MSX1 G/Ac,e 0.44 0.55 0.95 0.00 0.51 0.95 0.00
rs2674394 Gene desert A/Cb 0.17 0.06 1.22 0.00 0.42 0.91 0.00
rs651333 TULP4 C/Tb,d,g 0.34 0.63 0.96 0.00 0.74 0.97 0.00
rs6558002 EPHX2 C/Tb,g 0.24 0.82 1.02 0.00 0.11 0.11 0.00
rs987525 8q24 A/Cb,g 0.38 5.38E-03f 1.28 0.00 0.01f 0.80 54.21
rs894673 FOXE1 A/Tc 0.33 0.54 0.95 42.39 0.45 0.94 0.00
rs3758249 FOXE1 T/Cc 0.33 0.53 0.94 46.73 0.68 0.96 0.00
rs7078160 VAX1 A/Gb 0.25 0.03f 1.23 0.00 0.20 1.13 24.04
rs4752028 VAX1 C/Tb,g 0.45 0.55 1.05 16.64 0.50 0.95 0.00
rs10785430 ADAMTS20 G/Ab 0.32 0.88 1.01 41.30 0.86 0.98 3.00
rs9574565 SPRY2 T/Cc,g 0.35 0.53 1.06 72.62 0.43 1.07 65.44
rs8001641 SPRY2 G/Ac,d,e,g 0.10 0.99 1.00 0.00 0.26 1.13 0.00
rs17563 BMP4 A/Gb,d,e,g 0.18 0.89 0.99 25.84 0.98 1.00 0.00
rs1258763 GREM1 C/Tc,d,e,g 0.49 0.22 0.90 0.00 0.10 1.15 0.00
rs8049367 ADCY9 C/Tc,d,e 0.30 0.36 1.09 10.19 0.35 1.08 0.00
rs16260 CDH1 A/Cb 0.13 0.46 0.91 10.51 0.20 1.16 0.00
rs11642413 CDH1 G/Ab,e,g 0.28 0.98 1.00 0.00 0.55 1.05 0.00
rs1546124 CRISPLD2 G/Cb,e 0.25 0.26 0.90 0.00 0.88 1.01 0.00
rs4783099 CRISPLD2 T/Cb 0.33 0.85 1.02 0.00 0.32 1.09 0.00
rs8069536 NTN1 T/Gb 0.32 0.72 1.03 3.47 0.04f 1.20 0.00
rs8081823 NTN1 A/Gc 0.24 0.55 0.95 0.00 0.05 0.83 0.00
rs17760296 NOG1 G/Tb 0.02 0.83 1.04 5.85 0.85 0.97 0.00
rs227731 NOG1 G/Tb,g 0.22 0.38 0.92 0.00 0.59 1.05 0.00
rs7224837 AXIN2 G/Ab 0.11 0.61 1.08 0.00 0.81 1.04 0.00
rs3923086 AXIN2 A/Cb,d,e,g 0.02 0.62 1.10 40.28 NA NA 0.00
rs17820943 MAFB T/Cc 0.25 0.25 0.89 15.55 0.43 0.93 0.00
rs13041247 MAFB C/Tc 0.25 0.25 0.89 31.03 0.54 0.94 0.00
rs11696257 MAFB T/Cc 0.25 0.24 0.89 27.17 0.40 0.92 0.00

All P values reported are for the minor alleles. All initial studies were carried out in Asians and/or Caucasians but not Africans. Source of minor alleles and MAF: http://browser.1000genomes.org.

I, test of heterogeneity of which 0 to 40 represents no heterogeneity; MAF, minor allele frequency; NA, not applicable; NSCL, nonsyndromic cleft lip; NSCL/P, nonsyndromic cleft lip with or without cleft palate; NSCLP, nonsyndromic cleft lip and palate; NSCPO, nonsyndromic cleft palate only; OR, odds ratio; SNP, single-nucleotide polymorphism.

a

The first allele is the minor allele in Europeans unless otherwise indicated. The first allele is also the minor allele in East Asians, South Asians, and Africans.

b

Minor allele was the risk allele in initial study.

c

Minor allele was protective in initial study.

d

The first allele is the major allele, while the second allele is the minor allele in South Asians.

e

The first allele is the major allele, while the second allele is the minor allele in East Asians.

f

Loci that reached nominal significance in meta-analyses (in bold).

g

The first allele is the major allele, while the second allele is the minor allele in Africans.

h

The first allele is the minor allele, and the variation exists only in Africans.