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. Author manuscript; available in PMC: 2012 Feb 1.
Published in final edited form as: Cancer Epidemiol Biomarkers Prev. 2011 Jun 2;20(8):1793–1797. doi: 10.1158/1055-9965.EPI-11-0397

Table 2.

Association between selected miRNA processing and miRNA binding site SNPs and epithelial ovarian cancer risk in a pooled analysis.

Gene (locus) SNP (maj/min allelea) Location (putative miRs) b OR (95% CI) reported by Liang et al (Ref. 3) MAF c Pooled OR (95% CI), adjusted for study d P Pooled OR (95% CI), adjusted for study and ancestry e P
miRNA processing
DDX20 (1p21,1-p13.2) rs197414 (C/A) f Missense 0.69 (0.48–0.99) 0.13 1.02 (0.92,1.12) 0.70 1.04 (0.94,1.15) 0.49
DROSHA (5p13.3) rs9292427 (C/T)g Intron 0.71 (0.51–0.99) 0.46 1.01 (0.95,1.08) 0.72 1.01 (0.94,1.08) 0.79
GEMIN4 (17p13) rs2740349 (A/C) h exon 1, ns 0.70 (0.51–0.96) 0.18 0.99 (0.92,1.09) 0.97 1.02 (0.93,1.11) 0.71
rs2740351 (T/C) i flanks 5′UTR 0.71 (0.57–0.87) 0.45 0.98 (0.91,1.04) 0.46 1.00 (0.94,1.07) 0.98
rs7813 (T/G) i exon 1, ns 0.71 (0.57–0.88) 0.46 0.97 (0.91,1.04) 0.38 1.00 (0.93,1.07) 0.91
XPO5 (6p21.1) rs2257082 (C/A) exon 1, ss 0.73 (0.54–0.99) 0.27 0.99 (0.92,1.07) 0.87 1.00 (0.93,1.08) 0.95
miRNA binding sites
CAV1 (7q31.1) rs9920 (G/A) 3′UTR (miR 630) 1.50 (1.04–2.17) 0.10 1.13 (1.10,1.26) 0.03 1.06 (0.95,1.19) 0.29
COL18A1 (21q22.3) rs7499 (G/A) 3′UTR (miR-594) 1.47 (1.07–2.02) 0.42 c 0.98 (0.92,1.05) 0.57 0.98 (0.92,1.05) 0.50
E2F2 (1p36) rs2075993 (A/C) j 3′UTR (miR-663,486-3p) 1.24 (1.00–1.54) 0.48 1.01 (0.95,1.08) 0.67 1.01 (0.94,1.08) 0.87
ILIR1 (2q12) rs3917328 (C/T) 3′UTR (miR-335, 31) 1.65 (1.03–2.64) 0.05 c 1.06 (0.91,1.23) 0.49 1.00 (0.86,1.17) 0.99
KRAS (12p12.1) rs13096 (A/G) k 3′UTR (miR-1244) 1.26 (1.01–1.57) 0.45 1.00 (0.94,1.07) 0.94 0.99 (0.93,1.06) 0.85
UGT2A3 (4q13.2) rs17147016 (T/A) h 3′UTR (miR-224, 1279) 1.47 (1.08–2.01) 0.19 c 1.02 (0.93,1.11) 0.70 1.01 (0.93,1.10) 0.88

Abbreviations: US-CAN=United States-Canada; UK=United Kingdom; POL=Poland; maj=major; min=minor; miR=miRNA; UTR= untranslated region; ns=non- synonymous SNP; ss=synonymous SNP; OR (CI) =odds ratio (confidence interval); MAF=minor allele frequency among all controls; all P-values are two-sided.

a

The major allele represents the most frequently-occurring allele and serves as the reference allele during modeling.

b

SNP location derived from Illumina annotation files, HapMap2 data (http://hapmap.ncbi.nlm.nih.gov/), and dbSNP (http://www.ncbi.nlm.nih.gov/projects/SNP/). SNPinfo http://snpinfo.niehs.nih.gov/ and the PolymiRTS database (http://compbio.uthsc.edu/miRSNP) were used to predict miRNAs whose binding activity may be altered due to the SNP location.

c

Genotype data was imputed for all participants using MACH version 1.0.16 using phased data from HapMap release 22 (genome build 36) derived from individuals with European ancestry (CEU).

d

Pooled OR and 95% CI estimated using a log-additive model adjusted for study (US-CAN, UK, POL)

e

Pooled OR and 95% CI estimated using a log-additive model adjusted for study and the first two principal components representing European ancestry

f

DDX20 rs19714 is in linkage disequilibrium (LD) (r2 =0.90) with rs197383 identified by Liang et al.

g

DROSHA rs9292427 is in LD (r2 =0.98) with rs4867329 identified by Liang et al.

h

SNP deviates from Hardy Weinberg Equilibrium among all controls with PHWE values of 0.020 for rs607613, 0.040 for rs615435, 0.013 for rs2740349, 0.004 for rs3732133, and 0.034 for rs17147016, respectively.

i

GEMIN4 SNP pair in LD (r2 =1)

j

E2F2 SNP pair in LD (r2 =0.97)

k

KRAS rs13096 is in LD (r2 =1) with rs10771184 identified by Liang et al.