Supplementary Figure 1. Flow Diagram Showing Split up of the Study Participants
dbSNPa / Allelesb / Polymorphismb / Domain / Exon2 / Intron8 / Intron8 / Exon9
rs2228570 / F/f / C>T / Exon2 / ---- / 0.001 / 0.001 / 0.021
rs1544410 / B/b / G>A / Intron8 / 0.023 / ---- / 0.587* / 0.528*
rs17879735 / A/a / GT / Intron8 / 0.034 / 0.816 / ---- / 0.565*
rs731236 / T/t / T>C / Exon9 / 0.142 / 0.793 / 0.952 / ----
aSNP IDs according to the database dbSNP ( bUnderlined letters are minor alleles. Upper matrix denotes R2 values (correlation coefficient) and lower matrix denotes D’ values (standardized disequilibrium coefficient). *P<0.01 for the SNP pairs
Supplementary Table 2. Meta-analyses of VDR gene polymorphisms in relation to BMD, fracture risk or risk of osteoporosis.Number of Studies analysed / Polymorphism / Major Inference / Reference
41 Studies / BsmI / VDRBsmIB/bgenepolymorphismis not associated with the susceptibility ofosteoporosisin overall populations, Caucasians and Asians. / 1
25 Studies
4,075 women / BsmI, Ap I / Modest but statistically significant association with BMD in Chinese postmenopausal women with higher BMD in heterozygotes. / 2
17 Studies
2,112 fracture cases
4,521 controls / FokI, BsmI, Apa I, Taq I / Modest but statistically significant association between BsmI (bb) genotypes and fracture risk. (OR 0.87 95%CI 0.76-0.98) / 3
26,242 participants
18,405 women / Cdx2, FokI, Bsm I, ApaI, TaqI / No association of these polymorphisms with BMD except Cdx2 which shows mild association. / 4
13 Studies
1,632 fracture cases
3,203 controls / BsmI, Taq I / No relationship of VDR Bsm I and Taq I with fracture risk. / 5
14 Studies / FokI, BsmI, ApaI, TaqI / No association with the risk of osteoporosis except ‘b’allele in BsmI polymorphism in East Asian population in both dominant model (OR 0.14, 95%CI 0.04-0.50) and Random effect model (OR0.16, 95%CI 0.03-0.84) indicating prevention / 6
39 studies / BsmI / B allele was significantly associated with BMD at spine which follow recessive model with BB genotype having lower BMD than Bb/bb genotypes at baseline which led to greater bone mineral loss over time / 7
47 studies / FokI, BsmI, ApaI, TaqI / Although these polymorphisms were not significantly associated with osteoporosis individually but haplotype BAT (OR 4.21, P0.001) and BaT (OR3.71, P=0.031) were significantly associated with risk of osteoporosis. / 8
75 studies / FokI, BsmI, ApaI, TaqI / BMD is associated with VDR gene polymorphism with high levels of confidence. Non genetic factors and genetic heterogeneity interfere with the detection of effects of VDR gene polymorphism on bone phenotypes / 9
Supplementary Table 3. Haplotype studies on VDR gene polymorphism in relation to osteoporosis and fracture risk.
Population/Study / No. Tested / Marker / Haplotype Frequencies / Remarks / Reference
Chinese Nuclear Families / 400 families,
1215 subjects / ApaI
FokI
Cdx2 / aFG
aFA
afG
afA
AFG
AFA
AfG
AfA / 0.20
0.17
0.17
0.15
0.08
0.08
0.08
0.07 / No Significance within family associations were obtained between genotypes and haplotypes of VDR gene and peak BMD / 10
Swedish and Hongkong Chinese (MrOS) / 3014 (Swedish)
2000 (Chinese) / BsmI
ApaI
TaqI / baT
BAt
bAT / Swedish
0.23
0.15
0.02 / Chinese
0.50
0.07
0.004 / baT haplotype is independently associated with increased risk of vertebral fracture in Swedish subjects (OR1.65, 95% CI 1.15-2.4, P0.01) and with lower spine BMD in Swedish and Chinese subjects (P<0.05). / 11
Spanish / 719 postmenopausal women / BsmI
ApaI
TaqI / baT
BAt
bAt
BaT
BAT
bAt / 0.42
0.37
0.11
0.03
0.03
0.03 / Interaction of VDR (ApaI) and Col1A1(-1663IndelT) polymorphisms were associated with femoral neck BMD (P0.01) / 12
GENOMOS / 26,242 subjects
18,405 Women / Cdx2
FokI
BsmI
ApaI
TaqI / GGT
ATC
GTT
ATT
GGC
AGT / 0.45
0.39
0.11
0.02
0.01
0.01 / FokI, BsmI, ApaI and TaqI polymorphisms are not associated with BMD or fracture risk but Cdx2 polymorphism may be associated with the risk of fracture / 4
Indian
(South India) / 246 postmenopausal women / BsmI
ApaI
TaqI / BAT
BAt
BaT
Bat
bAT
bAt
baT
bat / 0.27
0.18
0.09
0.07
0.13
0.09
0.09
0.09 / VDR gene polymorphism is associated with BMD in Indian women but disease association analysis of haplotypes is not given. / 13
UK / 3100 British Women (50-63 years) / BsmI
ApaI
TaqI / BAt
bAT
baT / 0.37
0.13
0.42 / VDR does not seem to influence BMD or bone turnover in early postmenopausal women with adequate calcium intake / 14
------/ 47 studies
(Meta analysis) / BsmI
ApaI
TaqI / BAt
bAT
baT
BaT
BAT / Normal
0.41
0.11
0.46
0.001
0.005 / Osteoporotic
0.42
0.11
0.43
0.005
0.02 / Individually BsmI, TaqI and ApaI were not significantly associated with osteoporosis but haplotypes BAT (OR 4.21, P0.001) and BaT (OR 3.71, P=0.031) were significantly associated with the risk of osteoporosis / 8
Greece
(Hellenic) / 126 postmenopausal women / BsmI
ApaI
TaqI / BAT
Bat
bAT
baT
bAT / Normal
0.046
0.51
0.1
0.32
---- / Osteoporotic
-----
0.26
0.24
0.49
0.01 / bAT and baT haplotypes were associated with lower BMD at forearm (P=0.0047) / 15
Netherlands / 634 postmenopausal women / BsmI
ApaI
TaqI / baT
BAt
bAT / 0.493
0.403
0.104 / VDR haplotype baThomozygotes are associated with femoral neck and lumbar spine BMD (P0.001) / 16
Netherlands / 1004 postmenopausal women / BsmI
ApaI
TaqI / baT
BAt
bAT / 0.48
0.40
0.10 / baT haplotype was overrepresented in fracture cases (P=0.009). OR for heterozygous carriers=1.8, 95%CI 1.0-3.3, OR for homozygous carriers=2.6, 95%CI 1.4-5.0. This effect was independent of BMD / 17
Canada
(Caucasians) / 677 young women
(18-35 years) / BsmI
ApaI
TaqI / baT
Bat
bAT
BAT
Others / 0.45
0.39
0.14
0.01
0.001 / Significant association of VDR haplotypes, baT and BAt with BMD at hip. Greatest correlation with TaqI (P=0.001) / 18
India
(Northwest India) / 450 postmenopausal females (147 normals, 115 osteopenics and 188 osteoportics) / BsmI
ApaI
TaqI / baT
BAt
bAT
BaT
BAT
bAt / Normal
0.30
0.09
0.13
0.14
0.14
0.14 / Osteoporotic
0.28
0.07
0.12
0.31
0.08
0.13 / Significant influence of susceptibility haplotype AGT (BaT) for the risk of osteopenia (OR 2.04, 95%CI 1.03-4.08, P=0.036) and osteoporosis (OR 2.90, 95%CI 1.61-5.38, P=0.00005) has been revealed, which manifest in its recessive mode of inheritance. / Present Study
Supplementary Figure 1. Flow diagram showing split up of the study participants.
Supplementary Figure 2.Association of BMD by number of copies of the susceptible haplotype AGT of VDR SNPs in the order of rs1544410, rs17879735 and rs731236.A) BMD of the lumbar spine and B) BMD of the femoral neck. The BMD was corrected with age, BMI and years since menopause. Double and triple heterozygotes (n=65) were excluded for the analysis. Error bars represent 95% confidence intervals
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