| Literature DB >> 34917354 |
Seyedeh Maryam Kazemi1,2, Aghil Esmaieli-Bandboni3, Ziba Veisi Malekshahi4, Mohammad Shahbaz Sardood4, Mehrdad Hashemi1, Keivan Majidzadeh5, Maryam Kadkhodazadeh6, Rezvan Esmaili5, Babak Negahdari4.
Abstract
OBJECTIVES: Vitamin D deficiency is a driving force of common cancers like breast cancer. Vitamin D receptor (VDR) can play a tumor suppressor role by helping the precise function of vitamin D in cells such as modulation TGF-β signaling pathway. This study aimed to investigate the association of VDR gene variants and susceptibility to breast cancer in Iranian women.Entities:
Keywords: BMD, Bone mineral density; Breast cancer; Genetics; HWE, Hardy-Weinberg equilibrium; LD, Linkage disequilibrium; LOH, Loss of heterozygosity; PCR, Polymerase chain reaction; Polymorphism; RFLP, Restriction fragment length polymorphism; VDR, Vitamin D receptor; Vitamin D receptor
Year: 2021 PMID: 34917354 PMCID: PMC8666522 DOI: 10.1016/j.amsu.2021.103150
Source DB: PubMed Journal: Ann Med Surg (Lond) ISSN: 2049-0801
The sequences of used primers for PCR.
| SNP Polymorphism (SNP ID | Primers |
|---|---|
| For: CTGAAGGGAGACGTAGCAAAAG | |
| Rev: ATGTCCCCAAGGTCACAATAAC | |
| For: CTTCTGGATCATCTTGGCATAGAG | |
| Rev: AAGATAGCAGAGCAGAGTTCCAAG | |
| For: GCAAAGATAGCAGAGCAGAGTTC | |
| Rev: CTTCTGGATCATCTTGGCATAGAG | |
| For: GGGCTGTGAAATAAATTTGGTGGA | |
| Rev: TAAACACCCAGAGAACATTCTGAGAG |
SNP ID is extracted from miRBase database (http://www.mirbase.org/).
Forward primer.
Reverse primer.
Allelic frequency and genotype distribution for 5 variants of VDR polymorphism.
| allele/Genotype | Frequency (number) | Frequency (%) | Frequency (number) | Frequency (%) | ||
|---|---|---|---|---|---|---|
| A | 155 | 64 | 196 | 71 | ||
| C | 87 | 36 | 82 | 29 | ||
| 53 | 44 | 83 | 60 | <0.0001 | ||
| 49 | 40 | 30 | 22 | |||
| 19 | 16 | 26 | 19 | |||
| A | 171 | 63 | 143 | 53 | ||
| G | 99 | 37 | 125 | 47 | ||
| 52 | 39 | 42 | 31 | 0.53 | ||
| 67 | 5 | 59 | 44 | |||
| 16 | 12 | 33 | 25 | |||
| T | 143 | 52 | 207 | 78 | ||
| C | 133 | 48 | 57 | 22 | ||
| 45 | 33 | 25 | 19 | <0.0001 | ||
| 43 | 31 | 7 | 5 | |||
| 50 | 36 | 100 | 76 | |||
| G | 157 | 64 | 142 | 55 | ||
| A | 87 | 36 | 118 | 45 | ||
| 54 | 44 | 43 | 33 | <0.0001 | ||
| 49 | 40 | 56 | 43 | |||
| 19 | 16 | 31 | 24 | |||
| T | 134 | 58 | 171 | 65 | ||
| C | 96 | 42 | 93 | 35 | ||
| 15 | 13 | 16 | 12 | 0.23 | ||
| 66 | 57 | 61 | 46 | |||
| 34 | 30 | 55 | 42 | |||
BC group; breast cancer group.
Association between SNPs of VDR variants and breast cancer in our population.
| SNP | Inheritance state | Genotype | Frequency in control group (number/%) | Frequency in BC group (number/%) | OR, | |
|---|---|---|---|---|---|---|
| Recessive | AA-AG | 119 (88.2%) | 101 (75.4%) | 1.00 | 0.0062 | |
| GG | 16 (11.8%) | 33 (24.6%) | 2.43 (1.26–4.67) | |||
| Dominant | AA | 52 (38.5%) | 42 (31.3%) | 1.00 | 0.22 | |
| AG-GG | 83 (61.5%) | 92 (68.7%) | 1.37 (0.83–2.27) | |||
| Codominant | AA | 52 (38.5%) | 42 (31.3%) | 1.00 | 0.022 | |
| AG | 67 (49.6%) | 59 (44%) | 1.09 (0.64–1.86) | |||
| GG | 16 (11.8%) | 33 (24.6%) | 2.55 (1.24–5.26) | |||
| Recessive | AA-AC | 102 (84.3%) | 113 (81.3%) | 1.00 | 0.52 | |
| CC | 19 (15.7%) | 26 (18.7%) | 1.24 (0.65–2.36) | |||
| Dominant | AA | 53 (43.8%) | 83 (59.7%) | 1.00 | 0.01 | |
| AC-CC | 68 (56.2%) | 56 (40.3%) | 0.53 (0.32–0.86) | |||
| Codominant | AA | 53 (43.8%) | 83 (59.7%) | 1.00 | 0.0038 | |
| AC | 49 (40.5%) | 30 (21.6%) | 0.39 (0.22–0.69) | |||
| CC | 19 (15.7%) | 26 (18.7%) | 0.87 (0.44–1.73) | |||
| Recessive | TT-CT | 92 (67.2%) | 107 (81.1%) | 1.00 | 0.0089 | |
| CC | 45 (32.9%) | 25 (18.9%) | 0.48 (0.27–0.84) | |||
| Dominant | TT | 49 (35.8%) | 100 (75.8%) | 1.00 | <0.0001 | |
| CT-CC | 88 (64.2%) | 32 (24.2%) | 0.18 (0.10–0.30) | |||
| Codominant | TT | 49 (35.8%) | 100 (75.8%) | 1.00 | <0.0001 | |
| CT | 43 (31.4%) | 7 (5.3%) | 0.08 (0.03–0.19) | |||
| CC | 45 (32.9%) | 25 (18.9%) | 0.27 (0.15–0.49) | |||
| Recessive | TT-TC | 101 (87.1%) | 116 (87.9%) | 1.00 | 0.85 | |
| CC | 15 (12.9%) | 16 (12.1%) | 0.93 (0.44–1.97) | |||
| Dominant | TT | 35 (30.2%) | 55 (41.7%) | 1.00 | 0.06 | |
| TC-CC | 81 (69.8%) | 77 (58.3%) | 0.60 (0.36–1.02) | |||
| Codominant | TT | 35 (30.2%) | 55 (41.7%) | 1.00 | 0.16 | |
| TC | 66 (56.9%) | 61 (46.2%) | 0.59 (0.34–1.02) | |||
| CC | 15 (12.9%) | 16 (12.1%) | 0.68 (0.30–1.54) | |||
| Cdx2 | Recessive | GG-AG | 98 (80.3%) | 92 (73.6%) | 1.00 | 0.21 |
| AA | 24 (19.7%) | 33 (26.4%) | 1.46 (0.81–2.66) | |||
| Dominant | GG | 64 (52.5%) | 61 (48.8%) | 1.00 | 0.57 | |
| AG-AA | 58 (47.5%) | 64 (51.2%) | 1.16 (0.70–1.91) | |||
| Codominant | GG | 64 (52.5%) | 61 (48.8%) | 1.00 | 0.45 | |
| AG | 34 (27.9%) | 31 (24.8%) | 0.96 (0.53–1.74) | |||
| AA | 24 (19.7%) | 33 (26.4%) | 1.44 (0.77–2.71) |
BC group: breast cancer group, OR: odds ratio, CI: confidence interval.
Linkage disequilibrium for five SNPs of VDR gene.
| Cdx2 | |||||
|---|---|---|---|---|---|
| . | 0 | 0.0523 | 0.0441 | 0.0817 | |
| 0.9999 | . | 0.1099 | 0.0237 | 0.1405 | |
| 0.2899 | 0.1379 | . | 0.1251 | 0.0036 | |
| Cdx 2 | 0.3972 | 0.7534 | 0.1466 | . | 0.0508 |
| 0.1289 | 0.0508 | 0.9439 | 0.5401 | . |
Upper diagonal: D′-values for the SNP combinations; lowr diagonal: P-values for pair wise LD.
Haplotypes frequency in case and control groups, and their association with breast cancer.
| Cdx2 | Total | BC group | Control group | OR (95% CI) | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | A | A | T | G | T | 0.1176 | 0.1037 | 0.1285 | 1.00 | – | |
| 2 | A | G | T | A | T | 0.0702 | 0 | 0.1119 | 1.37 (0.47–3.99) | 0.56 | |
| 3 | A | G | T | G | T | 0.0679 | 0.0546 | 0.088 | 2.60 (0.62–10.94) | 0.19 | |
| 4 | A | A | C | G | T | 0.0588 | 0.0532 | 0.0674 | 0.08 (0.01–1.04) | 0.055 | |
| 5 | A | A | T | G | C | 0.0547 | 0 | 0.0678 | 1.03 (0.17–6.27) | 0.97 | |
| 6 | C | G | T | G | T | 0.053 | 0.0716 | 0.0252 | 0.47 (0.13–1.75) | 0.26 | |
| 7 | A | G | C | G | C | 0.0493 | 0.0648 | 0.05 | 0.02 (0.00–0.53) | 0.02 | |
| 8 | C | A | T | G | C | 0.0455 | 0.0334 | 0.0525 | 1.40 (0.30–6.53) | 0.67 | |
| 9 | A | A | T | A | C | 0.0454 | 0.0735 | 0.0213 | 3.31 (0.26–41.96) | 0.36 | |
| 10 | A | A | C | A | T | 0.0436 | 0.0404 | 0.0252 | 0.31 (0.06–1.53) | 0.15 | |
| 11 | A | A | T | A | T | 0.0367 | 0.0406 | 0.0438 | 0.95 (0.08–11.51) | 0.97 | |
| 12 | C | A | C | G | C | 0.0356 | 0.0325 | 0.0412 | 0.08 (0.01–0.66) | 0.019 | |
| 13 | A | G | T | G | C | 0.035 | 0.0508 | 0.0446 | 1.25 (0.28–5.49) | 0.77 | |
| 14 | A | G | C | G | T | 0.032 | 0.0778 | 0.0055 | 11.80 (0.49–285.35) | 0.13 | |
| 15 | C | A | T | A | T | 0.0306 | 0.0595 | 0.0222 | 0.54 (0.11–2.54) | 0.44 | |
| 16 | C | A | C | G | T | 0.029 | 0.0289 | 0.0273 | 1.20 (0.17–8.68) | 0.85 | |
| 17 | C | A | C | A | T | 0.0266 | 0 | 0.0478 | 0.02 (0.00–0.78) | 0.037 | |
| 18 | A | A | C | G | C | 0.0258 | 0.0201 | 0.0135 | 3.62 (0.12–111.21) | 0.46 | |
| 19 | C | G | T | A | T | 0.0239 | 0.0205 | 0.0129 | 5.64 (3.64–7.43) | <0.0001 | |
| 20 | C | G | C | G | T | 0.02 | 0 | 0.0252 | 1.55 (0.20–11.97) | 0.67 | |
| 21 | A | G | C | A | C | 0.0191 | 0.0281 | 0.0107 | 0.33 (0.01–11.32) | 0.54 | |
| 22 | A | G | T | A | C | 0.0183 | 0.017 | 0.0204 | 0.76 (0.06–9.46) | 0.83 | |
| 23 | C | A | T | A | C | 0.0182 | 0.0216 | 0.0061 | 0.22 (0.01–6.39) | 0.38 | |
| 24 | C | G | T | G | C | 0.0153 | 0.0291 | 0.0178 | 0.09 (0.00–1.92) | 0.12 | |
| Rare | * | * | * | * | * | 0.0281 | 8.39 (0.29–243.29) | 0.22 | |||
Rare (*): All haplotypes with estimated frequencies <0.01% in total population.
BC group: breast cancer group, OR: odds ratio, CI: confidence interval.