| Literature DB >> 19822020 |
Feng Zhu1, Marie Loh, Jeffrey Hill, Sumarlin Lee, King Xin Koh, Kin Wai Lai, Manuel Salto-Tellez, Barry Iacopetta, Khay Guan Yeoh, Richie Soong.
Abstract
BACKGROUND: Intestinal metaplasia (IM) is an important precursor lesion in the development of gastric cancer (GC). The aim of this study was to investigate genetic factors previously linked to GC risk for their possible association with IM. A total of 18 polymorphisms in 14 candidate genes were evaluated in a Singapore-Chinese population at high risk of developing GC.Entities:
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Year: 2009 PMID: 19822020 PMCID: PMC2766386 DOI: 10.1186/1471-230X-9-76
Source DB: PubMed Journal: BMC Gastroenterol ISSN: 1471-230X Impact factor: 3.067
PCR primers and dispensation sequences for pyrosequencing of 17 SNPs evaluated for association with IM.
| PCR | Pyrosequencing | |||||
|---|---|---|---|---|---|---|
| Locus | Forward Primer | Reverse Primer | °C | bp | Sequencing Primer | Dispensation |
| IL10 -- 1082 A/G | CTCAATCAAAGGATCCCCAGAGAC | AGGCTGGATAGGAGGTCCCTTACT | 60 | 253 | ACACTACTAAGGCTTCTTTG | cgagcagta |
| IL10 -- 819 T/C | GGCCAATTTAATCCAAGGTTT | TCTGCACTTGCTGAAAGCTTCTTA | 60 | 207 | CCTTGTACAGGTCATGTAA | gtcgatctc |
| IL-1B -- 511 T/C | CATGAGATTGGCTAGGGTAACAG | GCCCTCCCTGTCTGTATTGA | 60 | 230 | CAATTGACAGAGAGCTCC | atctgagca |
| MMP2 -- 1306 T/C | TTTCATCTCTGGGCCATTGT | TGAAGTTCTCCCTGTGACAACC | 60 | 265 | TCCCCACCCAGCACT | gctgactct |
| EGF +61 A/G | GTCATCCCTGCTTTCCTGTGTG | CAGAGCAAGGCAAAGGCTTAGA | 60 | 266 | CCCAATCCAAGGGTTGT | cagactgac |
| PTPN11 (int1) A/G | TGGACGAATGGCAAATTG | GATCAATCCCACCTGAGACAGA | 60 | 182 | TTGTCTCTAAAGGACTGTG | tgagctcat |
| NQ01 C609T | AACTGCATGGAATTGGTTGACTTA | TGGTGTCTCATCCCAAATATTCT | 60 | 191 | GTGGCTTCCAAGTCTTA | cgatcgtca |
| STCH rs2242661 | AACTCGAATCCTGGACCTGATTAG | CTGGCGTTTATAATCAAACCTGTG | 65 | 203 | GCGGAAAGAGAAAGG | gctagtact |
| STCH rs1882881 | CTATGGAAGGCTGCGAGAAC | ACTTCCAGCTACAGGCAACATT | 65 | 213 | GAGGCTTTTTCCATCA | gcagtcgtg |
| STCH rs12479 | CTTGAAGGACCGTGTTGATGT' | GCAAAGGTCTCGGATAACAAAAA | 60 | 312 | ATGTTTCAGCACCAT | gatagctag |
| STCH rs9982492 | TCGTGCTTACCTTGTTCACATT | AGTATGAGCCCTGCCATGA | 60 | 193 | CCACTTGTCCTTTAAGTCC | actcgactc |
| SULT1A1 G638A | GCCAGATCGCCTCTGAGGT | TGGGGGACGGTGGTGTAGT | 65 | 233 | CCTGGAGTTTGTGGG | tgcgagctc |
| ADPRT T2285C | GATACCTAAGTCGGGGGCTTTC | ACAAGCTTTCCAGGAGATCCTAAC | 65 | 262 | TGCTCCTCCAGGCCA | cagtctgat |
| HER2 +17ex17 A/G | GTCCCTCCCACCCCAAACTA | CTGCCGTCGCTTGATGAG | 65 | 145 | CCCTCTGACGTCCAT | gtcagatct |
| TP53 C215G | TCCCAAGCAATGGATGATTTGA | AAGCCCAGACGGAAACCGTAG | 60 | 230 | CAGAGGCTGCTCCCC | tgcagtgct |
| FR-a A1314G | AAGTGGAGACTGAGGCCCAGA | TGACCCCTCCCCACCAAC | 60 | 183 | GTGTGGCCTGCTCAA | cgagtacga |
| MTHFR C677T | ACTGTCATCCCTATTGGCAGGTTA | TCGGTGCATGCCTTCACAA | 60 | 168 | GAAGGTGTCTGCGGG | cgagtacga |
Characteristics of study subjects in relation to the presence of IM.
| Total (%) | IM+ (%) | IM- (%) | |
|---|---|---|---|
| Subjects | 374 | 128 | 246 |
| Mean age ± SD (range) | 60.5 ± 7.8 | 62.9 ± 7.8 | 59.2 ± 7.5 |
| Age 50-59 yrs | 190 (51) | 48 (38)* | 142 (58)* |
| Age 60-69 yrs | 133 (36) | 55 (43) | 78 (32) |
| Age ≥70 yrs | 51 (13) | 25 (19) | 26 (10) |
| Male | 207 (55) | 72 (56) | 135 (55) |
| Family history of GC | 66 (18) | 23 (18) | 43 (17) |
| HP infection | 191 (51) | 84 (66)* | 107 (43)* |
| Drinker | 66 (18) | 22 (17) | 46 (19) |
| Smoker | 90 (24) | 30 (23) | 60 (24) |
| Chronic gastritis | 290 (78) | 115 (90) | 175 (71) |
| Atrophy gastritis | 194 (52) | 97 (76) | 97 (39) |
| Dysplasia | 1 (0.3) | 1 (0.8) | 0 |
* P < 0.05
Distribution of genotype frequencies according to IM and HP infection status
| Gene polymorphism | Genotype | IM- | IM+ | HP- | HP+ | ||
|---|---|---|---|---|---|---|---|
| IM- | IM+ | IM- | IM+ | ||||
| TT | 71 | 31 | 33 | 9 | 38 | 22 | |
| TC | 117 | 60 | 64 | 24 | 53 | 36 | |
| CC | 33 | 16 | 13 | 6 | 20 | 10 | |
| AA | 22 | 5 | 13 | 1 | 9 | 4 | |
| AG | 103 | 55 | 54 | 20 | 49 | 35 | |
| GG | 110 | 58 | 50 | 18 | 60 | 40 | |
| GG | 164 | 95 | 74 | 30 | 90 | 65 | |
| GA | 74 | 31 | 43 | 12 | 31 | 19 | |
| AA | 6 | 1 | 5 | 0 | 1 | 1 | |
| AA | 174 | 92 | 87 | 32 | 87 | 60 | |
| AG | 60 | 30 | 29 | 8 | 31 | 22 | |
| GG | 1 | 1 | 1 | 1 | 0 | 0 | |
| 44 | 212 | 101 | 112 | 33 | 100 | 68 | |
| 24 | 28 | 18 | 9 | 4 | 19 | 14 | |
| 34 | 1 | 2 | 0 | 2 | 1 | 0 | |
| 54 | 0 | 1 | 0 | 0 | 0 | 1 | |
| 22 | 2 | 2 | 0 | 1 | 2 | 1 | |
| CC | 64 | 35 | 33 | 10 | 31 | 25 | |
| CT | 119 | 62 | 63 | 21 | 56 | 41 | |
| TT | 48 | 23 | 20 | 10 | 28 | 13 | |
| TT | 131 | 55 | 57 | 21 | |||
| TC | 78 | 46 | 39 | 15 | 39 | 31 | |
| CC | 22 | 16 | 17 | 3 | 5 | 13 | |
| AA | 207 | 100 | 98 | 37 | 109 | 63 | |
| AG | 21 | 14 | 13 | 3 | 8 | 11 | |
| GG | 2 | 0 | 2 | 0 | 0 | 0 | |
| CC | 178 | 79 | 85 | 28 | 93 | 51 | |
| CT | 46 | 22 | 26 | 8 | 20 | 14 | |
| TT | 3 | 2 | 2 | 0 | 1 | 2 | |
| CC | 132 | 77 | 64 | 23 | 68 | 54 | |
| CT | 98 | 42 | 50 | 16 | 48 | 26 | |
| TT | 14 | 7 | 8 | 2 | 6 | 5 | |
| CC | 27 | 10 | |||||
| CT | 143 | 80 | 78 | 25 | 65 | 55 | |
| TT | 28 | 22 | 13 | 4 | 5 | 18 | |
| CC | 45 | 16 | 22 | 7 | 23 | 9 | |
| CG | 126 | 78 | 66 | 23 | 60 | 55 | |
| GG | 51 | 26 | 24 | 10 | 27 | 16 | |
| GG | 175 | 85 | |||||
| GA | 58 | 28 | 26 | 16 | 32 | 12 | |
| AA | 4 | 2 | 0 | 1 | 4 | 1 | |
| GG | 102 | 58 | 51 | 20 | 51 | 38 | |
| GA | 106 | 39 | 52 | 12 | 54 | 27 | |
| AA | 22 | 15 | 10 | 8 | 12 | 7 | |
| AA | 58 | 34 | 24 | 13 | 34 | 21 | |
| AC | 123 | 58 | 67 | 15 | 56 | 43 | |
| CC | 57 | 31 | 26 | 13 | 31 | 18 | |
| AA | 69 | 31 | 34 | 12 | 35 | 19 | |
| AG | 106 | 46 | 52 | 13 | 54 | 33 | |
| GG | 44 | 26 | 22 | 13 | 22 | 13 | |
| CC | 85 | 45 | 41 | 15 | 44 | 30 | |
| CT | 105 | 39 | 53 | 12 | 52 | 27 | |
| TT | 28 | 18 | 14 | 9 | 14 | 9 | |
| GG | 221 | 108 | 112 | 33 | 109 | 75 | |
| GA | 16 | 10 | 6 | 6 | 10 | 4 | |
| AA | 1 | 0 | 1 | 0 | 0 | 0 | |
* Bold type denotes significant difference in genotype frequencies
Multivariate logistic regression analysis for associations with IM.
| OR for IM | ||
|---|---|---|
| All cases | ||
| HP (positive | 2.16 (1.35 - 3.45) | 0.001 |
| Age (>60 | 2.21 (1.40 - 3.49) | 0.001 |
| | 1.74 (0.99 - 3.06) | 0.056 |
| HP- cases | ||
| Age (>60 | 1.92 (0.92 - 4.00) | 0.082 |
| | 2.51 (1.16 - 5.40) | 0.019 |
| HP+ cases | ||
| Age (≥60 | 2.19 (1.15 - 4.17) | 0.017 |
| | 2.61 (1.18 - 5.80) | 0.018 |
| | 2.32 (1.21 - 4.43) | 0.011 |
| | 0.46 (0.21 - 0.99) | 0.048 |