| Literature DB >> 32273741 |
Kazem Vatankhah Yazdi1, Seyed Mehdi Kalantar1, Massoud Houshmand2,3, Masoud Rahmanian4, Masoud Reza Manaviat5, Mohammad Reza Jahani6, Behnam Kamalidehghan2,7, Amir Almasi-Hashiani8.
Abstract
BACKGROUND: Type 2 diabetes mellitus (T2DM) is a serious public health issue with significantly increasing rates across the world. The genome-wide association studies (GWAS) have previously manifested involved genes that remarkably enhance the risk of T2DM. In this study, the association of common variants with T2DM risk has been identified among Iranian population from Tehran province of Iran.Entities:
Keywords: ARMS; GWAS; Iranian populations; T2DM; the genome-wide association studies; the tetra amplification refractory mutation system; type 2 diabetes mellitus
Year: 2020 PMID: 32273741 PMCID: PMC7102914 DOI: 10.2147/DMSO.S225968
Source DB: PubMed Journal: Diabetes Metab Syndr Obes ISSN: 1178-7007 Impact factor: 3.168
Represents List of Forward and Reverse Primers (Inner and Outer) Applied for Detection of SNPs
| SNP ID | Forward and Reverse Primer Sequences (Outer & Inner) | Primer Tm (C°) | Product Size(bp) | ||
|---|---|---|---|---|---|
| 1470579 | FO | 5ʹ-ACA GAA ACA CAA TAA GAT CAT CAC AT-3’ | 57.43 | FO-RO | 391 |
| RO | 5ʹ-AAA TTT TTT ATG GAC ACT GAA GGT C-3’ | 56.51 | FO-RI | 205 | |
| FI | 5ʹ-ATC ATT AGA TAA GAT CCA TAC GAG CTA-3’ | 57.37 | FI-RO | 233 | |
| RI | 5ʹ-CTT TTC TTG ATA GGC AGG GTG-3’ | 56.59 | |||
| 2237892 | FO | 5ʹ-CTG TGG GTA CAC AGC TTC CCT-3’ | 61.72 | FO-RO | 467 |
| RO | 5ʹ-CCT GGG TCA TCA GAC TAG GGT AG-3’ | 61.01 | FO-RI | 267 | |
| FI | 5ʹ-GTC ACA GGA CTT TGC CAA CC-3’ | 59.33 | FI-RO | 239 | |
| RI | 5ʹ-TTT CTA GGC CCC TCA CCA CA-3’ | 60.47 | |||
| 7903146 | FO | 5ʹ-TTT TTC ACA TGT GAA GAC ATA CAC-3’ | 56.15 | FO-RO | 429 |
| RO | 5ʹ-TTT ATA GCG AAG AGA TGA AAT GTA G-3’ | 55.10 | FO-RI | 269 | |
| FI | 5ʹ-ATT AGA GAG CTA AGC ACT TTT TAG AGA T-3’ | 58.59 | FI-RO | 212 | |
| RI | 5ʹ-CTC ATA CGG CAA TTA AAT TAT AGA G-3’ | 54.04 | |||
| 8050136 | FO | 5ʹ-CCA TAC CAA CCA AGG TCC T-3’ | 56.29 | FO-RO | 388 |
| RO | 5ʹ-CAC ACC AAG ATG GTC ATG TC-3’ | 56.43 | FO-RI | 237 | |
| FI | 5ʹ-GTT GCC CAC TGT GGC AGT A-3’ | 60.23 | FI-RO | 189 | |
| RI | 5ʹ-AAC CAC AGG CTC AGA TAC TG-3’ | 56.93 | |||
| 10830963 | FO | 5ʹ-GGT TAA AGA GGC TGT CTG GGA GG-3’ | 62.51 | FO-RO | 421 |
| RO | 5ʹ-AGC CTT TGT TCA GAA CCA TGC TG-3’ | 61.87 | FO-RI | 254 | |
| FI | 5ʹ-AGT GAT GCT AAG AAT TCA CAC CAT GTG-3’ | 61.97 | FI-RO | 216 | |
| RI | 5ʹ-GGC AGT TAC TGG TTC TGG ATT GG-3’ | 61.43 | |||
| 10946398 | FO | 5ʹ-CAG GAT CTT GTG CTC CTC AC-3’ | 57.98 | FO-RO | 424 |
| RO | 5ʹ-CCA ACA GCA AGC AGT TGA TT-3’ | 57.19 | FO-RI | 255 | |
| FI | 5ʹ-GGA AAA GGG TTT AGT ATC GCT C-3’ | 55.67 | FI-RO | 214 | |
| RI | 5ʹ-GAT GAC TTG ATG CAA TGA CAG TAT-3’ | 57.38 | |||
| 13266634 | FO | 5ʹ-CTG CTG ATA GCA TTT GGG ACA GG-3’ | 61.55 | FO-RO | 826 |
| RO | 5ʹ-CCA ATT GAT TGA TGG ATC TCA GTG C-3’ | 60.51 | FO-RI | 520 | |
| FI | 5ʹ-GCT TCT TTA TCA ACA GCA GCC AGC T-3’ | 64.04 | FI-RO | 350 | |
| RI | 5ʹ-CGA ACC ACT TGG CTG TCC CG-3ʹ | 63.66 | |||
Figure 1ARMS-PCR analysis of the (A) rs2237892 C > T, (B) rs1470579 C > A, (C) rs10946398 C > A, (D) rs8050136 A>C, (E) rs10830963 C > G, (F) rs13266634 C > T and (G) rs7903146 T > C on 1.5% agarose gel. Note: Lanes 1, 2, 3 and 4 represent fo-ro/fo-ri/fi-ro, fo-ro/fo-ri, fo-ro/fi-ro and DNA molecular marker, respectively.
Figure 2PCR-sequencing of (A) rs2237892 C > T, (B) rs1470579 C > A, (C) rs10946398 C > A, (D) rs8050136 A>C, (E) rs10830963 C > G, (F) rs13266634 C > T and (G) rs7903146 T > C. The highlighted blue area marks the polymorphisms.
The Clinical and Biomedical Characteristics of Individuals in This Study
| Clinical Parameters | Controls (n=106) | T2DM Subjects (n=162) | P-value |
|---|---|---|---|
| Age | 65.5±7.3 | 65±7.5 | 0.64 |
| BMI (Body Mass Index) | 23.07±1.03 | 24.00±1.23 | <0.001* |
| SBP (Systolic Blood Pressure) | 120.36±4.23 | 130.03±7.43 | <0.001* |
| DBP (Diastolic Blood Pressure) | 84.89±3.01 | 88.75±4.59 | <0.001* |
| LDL (Low-Density Lipoprotein) | 110.97±13.00 | 129.83±9.06 | <0.001* |
| HDL (High-Density Lipoprotein) | 46.07±4.16 | 44.28±4.29 | 0.002* |
| TG (Triglyceride) | 118.64±12.11 | 176.69±11.59 | <0.001* |
| 2hpp (Two-Hour Postprandial Glucose) | 121.56±3.60 | 235.35±12.97 | <0.001* |
| FBS (Fasting Blood Sugar) | 87.32±4.35 | 165.20±22.51 | <0.001* |
| HbA1c (Glycated hemoglobin) | 5.40±0.16 | 8.34±0.49 | <0.001* |
Notes: Data are mean±S.D values; *Statistically significant.
Abbreviations: BMI, Body Mass Index; SBP, Systolic Blood Pressure; DBP, Diastolic Blood Pressure; LDL, Low-Density Lipoprotein; TG, Triglyceride; 2hpp, Two-Hour Postprandial Glucose; FBS, Fasting Blood Sugar; HbA1c, Hemoglobin A1c.
The Genotypic Frequency of Polymorphisms Between T2DM and Control Groups
| SNP | Control | T2DM | p-value | |
|---|---|---|---|---|
| rs1470579 IGF2BP2 | AA | 55 (51.89%) | 67 (41.36%) | 0.001* |
| CC | 11 (10.38%) | 55 (33.95%) | ||
| AC | 40 (37.74%) | 40 (24.69%) | ||
| rs2237892 KCNQ1 | TT | 6 (5.66%) | 1 (0.62%) | 0.002* |
| CC | 85 (80.19%) | 152 (93.83%) | ||
| CT | 15 (14.15%) | 9 (5.56%) | ||
| rs7903146 TCF7L2 | CC | 51 (48.11%) | 26 (16.05%) | 0.001* |
| CT | 39 (36.79%) | 76 (46.91%) | ||
| TT | 16 (15.09%) | 60 (37.04%) | ||
| rs8050136 FTO | CC | 25 (23.58%) | 42 (25.93%) | 0.132 |
| AA | 60 (56.60%) | 73 (45.06%) | ||
| AC | 21 (19.81%) | 47 (29.01%) | ||
| rs10830963 MTNR1B | CC | 52 (49.06%) | 58 (35.80%) | 0.079 |
| CG | 44 (41.51%) | 80 (49.38%) | ||
| GG | 10 (9.43%) | 24 (14.81%) | ||
| rs10946398 CDKAL1 | AA | 46 (43.40%) | 31 (19.14%) | 0.001* |
| CC | 10 (9.43%) | 27 (16.67%) | ||
| AC | 50 (47.17%) | 104 (64.20%) | ||
| rs13266634SLC30A8 | TT | 78 (73.58%) | 82 (50.62%) | 0.001* |
| CC | 5 (4.72%) | 16 (9.88%) | ||
| CT | 23 (21.70%) | 64 (39.51%) | ||
Note: *statistically significant.
The Genotypic Frequency of Polymorphisms Between T2DM and Control Groups with Odds Ratio
| SNP | Control | T2DM | Odds Ratioa | p-value | |
|---|---|---|---|---|---|
| rs1470579 IGF2BP2 | AA | 55 (51.89%) | 67 (41.36%) | Ref. | - |
| CC | 11 (10.38%) | 55 (33.95%) | 4.1 (1.96–8.59) | 0.001* | |
| AC | 40 (37.74%) | 40 (24.69%) | 0.82 (0.46–1.44) | 0.494 | |
| rs2237892 KCNQ1 | TT | 6 (5.66%) | 1 (0.62%) | Ref. | - |
| CC | 85 (80.19%) | 152 (93.83%) | 10.79 (1.27–90.6) | 0.029* | |
| CT | 15 (14.15%) | 9 (5.56%) | 3.6 (0.37–34.93) | 0.269 | |
| rs7903146 TCF7L2 | CC | 51 (48.11%) | 26 (16.05%) | Ref. | - |
| CT | 39 (36.79%) | 76 (46.91%) | 3.82 (2.07–7.03) | 0.001* | |
| TT | 16 (15.09%) | 60 (37.04%) | 7.35 (3.55–15.2) | 0.001* | |
| rs8050136 FTO | CC | 25 (23.58%) | 42 (25.93%) | Ref. | - |
| AA | 60 (56.60%) | 73 (45.06%) | 0.72 (0.39–1.32) | 0.293 | |
| AC | 21 (19.81%) | 47 (29.01%) | 1.33 (0.65–2.72) | 0.431 | |
| rs10830963 MTNR1B | CC | 52 (49.06%) | 58 (35.80%) | Ref. | - |
| CG | 44 (41.51%) | 80 (49.38%) | 1.63 (0.96–2.75) | 0.068 | |
| GG | 10 (9.43%) | 24 (14.81%) | 2.15 (0.94–4.92) | 0.069 | |
| rs10946398 CDKAL1 | AA | 46 (43.40%) | 31 (19.14%) | Ref. | - |
| CC | 10 (9.43%) | 27 (16.67%) | 4.0 (1.70–9.43) | 0.001* | |
| AC | 50 (47.17%) | 104 (64.20%) | 3.08 (1.75–5.43) | 0.001* | |
| rs13266634 SLC30A8 | TT | 78 (73.58%) | 82 (50.62%) | Ref. | - |
| CC | 5 (4.72%) | 16 (9.88%) | 3.04 (1.06–8.70) | 0.038* | |
| CT | 23 (21.70%) | 64 (39.51%) | 2.64 (1.49–4.67) | 0.001* | |
Notes: aCrude odds ratio (95% CI); *statistically significant.