| Literature DB >> 32547144 |
Laith N Al-Eitan1,2, Hatem Aman2, Rami Alkhatib1,2, Mansour A Alghamdi3.
Abstract
OBJECTIVE: To investigate the genotypic and allelic association of Src homology 2 B adapter protein 1 (SH2B1) gene polymorphisms with type 2 diabetes mellitus (T2DM) in Jordanian patients. PATIENTS AND METHODS: Three hundred patients were screened, but only 200 adult Jordanian patients diagnosed with T2DM (53.5% male and 46.5% female) have participated in this study. Blood samples were collected from both patients and healthy individuals for DNA extraction according to well-established procedures. Exon 1 and exon 9 of the SH2B1 gene were sequenced using an efficient and sensitive DNA sequencing method in order to identify specific single nucleotide polymorphisms (SNPs) in the SH2B1 gene associated with T2DM. Genetic and haplotype correlation analysis was performed for the chosen SNPs to detect any association if existent. In addition, SNPStats Web Tool and Hardy-Weinberg equilibrium (HWE) analyses for the genotype distribution were used. The significance was determined according to the P-value, and the level of significance taken as P < 0.05. The normality of the data distribution was statically analysed by the Shapiro-Wilk test with a P-value >0.05. Also, the patient's characteristics and clinical data about all participants were mentioned.Entities:
Keywords: Arab; Jordan; SH2B1; type 2 diabetes mellitus
Year: 2020 PMID: 32547144 PMCID: PMC7250702 DOI: 10.2147/DMSO.S245843
Source DB: PubMed Journal: Diabetes Metab Syndr Obes ISSN: 1178-7007 Impact factor: 3.168
Figure 1Flowchart of T2DM patients.
Figure 2Schematic structure of the human SH2B1 gene. The positions of the seven SNPs genotyped and their dbSNP IDs are also shown.
Figure 3Gel Electrophoresis Results. (A) Separation of PCR products of SH2B1 gene by 2% agarose gel for exon1. The first lane from the left corresponds to the 1 kb DNA ladder. Lane –Ve: represent of negative blank. Lanes 1–30: the 1240 bp amplified product for samples that represent the DNA samples for T2DM patients. (B) Separation of PCR products of SH2B1 gene by 2% agarose gel for exon9. The first lane from the left corresponds to the 1 kb DNA ladder. Lane –Ve: represent of negative blank. Lanes 160–200: the 722 bp amplified product for samples that represent the DNA samples for T2DM patients.
Figure 4Capillary Electrophoresis and DNA-Sequencing Results. (1) Partial sequence Electropherograms of (NOVEL) SNP C827G for exon1.
Notes: Reverse primer use here in PCR-sequencing step. (A) The wild type allele shows a conserved C at position 827 in DM-34 sample. Vertical arrow points to the conserved nucleotide C (blue peak) to G (black peak). (B) A sample showing a heterozygous C827G sequence variant. (2) Partial sequence Electropherograms of (NOVEL) SNP G2026A for exon9. Reverse primer use here in PCR-sequencing step. (A) The wild type allele shows a conserved G at position 2026 in DM-200 sample. Vertical arrow points to the conserved nucleotide G (black peak) to A (Green peak). (B) A sample showing a heterozygous G2026A sequence variant. (3) Partial sequence Electropherograms of G3241A SNP for exon1. Forward primer use here in PCR-sequencing step. (A) The wild-type allele shows a conserved G at position 3241 in DM-34 sample. Vertical arrow points to the conserved nucleotide G (black peak) to A (Green peak). (B) A sample showing a homozygous G3241A sequence variant. (4) Partial sequence Electropherograms of T361A SNP for exon9. This primer covers the T361A SNP. Reverse primer use here in PCR-sequencing step. (A) The wild type allele shows a conserved T at position 361 in DM-198 sample. Vertical arrow points to the conserved nucleotide T (red peak) to A (Green peak). (B) A sample showing a heterozygous T361A sequence variant. (5) Partial sequence Electropherograms of C1930T SNP for exon9. This primer covers the C1930T SNP. Forward primer use here in PCR-sequencing step. (A) The wild type allele shows a conserved C at position 1930 in DM-198 sample. Vertical arrow points to the conserved nucleotide C (blue peak) to T (red peak). (B) A sample showing a heterozygous C1930T sequence variant. (6) Partial sequence Electropherograms of G2161A SNP for exon9. This primer covers the G2161A SNP. Forward primer use here in PCR-sequencing step. (A) Sample showing homozygous G2161A in sequence variant for DM-87. (B) Sample showing heterozygous G2161A in sequence variant for DM-101. (C) The wild type allele shows a conserved G at position 2161 in DM-198 sample. Vertical arrow points to the conserved nucleotide G (blue peak) to A (red peak). (7) Partial sequence Electropherograms of T2221C SNP for exon9. This primer covers the T2221C SNP. Forward primer use here in PCR-sequencing step. (A) The wild-type allele shows a conserved T at position 2221 in DM-200 sample. Vertical arrow points to the conserved nucleotide T (blue peak) to C (red peak). (B) A sample showing a heterozygous T2221C sequence variant.
SH2B1 SNPs, Their Minor Allele Frequencies, and HWE p-values in T2DM and Controls
| Gene | SNP _ID | Cases (n =200) | Controls (n = 200) | ||||
|---|---|---|---|---|---|---|---|
| MA | MAF | HWE | MA | MAF | HWE | ||
| C.827C>G | G | 0.01 | 0.915 | G | 0.00 | – | |
| C.2026G>A | A | 0.00 | 0.972 | A | 0.00 | – | |
| rs146946750 | A | 0.06 | <0.0001 | A | 0.02 | <0.0001 | |
| rs565131715 | A | 0.11 | 0.14 | A | 0.02 | 1 | |
| rs370302573 | T | 0.00 | 1 | T | 0.00 | 1 | |
| rs143212778 | A | 0.04 | 0.21 | A | 0.01 | 1 | |
| rs200470848 | C | 0.01 | 1 | C | 0.01 | 1 | |
Abbreviations: MA, minor allele; MAF, minor allele frequency; HWE, Hardy–Weinberg equilibrium.
Allele and Genotype Distributions of the Exon1 and Exon 9 Polymorphisms Within the SH2B1 Gene in T2DM Patients and Controls
| SNP_ID | Allele/Genotype | T2DM | Controls | T2DM vs Controls | |
|---|---|---|---|---|---|
| Chi-Square | p-value | ||||
| C | 99.25% | 100.0% | 3.011 | 0.083 | |
| G | 0.75% | 0.0% | |||
| C.827C>G | CC | 98.5% | 100.0% | ||
| CG | 1.5% | 0.0% | 3.023 | 0.082 | |
| GG | 0.0% | 0.0% | |||
| G | 99.75% | 100.0% | 1.004 | 0.316 | |
| A | 0.25% | 0.0% | |||
| C.2026G>A | GG | 99.5% | 100.0% | ||
| GA | 0.5% | 0.0% | 1.003 | 0.317 | |
| AA | 0.0% | 0.0% | |||
| G | 94% | 98% | 7.446 | ||
| A | 6.0% | 2.0% | |||
| rs146946750 | GG | 93.5% | 97.5% | ||
| GA | 0.0% | 0.0% | 3.723 | ||
| AA | 6.5% | 2.5% | |||
| T | 89% | 98% | 27.648 | ||
| A | 11% | 2.0% | |||
| rs565131715 | TT | 78.5% | 96.5% | ||
| TA | 21.5% | 3.5% | 29.623 | ||
| AA | 0.0% | 0.0% | |||
| C | 99.75% | 100.0% | 1.004 | 0.316 | |
| T | 0.25% | 0.0% | |||
| rs370302573 | CC | 99.5% | 100.0% | ||
| CT | 0.5% | 0.0% | 1.003 | 0.317 | |
| TT | 0.0% | 0.0% | |||
| G | 96% | 99% | 7.272 | ||
| A | 4.0% | 1.0% | |||
| rs143212778 | GG | 93.5% | 98.5% | ||
| GA | 6.0% | 1.5% | 6.66 | ||
| AA | 0.5% | 0.0% | |||
| T | 100% | 99% | 0.672 | 0.412 | |
| C | 0.0% | 1.0% | |||
| rs200470848 | TT | 99% | 98% | ||
| TC | 1.0% | 2.0% | 0.677 | 0.411 | |
| CC | 0.0% | 0.0% | |||
Notes: Allelic and genotypic association p-value, calculated using the Pearson Chi-squared test for a 23 contingency table with 1 df for allelic, 2 df for genotypic comparisons; P < 0.05 is significant, in bold.
Genetic Association Analysis of rs146946750, rs565131715 and rs143212778 Polymorphisms in T2DM Cases and Controls Using Different Genetic Models
| Gene | SNP_ID | Category Test | Odds Ratio | 95% CI | Chi-Square* |
|---|---|---|---|---|---|
| Het (GA) vs Common Hz (GG) | n/a | 1.00 | 1.05 | ||
| rs146946750 | Rare Hz (AA) vs Het (GA) | n/a | n/a | n/a | |
| Rare Hz (AA) vs Common Hz (GG) | 2.71 | 0.95–7.75 | 3.72 | ||
| Het (TA) vs Common Hz (TT) | 7.55 | 3.31–17.25 | 29.62 | ||
| rs565131715 | Rare Hz (AA) vs Het (TA) | n/a | n/a | n/a | |
| Rare Hz (AA) vs Common Hz (TT) | n/a | 1.00 | 1.05 | ||
| Het (GA) vs Common Hz (GG) | 4.21 | 1.17–15.17 | 5.66 | ||
| rs143212778 | Rare Hz (AA) vs Het (GA) | n/a | n/a | n/a | |
| Rare Hz (AA) vs Common Hz (GG) | n/a | 1.00 | 1.05 |
Notes: n/a: Not applicable. *For significant association chi-squared should be >3.84 with p-value <0.003.
Haplotype Association with Response (n=400, Crude Analysis) Within SH2B1 Gene in Patients with T2DM Compare to Healthy Controls
| Gene | Haplotypes | T2DM (%) | Controls (%) | Odds Ratio (95% CI) | P-value* |
|---|---|---|---|---|---|
| GTTCG | 0.7962 | 0.9425 | 1.00 | – | |
| GTACG | 0.0963 | 0.0175 | 7.28 (3.15–16.80) | <0.0001 | |
| GTTCA | 0.0575 | 0.0225 | 1.85 (1.04–3.31) | 0.037 | |
| ATTCG | 0.0313 | 0.0075 | 4.46 (1.25–15.87) | 0.022 |
Notes: *Chi-square test with P< 0.05 is considered significant. Global haplotype association p-value: <0.0001.
Figure 5Linkage disequilibrium analysis for SH2B1 gene.
Association Between Single Nucleotides Polymorphisms Within SH2B Gene and T2DM Clinical Factors
| Characteristics | rs1801516 | rs6760993 | rs1219648 | rs2981582 | rs10207245 | rs2373721 | rs661348 |
|---|---|---|---|---|---|---|---|
| Gender* | 0.470 | 0.430 | 0.372 | 0.725 | 0.372 | 0.869 | 0.488 |
| BMI (kg/m2)** | 0.137 | 0.955 | 0.001 | 0.818 | 0.746 | 0.319 | 0.558 |
| HbA1c (%) ** | 0.770 | 0.328 | NA | 0.963 | 0.575 | 0.381 | 0.078 |
| Total cholesterol (mmol/L)** | 0.084 | 0.380 | NA | 0.265 | 0.614 | 0.475 | 0.812 |
| HDL cholesterol (mmol/L)** | 0.151 | 0.466 | NA | 0.006 | 0.676 | 0.553 | 0.916 |
| LDL cholesterol (mmol/L)** | 0.289 | 0.590 | NA | 0.706 | 0.757 | 0.661 | 0.670 |
| Triglyceride (mmol/L)** | 0.911 | 0.765 | NA | 0.812 | 0.554 | 0.400 | 0.829 |
| Creatinine (umol/l)** | 0.217 | 0.760 | 0.861 | 0.304 | NA | 0.803 | 0.850 |
Notes: *Pearson’s chi-squared test was used to determine genotype-phenotype association. **Analysis of variance (ANOVA) was used to determine genotype-phenotype association. P-value <0.05 was considered as significant. NA, not applicable