Polymorphism In Chinese Han Population Research Articles

Establishment of sequence-based typing assay for KIR2DS4 gene and identification of a new allele KIR2DS4*016

To establish a reliable sequence-based typing method for KIR2DS4 and study its allele polymorphism in Chinese Han population. Using PCR-SSP method to detect the positive or negative of KIR2DS4 gene in 222 random Chinese Han individuals, and then using the method of high fidelity and long-fragment PCR-SBT to amplify, sequence and genotype the exons 4 and 5 of KIR2DS4 positive individuals. We successfully amplified the fragment with 3.2 kb length contains exons 4 and 5 of KIR2DS4 and detected the KIR2DS4 allele frequency in Chinese Han population. 209 KIR2DS4 positive individuals were detected, and the positive rate is 94.1%. By sequence-based typing, we identified 12 genotypes and 7 alleles of KIR2DS4. The 6 known alleles and their detection frequency is as follows: KIR2DS4* 00101/011 (180, 81.1%), KIR2DS4* 010 (53, 23.9%), KIR2DS4* 004 (34, 15.3%), KIR2DS4* 003 (15 and 6.8%), KIR2DS4* 006 (2, 0.9%) and KIR2DS4* 015 (1, 0.5%). In this study, we found a new allele, KIR2DS4* 016, with the difference in exon 5 comparing its most similar allele KIR2DS4* 010. In the exon 5 of KIR2DS4* 010, there is a 22bp-deletion, while the exon 5 of KIR2DS4* 016 is normal. This is not a rare allele because it was detected 3 times in studied population and with the frequency of 1.4%. The sequence of the new allele sequence has been submitted to GenBank (accession no.: KC414890) and the IPD -KIR database (submission no.: IWS40001804), and was nominated by WHO nomenclature committee for HLA system. In this study, a sequence-based typing method for KIR2DS4 was established, and the polymorphism data of KIR2DS4 in Chinese Han population was enriched by studying the allele polymorphism and new allele.

Interleukin gene polymorphisms in Chinese Han population with breast cancer, a case-control study.

Cytokines are known as important regulators of the cancer involved in inflammatory and immunological responses. This fact and plethora of gene polymorphism data prompted us to investigate IL1 gene polymorphisms in breast cancer (BC) patients. Totally, 530 patients with BC and 628 healthy control women were studied. The genetic polymorphisms for IL1 were analyzed by Massarray Sequencing method. Three single nucleotide polymorphisms (SNPs) identified in IL1B, IL1R1 gene are thought to influence breast cancer risk. The results of the association between IL-1B, IL1R1 polymorphisms and breast cancer risk have significant. We found that the variant TT genotype of rs10490571 was associated with a significantly increased breast cancer risk (TT vs. CC: OR = 2.82, 95% CI = 1.12–7.08, P = 0.047 for the codominant model). For rs16944 (AG vs. GG: OR = 0.60, 95% CI = 0.41–0.90, P = 0.034 for the codominant model) and rs1143623 (CG vs. CC: OR = 0.65, 95% CI = 0.45–0.94, P = 0.023 for the codominant model) have significant associations were found in genetic models. In conclusion, the present analysis suggests a correlation of polymorphic markers within the IL-1 gene locus with the risk in developing breast cancer. Taken together with our finding that IL1B, IL1R1 gene three SNP are also associated with the risk for the disease, we suggest that inflammation via innate and adaptive immunity contributes to multifactorial hereditary predisposition to pathogenesis of the breast cancer.

ABCB1 3435TT and ABCG2 421CC genotypes were significantly associated with longer progression-free survival in Chinese breast cancer patients.

ObjectiveTo investigate the distribution of ABCB1 C3435T and ABCG2 C421A gene polymorphisms in Chinese Han population and their influences on the susceptibility and prognosis of breast carcinoma.MethodsA total of 200 female subjects were enrolled in this study, comprising 100 breast cancer patients and 100 healthy controls. Carcinoma and para-carcinoma tissues were collected from the breast cancer patients, while peripheral blood was collected from healthy controls. Single nucleotide polymorphisms (SNPs) were detected by the Taqman method. Progression-free survival (PFS) and 5-year survival rate of the patients were calculated.ResultsABCB1 C3435T and ABCG2 C421A polymorphisms were not associated with disease susceptibility and 5-year survival rate in the study population (p>0.05). However, a high mutation rate of both ABCB1 C3435T and ABCG2 C421A (16% and 17%, respectively) was observed in breast cancer tissues. Patients with ABCB1 3435TT genotype or ABCG2 421CC genotype had longer PFS (p<0.05).ConclusionABCB1 3435TT and ABCG2 421CC were significantly associated with longer PFS in Chinese breast cancer patients.

Developing eight SNP-STR markers for DNA mixture detection

SNP-STR marker is a compound marker constituted by a STR marker and a SNP in the flanking sequence. SNP-STR marker has been introduced to improve the discrimination power of STR markers in previous reports. Recently, some researchers have reported that SNP-STR markers performed well in detecting unbalanced DNA mixtures by designing two allele-specific primers. In this study, STR markers were selected from previously reports which had a high polymorphism in Chinese Han population. Then SNP markers with minor allele frequency (MAF) above 0.10 and locate no more than 250bp from the repeat sequence of STR markers were screened from SNP database. Based on these criteria, eight SNP-STR markers were finally selected and amplification refractory mutation system (ARMS-PCR) method was used to achieve allele-specific amplification. 20 samples were used to estimate the polymorphism of SNPs in Chinese Han population. Six of the eight loci had a high polymorphism in SNP (above 0.20) which indicated the potential of discriminating DNA mixtures. Most of the primers target minor DNA at an excess of 100-fold major DNA. However, discrimination power is not high enough using these six loci. Therefore, further studies are necessary in developing more SNP-STR markers.

ASSA13-01-11 The Correlation of the Serum C-Reactive Protein Leve with Its Gene T-757C Polymorphism in Patients with Acute Myocardial Infarction

<h3>Objective</h3> To explore the association of the serum C-reactive protein (CRP) level with the CRP gene T-757C polymorphism and risk of acute myocardial infarction (AMI) in Chinese Han population of Sunan region. <h3>Methods</h3> The CRP gene T-757C polymorphism was genotyped by polymerase reaction restriction-fragment length polymorphism analysis, and the serum CRP level was measured by enzyme-linked immune sorbent assay in 213 AMI patients (AMI group) and 173 subjects without coronary heart disease (CHD) (control group). <h3>Results</h3> ➀In Chinese Han population of Sunan region, there were CRP gene T-757C polymorphisms in patients with AMI and in subjects without CHD; ➁The serum CRP level in AMI patients (5.985/6.527μg/ml) was significantly higher than those in non CHD subjects (3.262/1.356μg/ml) (<i>P</i> &lt; 0.01) and there were still significant differences after adjustment for gender, age, smoking, hypertension, diabetes and dyslipidemia (<i>P</i> &lt; 0.01); ➂In AMI patients, no significant differences were found in the serum CRP level among any genotype (CC, TC or TT) of the CRP gene T-757C (4.069/2.493 pg/ml <i>vs</i> 5.745/6.321 pg/ml <i>vs</i> 6.127/6.629 pg/ml), and there also were no significant differences in the serum CRP level among any genotypes in this locus within the same gender and age (<i>P</i> &gt; 0.05). <h3>Conclusions</h3> The serum CRP level in AMI patients is significantly higher than those in non CHD subjects but not influenced by CRP gene T-757C polymorphism in Chinese Han population of Sunan region.

Lack of association between NR3C1 polymorphism and glucocorticoid resistance in Chinese patients with immune thrombocytopenia

Resistance to glucocorticoids (GCs) is a tricky problem in therapy for immune thrombocytopenia (ITP). As GCs exert their effects through glucocorticoid receptor (GR), being a GR gene, NR3C1 is thought to connect with individual differences in GC responsiveness during GCs treatments. We analyzed the frequency of three novel single nucleotide polymorphisms (SNPs) of NR3C1 in ITP patients and evaluated the role of these genetic variants in GCs therapy. Four hundred and seventy-three patients with ITP and 160 healthy controls were recruited. Patients were allocated into GCs-responsive (n = 358) and -non-responsive group (n = 115). All subjects of the three groups were genotyped by the PCR-RFLP (restriction fragment length polymorphism) method for the BclI, N363S and ER22/23EK polymorphisms. Assess the statistical differences of genotypes between ITP and controls, and those between GCs- responsive and non-responsive groups. In healthy controls, BclI-GG/GC/CC occurred with 0.581/0.35/0.069 frequency. In ITP patients, BclI-GG/GC/CC was found with 0.617/0.353/0.03 frequency. There was no statistically differences between ITP and controls (p = 0.070). In GCs-responsive and -non-responsive group, BclI-GG, GC, CC occurred with frequencies of 0.628/0.352/0.02 and 0.583/0.357/0.061, respectively. No correlations in the variants of BclI was found between the GCs-responsive and -non-responsive group (p = 0.086). Neither N363S nor ER22/23EK polymorphism was observed in all 636 participants. The BclI polymorphism is not related to the response of GCs in patients with ITP. Furthermore, we did not observe N363S and ER22/23EK polymorphism in Chinese Han population.

Replication of Association between Schizophrenia and Chromosome 6p21-6p22.1 Polymorphisms in Chinese Han Population

Chromosome 6p21-p22.1, spanning the extended major histocompatibility complex (MHC) region, is a highly polymorphic, gene-dense region. It has been identified as a susceptibility locus of schizophrenia in Europeans, Japanese, and Chinese. In our previous two-stage genome-wide association study (GWAS), polymorphisms of zinc finger with KRAB and SCAN domains 4 (ZKSCAN4), nuclear factor-κB-activating protein-like (NKAPL), and piggyBac transposable element derived 1 (PGBD1), localized to chromosome 6p21-p22.1, were strongly associated with schizophrenia. To further investigate the association between polymorphisms at this locus and schizophrenia in the Chinese Han population, we selected eight other single-nucleotide polymorphisms (SNPs) distributed in or near these genes for a case-control association study in an independent sample of 902 cases and 1,091 healthy controls in an attempt to replicate the GWAS results. Four of these eight SNPs (rs12214383, rs1150724, rs3800324, and rs1997660) displayed a nominal difference in allele frequencies between the case and control groups. The association between two of these SNPs and schizophrenia were significant even after Bonferroni correction (rs12000: allele A>G, P = 2.50E-04, odds ratio [OR] = 1.27, 95% confidence interval [CI] = 1.12–1.45; rs1150722: allele C>T, P = 4.28E-05, OR = 0.55, 95% CI = 0.41–0.73). Haplotype ATTGACGC, comprising these eight SNPs (rs2235359, rs2185955, rs12214383, rs12000, rs1150724, rs1150722, rs3800324, and rs1997660), was significantly associated with schizophrenia (P = 6.60E-05). We also performed a combined study of this replication sample and the first-stage GWAS sample. The combined study revealed that rs12000 and rs1150722 were still strongly associated with schizophrenia (rs12000: allele G>A, P combined = 0.0019, OR = 0.81; rs1150722: allele G>A, P combined = 3.00E-04, OR = 0.61). These results support our findings that locus 6p21-p22.1 is significantly associated with schizophrenia in the Chinese Han population and encourage further studies of the functions of these genetic factors.

Screening of mtDNA SNPs in Chinese Han population using pyrosequencing

Mitochondrial DNA (mtDNA) single nucleotide polymorphisms (SNPs) have been extensively applied as supplement for HV I and HV II sequencing. They have been proved even more effective for detecting highly degraded samples, hair shaft and bone samples. However, some mtDNA SNPs which had high polymorphisms in database could not be used in Chinese Han population due to ethnic differences. The pyrosequencing (PSQ) technology, including universal primer applications and pooling samples, could reduce assay cost and improved efficiency of screening SNPs. In this study, we aimed to screen a set of mtDNA SNPs which has enough polymorphisms in Chinese Han population. We analyzed 21 candidate SNPs and estimated allelic frequencies using PSQ with pooling samples. Our results revealed that there were nine mtDNA SNPs with enough polymorphisms in Chinese Han population. In conclusion, PSQ was an effective method in screening mtDNA SNPs. A total of nine mtDNA SNPs would be used as candidate markers for forensic purpose.

ASSOCIATION OF THE SERUM LEVELS OF C-REACTIVE PROTEIN WITH ITS GENE POLYMORPHISMS AND ACUTE CORONARY SYNDROME

ASSOCIATION OF THE SERUM LEVELS OF C-REACTIVE PROTEIN WITH ITS GENE POLYMORPHISMS AND ACUTE CORONARY SYNDROME

THE CORRELATION OF THE SERUM C-REACTIVE PROTEIN LEVEL WITH THE C-REACTIVE PROTEIN GENE T-757C POLYMORPHISM AND RISK OF ACUTE MYOCARDIAL INFARCTION

ObjectivesTo explore the association of the serum C-reactive protein (CRP) leve with the CRP gene T-757C polymorphism and risk of acute myocardial infarction (AMI) in Chinese Han population of Sunan...

RELATIONSHIP OF THE SERUM LEUKOTRIENE B4 LEVEL WITH THE RISK OF UNSTABLE ANGINA PECTORIS AND THE ARACHIDONATE 5-LIPOXYGENASE ACTIVATING PROTEIN GENE SG13S114T/A POLYMORPHISM

ObjectivesTo investigate the association of the serum leukotrienes (LT) B4 level with the risk of unstable angina pectoris (UAP) and the arachidonate 5-lipoxygenase activating protein (ALOX5AP) gene SG13S114T/A polymorphism in...

A case-control study of interleukin-12 1188A/C polymorphism in obsessive-compulsive disorder in Chinese population.

Previous studies indicated that the levels of serum interleukin (IL)-12 at baseline were elevated in obsessive-compulsive disorder (OCD) patients compared with control subjects, suggesting that IL-12 maybe involved in the etiopathogenesis of OCD. Therefore, we study the relationship between 1188A/C polymorphism of IL-12(rs3212227) and OCD in Chinese Han population. We genotyped 194 OCD patients and 322 healthy individuals by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), then analyzed the data using case-control association test. No significant differences were found in 1188A/C genotypic and allelic frequencies between OCD cases and controls ( X 2 = 2.12, df = 2, P = 0.35 by genotype; X 2 = 0.005, df = 1, P = 0.94 by allele). Our results suggested that there may be lack of an association between OCD and IL-12 1188A/C polymorphism in Chinese Han population.

MICB polymorphism in a southern Chinese Han population: The identification of two new MICB alleles, MICB∗005:06 and MICB∗026

In this study, we investigated the major histocompatibility complex (MHC) class I chain-related gene B (MICB) allelic variation by sequence-based typing (SBT) in 201 healthy, unrelated Han subjects from Hunan province, southern China. Eleven MICB alleles were observed, among which MICB(∗)005:02 predominated with a frequency of 64.93%. Significant linkage disequilibrium (LD) was observed for 5 HLA-B-MICB and 6 MICA-MICB haplotypes. Compared with a northern Chinese Han population, several MICB-containing haplotypes appeared to be highly specific to this southern Chinese Han population. Two new MICB alleles, MICB(∗)005:06 and MICB(∗)026, were identified. Aligned with MICB(∗)005:02, MICB(∗)005:06 has a synonymous T replacement at nucleotide 762 in exon 4; MICB(∗)026 has probably arisen from MICB(∗)004:01 through a single nucleotide substitution from G to A at position 826 in exon 4, leading to an amino acid change from glutamic acid to lysine at codon 253. HLA-A(∗)02-C(∗)01-B(∗)46-MICA(∗)010-MICB(∗)005:02-DRB1(∗)09 was the most prevalent six-locus haplotype with a frequency of 8.49%. HLA-A(∗)30-C(∗)06-B(∗)13:02-MICA(∗)008:01-MICB(∗)005:02-DRB1(∗)07 appeared to be a conserved extended haplotype. Our results provide new information about MICB genetic polymorphism in Chinese Han populations, and will inform future studies of the potential role of MICB in allogeneic organ transplantation and disease susceptibility in related ethnic groups.

Racial difference in aldose reductase C-106T genetic polymorphism and association with essential hypertension.

To investigate the distribution of aldose reductase (AR) C-106T genetic polymorphism in Chinese Han population and its association with the risk for essential hypertension (EH). The AR C-106T polymorphism was genotyped in 148 Chinese EH patients and 137 controls by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). The genotype distribution between groups was contrasted by Χ(2)- test and the degree of genetic association was evaluated by 95% confidence interval (CI). Frequency of the variant AR C-106T allele was 13.9% (95% CI: 11.2%-16.6%) in the controls, which was significantly lower than that in the Japanese (18.4% in 712 individuals, P=0.0063), the Australians (37.9% in 240 individuals, P<0.0001) and the Brazilians (34.7% in 62 individuals, P<0.0001). The frequency of AR C-106T allele was 11.7% (95% CI: 7.9%-15.5%) in the EH patients. No significant difference in the allele frequency was observed between the EH patients and the controls (P=0.147). There is obvious racial difference in the distribution of AR C-106T polymorphism. The polymorphism is not associated with the risk for EH.

106-P: The Analysis of MICA Allele and Transmembrane Region Polymorphism in Chinese Han Population

106-P: The Analysis of MICA Allele and Transmembrane Region Polymorphism in Chinese Han Population

Absence of TLR4 Asp299Gly and Thr399Ile Polymorphisms in Chinese Han Population With Type 2 Diabetes

This study was performed to detect the association between the Asp299Gly and Thr399Ile polymorphisms of the TLR4 gene and type 2 diabetes in the Chinese Han population. The study included 856 unrelated individuals with type 2 diabetes and 672 healthy controls. The polymorphisms of the TLR4 gene were examined through denaturing high-performance liquid chromatography. Neither the Asp299Gly nor the Thr399Ile polymorphism was detected in any of the diabetic and healthy subjects. Our finding indicates the Asp299Gly and Thr399Ile polymorphisms of the TLR4 gene are very rare in the Chinese Han population.

MICA polymorphism in a northern Chinese Han population: The identification of a new MICA allele, MICA*059

The major histocompatibility complex class I chain-related gene A (MICA) in humans, located 46 kb centromeric to human leukocyte antigen (HLA)-B, is highly polymorphic. In addition to its primary role in immune surveillance, recent data highlight the importance of MICA in organ transplantation and in susceptibility to some diseases. In this study, 104 healthy, unrelated Han subjects recruited from central Inner Mongolia Autonomous Region, northern China, were investigated by sequence-based typing and fragment analysis for MICA allelic variation, MICA-HLA-B linkage disequilibrium, and HLA-A-Cw-B-MICA haplotypic diversity. Nineteen MICA alleles were observed, the most frequent of which were MICA*00801, MICA*010, MICA*00201, MICA*00901, and MICA*045, with gene frequencies of 23.08%, 18.75%, 12.02%, 12.02%, and 8.17%, respectively. The peculiarity in HLA-B-MICA haplotypic configurations was also uncovered. In particular, there was a clear-cut dichotomy between MICA*00801 and MICA*045 in their linkage to members of HLA-B*13 lineage, which was frequently represented in this population. A new MICA allele, MICA*059, was identified, which appeared to be evolutionarily linked to MICA*045. Haplotype HLA-A*30-Cw*06-B*1302-MICA*00801, previously not reported in other populations, was found with a frequency of 8.65% in this population. Our results provide new data about MICA genetic polymorphism in Chinese Han populations, which will form the basis for future studies of the potential role of MICA in allogeneic organ transplantation and disease susceptibility in related ethnic groups.

Relationship between polymorphism of platelet membrane glycoprotein Ⅲa and coronary heart disease with blood-stasis syndrome in Chinese Han population

To investigate the genotype distributions of PLA1/PLA2 polymorphism in Chinese Han population from Beijing and Hebei Province and to study the correlation between the platelet membrane glycoprotein IIIa polymorphism and coronary heart disease (CHD) or CHD with blood-stasis syndrome. A total of 110 CHD patients with blood-stasis syndrome and 102 CHD patients with non-blood stasis syndrome were enrolled in the case-control study. Thirty-nine healthy volunteers were included as normal control. Syndrome differentiation in traditional Chinese medicine was performed in all of the patients. The genomic DNA was isolated from the whole blood and the locus typing of PLA was determined by TaqMan probe technology. The locus typing of PLA1/PLA2 gene polymorphism was exclusively PLA1/PLA1 (TT) in healthy people, CHD patients and CHD patients with blood-stasis syndrome, while GPIIIa PLA1/PLA2 (TC) and PLA2/PLA2 (CC) were not found in all the selected objects. Statistical analysis of locus typing for other PLA1/PLA1 polymorphisms was not made in the study. The PLA1/PLA2 polymorphism of membrane glycoprotein IIIa is not a risk factor for CHD patients or CHD patients with blood-stasis syndrome in Chinese Han population, and the related genes may be some other gene polymorphisms.

Protective role of interlekin-1 alpha gene polymorphism in Chinese Han population with sporadic Parkinson’s disease

Parkinson’s disease is the second most common neurodegenerative disorders after Alzheimer’s disease in the elderly. Abundant evidence showed that proinflammatory factors were involved in the pathogenesis of sporadic Parkinson’s disease (SPD). Interleukin-1 (IL-1) is a cytokine that plays an important role in neurodegenerative disease. Previous association studies between genetic polymorphisms of IL-1 alpha and PD have showed conflicting results and no such study was done in Chinese. We recruited 533 SPD patients and 530 controls in Chinese Han population to investigate the association of IL-1α C-899T allele and risk for PD. Real-time PCR was used to detect the polymorphism, and multiple logistic regression, Chi square test and survival analysis were performed to explore the association. The distribution of IL-1α alleles was significantly different between the cases and controls, and the T allele was associated with a reduced risk of PD (OR: 0.72, 95%CI: 0.54–0.97, ρ = 0.033). However, survival analysis showed that the T allele did not delay the onset age of PD (T allele vs. non-T allele log rank: χ 2 = 0.14, p = 0.70). Our data suggest that the T allele carriers have less inclination to have PD in Chinese Han population.

Relationship between polymorphisms of plasminogen activator inhibitor-1 promoter gene and pulmonary thromboembolism in Chinese Han population

To determine the prevalence of polymorphisms in the plasminogen activator inhibitor-1 (PAI-1) promoter 4G/5G polymorphisms in Chinese Han population and to investigate whether they are associated with pulmonary thromboembolism (PTE). Samples of peripheral venous blood were collected from 101 patients with PTE diagnosed by high probability of lung ventilation/perfusion scan and/or multi-slice CT pulmonary angiography (CTPA) as well as medical history and clinical manifestations, 67 males and 34 females, aged 48 +/- 15, and 101 age and sex-matched healthy controls from the same geographic area as controls. The genome DNA was extracted from the whole blood using potassium iodide-phenol-chloroform method. Polymerase chain reaction (PCR), denaturing high performance liquid chromatography (DHPLC), and sequence analysis were used to screen the single nucleotide polymorphisms and the genotype distribution of -675 4G/5G located in the promoter region of the PAI-1 gene. The frequencies of the allele 4G of PAI-1 gene in the controls were 0.495, significantly lower than in the PTE patients (0.733, chi(2) = 24.060, P < 0.01). The frequencies of the allele 5G of PAI-1 gene in the controls were 0.505, significantly higher than that in the PET patients. The genotype frequency of 4G4G of the PET patients was 57.4%, significantly higher than that of the controls (30.7%, P = 0.000). The genotype frequencies of 4G5G and 5G5G of the PET patients were 31.7% and 10.9% respectively, not significantly different from those of the controls (37.6 and 31.7% respectively). The presence of 4G allele of PAI-1 gene was found to be a greater risk factor for PTE. In comparison with the controls, the OR of 4G4G + 4G5G, 4G4G, and 4G5G in the PET patients were 3.794 (1.786 - 8.060), 5.443 (2.416 - 12.260), and 2.450 (1.067 - 5.623) respectively with the P values of 0.001, 0.000, and 0.035 respectively. The 4G/5G and 4G/4G genotypes are associated with the pathogenesis of PET.T.