Analysis of pharmacogenomic very important pharmacogenomic variants: CYP3A5, ACE, PTGS2 and NAT2 genes in Chinese Bai population.

Aim: Our study aimed to screen the genotype frequencies of very important pharmacogenomic (VIP) mutations and identify their differences between Bai and other populations. Materials & methods: We selected 66 VIP variants from PharmGKB (www.pharmgkb.org/) for genotyping. χ2 test was used to identify differences in loci between these populations and FST values of Bai and the other 26 populations were analyzed. Results: Our study showed that the frequencies of SNPs of CYP3A5, ACE, PTGS2 and NAT2 differed significantly from those of the other 26 populations. At the same time, we found that some VIP variants may affect the metabolism of drugs and the genetic relationship between the Bai population and East Asian populations was found to be the closest. Conclusion: By comparing the genotype frequencies of different populations, the loci with significant differences were identified and discussed, providing a theoretical basis for individualized drug use in the Bai ethnic population.

Massively parallel sequencing of STRs using a 29-plex panel reveals stutter sequence characteristics.

Massively parallel sequencing of forensic STRs simultaneously provides length-based genotypes and core repeat sequences as well as flanking sequence variations. Here, we report primer sequences and concentrations of a next-generation sequencing (NGS)-based in-house panel covering 28 autosomal STR loci (CSF1PO, D1GATA113, D1S1627, D1S1656, D1S1677, D2S441, D2S1776, D3S3053, D5S818, D6S474, D6S1017, D6S1043, D8S1179, D9S2157, D10S1435, D11S4463, D13S317, D14S1434, D16S539, D18S51, D18S853, D20S482, D20S1082, D22S1045, FGA, TH01, TPOX, and vWA) and the sex determinant locus Amelogenin. Preliminary evaluation experiments showed that the panel yielded intralocus- and interlocus-balanced sequencing data with a sensitivity as low as 62.5 pg input DNA. A total of 203 individuals from Yunnan Bai population were sequenced with this panel. Comparative forensic genetic analyses showed that sequence-based matching probability of this 29-plex panel reached 2.37 × 10-29 , which was 23 times lower than the length-based data. Compound stutter sequences of eight STRs were compared with parental alleles. For seven loci, repeat motif insertions or deletions occurred in the longest uninterrupted repeat sequences (LUS). However, LUS and non-LUS stutters co-existed in the locus D6S474 with different sequencing depth ratios. These results supplemented our current knowledge of forensic STR stutters, and provided a sound basis for DNA mixture deconvolution.

Association between vitamin D receptor gene polymorphisms and idiopathic hypocitraturia in a Chinese Bai population.

Idiopathic hypocitraturia (IH) is a risk factor for urolithiasis. IH is associated with vitamin D receptor (VDR) gene single nucleotide polymorphisms (SNPs) in a Chinese Han population. However, this association between VDR SNPs and IH has not been recapitulated in a Chinese Bai population. The aim of this study is to investigate the association between VDR SNPs and IH in a Chinese Bai population. A total of 320 participants comprising of 200 Chinese Bai patients with IH and 120 Chinese Bai control participants with normal urinary citrate level were enrolled for this study. The VDR SNPs rs7975232, rs2228570, rs731236 and rs1544410 were detected by Sanger sequencing, and the association between these SNPs and the presence of IH in the Chinese Bai population was analyzed. The prevalence of VDR SNPs rs7975232 allele A and rs2228570 genotype TT was significantly higher in patients than in controls (p < 0.0125, after Bonferroni correction). The haplotype TCGC was a protective factor in the Chinese Bai population who otherwise might suffer from IH, while the haplotype TTGA was a risk factor. VDR SNPs rs731236 and rs1544410 have a linkage disequilibrium value of 0.811. VDR SNPs rs7975232, rs2228570, and haplotypes TCGC, TTGA are associated with IH in a Chinese Bai population.

Association of interleukin-6 gene -572C/G polymorphisms with type 2 diabetic retinopathy / 国际眼科杂志(Guoji Yanke Zazhi)

@#AIM: To investigate the relationship of IL-6 gene -572C/G polymorphism in patients with type 2 diabetic retinopathy(T2DM)and diabetic retinopathy(DR)in Dali Bai population.<p>METHODS: The polymorphisms of IL-6 gene -572C/G was analyzed by polymerase chain reaction-restriction fragment polymorphisms assay(PCR-RFLP)in 150 patients with T2DM \〖NDR(without DR)group 57 cases, NPDR(with non-proliferative diabetic retinopathy)group 77 cases, PDR(with proliferative diabetic retinopathy)group 16 cases\〗 and 100 healthy control group in Dali Bai population. The genotypes frequency, allele frequency of IL-6-572C/G gene and clinical data were compared between groups. The statistics software SPASS22.0 was used for statistical analysis.<p>RESULTS: The genotype and allele frequencies of IL-6 gene -572C/G between groups were compared statistically significantly(<i>P</i><0.05); the incidence of T2DM in healthy control subjects with C allele significantly decreased in comparison with the carriers of G allele(<i>OR</i>=1.182, <i>95% CI</i>: 1.059-1.319, <i>P</i>=0.004); the incidence of DR in T2DM with G allele significantly increased in comparison with the carriers of C allele(<i>OR</i>=1.667, 95% <i>CI</i>: 1.195-2.326, <i>P</i>=0.003), but there was no statistical difference between PDR group with NPDR group for -572C/G polymorphism(<i>P</i>>0.05). There was statistical significant between T2DM group, NPDR + PDR and control groups in fasting blood glucose, triglycerides, body mass index(<i>P</i><0.05), PDR group was compared with NPDR group only in difference between fasting plasma glucose(<i>P</i><0.05). The hypertension in individuals suffering from T2DM increased in comparison with not combing hypertension(<i>OR</i>=3.730, 95% <i>CI</i>: 2.060-6.754, <i>P</i>=0.000), and suffering from DR increased obviously(<i>OR</i>=3.997, 95%<i>CI</i>:2.099-7.612, <i>P</i>=0.000). The clinical data showed no significant difference(<i>P</i>>0.05)among different genotypes.<p>CONCLUSION: These results suggest that the -572C/G polymorphism in the promoter of IL-6 gene is associated with T2DM and DR in Dali Bai population, but the clinical data is not coordinative risk factor. G allele is a risk factor in the pathogenesis of T2DM and DR, but not for the progress in NPDR to PDR process, C alleles is a protective factor T2DM and DR. Hypertension, fasting blood glucose, triglycerides, body mass index were risk factors for T2DM and DR, fasting blood glucose condition in DR progress has an important role.

Association of interleukin-6 gene -572C/G polymorphisms with type 2 diabetic retinopathy / 国际眼科杂志(Guoji Yanke Zazhi)

@#AIM: To investigate the relationship of IL-6 gene -572C/G polymorphism in patients with type 2 diabetic retinopathy(T2DM)and diabetic retinopathy(DR)in Dali Bai population.<p>METHODS: The polymorphisms of IL-6 gene -572C/G was analyzed by polymerase chain reaction-restriction fragment polymorphisms assay(PCR-RFLP)in 150 patients with T2DM \〖NDR(without DR)group 57 cases, NPDR(with non-proliferative diabetic retinopathy)group 77 cases, PDR(with proliferative diabetic retinopathy)group 16 cases\〗 and 100 healthy control group in Dali Bai population. The genotypes frequency, allele frequency of IL-6-572C/G gene and clinical data were compared between groups. The statistics software SPASS22.0 was used for statistical analysis.<p>RESULTS: The genotype and allele frequencies of IL-6 gene -572C/G between groups were compared statistically significantly(<i>P</i><0.05); the incidence of T2DM in healthy control subjects with C allele significantly decreased in comparison with the carriers of G allele(<i>OR</i>=1.182, <i>95% CI</i>: 1.059-1.319, <i>P</i>=0.004); the incidence of DR in T2DM with G allele significantly increased in comparison with the carriers of C allele(<i>OR</i>=1.667, 95% <i>CI</i>: 1.195-2.326, <i>P</i>=0.003), but there was no statistical difference between PDR group with NPDR group for -572C/G polymorphism(<i>P</i>>0.05). There was statistical significant between T2DM group, NPDR + PDR and control groups in fasting blood glucose, triglycerides, body mass index(<i>P</i><0.05), PDR group was compared with NPDR group only in difference between fasting plasma glucose(<i>P</i><0.05). The hypertension in individuals suffering from T2DM increased in comparison with not combing hypertension(<i>OR</i>=3.730, 95% <i>CI</i>: 2.060-6.754, <i>P</i>=0.000), and suffering from DR increased obviously(<i>OR</i>=3.997, 95%<i>CI</i>:2.099-7.612, <i>P</i>=0.000). The clinical data showed no significant difference(<i>P</i>>0.05)among different genotypes.<p>CONCLUSION: These results suggest that the -572C/G polymorphism in the promoter of IL-6 gene is associated with T2DM and DR in Dali Bai population, but the clinical data is not coordinative risk factor. G allele is a risk factor in the pathogenesis of T2DM and DR, but not for the progress in NPDR to PDR process, C alleles is a protective factor T2DM and DR. Hypertension, fasting blood glucose, triglycerides, body mass index were risk factors for T2DM and DR, fasting blood glucose condition in DR progress has an important role.

Polymorphism Investigation on 15 STR Loci of Yunnan Bai Population / 昆明医科大学学报

Objective The study aimed to investigate 15 autosomal loci polymorphism(such as D3S1358 and TPOX)in Nujiang Bai nationality,in order to construct genetic basic data of Bai population and provide a foundation for population study and forensic cases. Methods Venous blood was collected from 124 unrelated Bai individuals in Nujiang,Yunnan province. DNA was extracted by classical organic solvent extraction. PCR technique was applied to amplify the sequence of autosomal loci. The products were measured by electrical fluoroscopy. The gene frequencies of 15 STR loci were investigated and genetic polymorphisms were analyzed. ResultsGene polymorphisms of 15 STR loci were detected and the distributions of genotype conformed with Hardy-Weinberg balance law(P > 0.05). The cumulative match probability(CPM)was 4.869×10-17,the cumulative excluding probability(CPE)was 99.999 99%,and the combined power of discrimination(CDP)was 99.999 97%. ConclusionThe 15 STR loci used in this study were highly polymorphic informative content in Bai population and could be applied to population study and forensic practice.

Association study of clusterin polymorphism rs11136000 with late-onset Alzheimer's disease in Bai population / 中华行为医学与脑科学杂志

Objective To explore the association between clusterin(CLU) gene rs11136000 poly-morphism and late-onset Alzheimer's disease ( LOAD) in Bai population from Dali Bai Autonomous Prefec-ture of Yunnan Province.Methods A case-control study including 109 LOAD patients and 120 normal con-trols matched for age,sex and level of education was taken in Dali Bai population.Polymerase chain reaction (PCR) and single nucleotide polymorphism (SNP) site testing were used to detect genotype and allele fre-quency of CLU SNP rs11136000.SPSS 17.0 was applied to analyze the data.Result ①The different fre-quency ( C:65.60%,T:34.40%,CC:38.53%,CT:54.13%,TT:7.34%) of CLU SNP rs11136000 genotypes and alleles distribution in Bai between LOAD patients and healthy controls showed no statistical significance (χ2=1.529, P=0.216;χ2=2.805, P=0.246) .②The serum total cholesterol ( TC) of LOAD patients was significantly higher than that in that of control group( t=2.508, P=0.013) .Conclusion The results suggest that CLU rs11136000 polymorphism may not be the susceptible gene of LOAD,and high serum total choles-terol is more common in LOAD patients.