亲缘群体单体型推断的研究进展

随着高通量的基因分型技术的出现,越来越多的单核苷酸多态性( single nucleotide polymorphism,SNP)可被检测。基因组研究中,单体型分析已被运用到SNP位点与复杂性状的关联分析中。现有的单体型推断方法包括基于非亲缘群体的方法,DNA pool样本方法和系谱资料方法。不过家庭及亲缘数据可为单体型推断提供很重要的信息,利用这些信息进行单体型推断会增加准确性。如今对亲缘群体单体型推断的算法和软件已有很多报道。该文的目的是回顾这些算法、软件以及它们的优缺点和适用的群体类型,同时探讨仍然存在的问题和面临的挑战。     

北京汉族人群ROR2基因SNPs等位基因及单体型频率研究

目的为病因学研究中ROR2基因SNPs的确定和分析提供依据。方法利用Hap loview软件对HapM ap数据库中北京汉族人群（CHB）ROR2基因SNPs基因型数据进行分析。结果和讨论ROR2基因404个SNPs中,103个（25.5%）SNPs为纯合基因型,在中国人群中进行研究时,应避免选择这些SNPs作为遗传标记。263个合格SNPs中,MAF高于10%的SNPs为189个,占71.9%,有足够的标记可供选择。利用263个合格SNPs,本研究共确定77个标签SNPs,构建了5个单体域,各单体域均以前两种单体型为主,累计频率在68.1%-92.3%之间。结论对北京汉族人群ROR2基因SNPs数据进行的全面分析,为该人群中基因与相关疾病的病因学研究打下了基础,也为其它基因的初步研究提供了方法。     

Tim-3基因多态性与乙型肝炎病毒感染转归的相关性

目的:研究中国汉族人群T淋巴细胞免疫球蛋白黏蛋白-3(Tim-3)基因标签单核苷酸多态性(tagSNP)rs11741184C/G和rs13170556A/G位点多态性与乙型肝炎病毒(HBV)感染转归的关系.方法:采用SNaPshot技术检测996例慢性乙型肝炎患者及301例急性HBV感染自限性恢复患者Tim-3基因rs11741184和rs13170556tagSNP位点的多态性,计算其基因型和等位基因分布频率及单体型分布频率.结果:Tim-3基因tagSNPrs11741184位点基因型CC、CG、GG在急性乙型肝炎患者中的分布频率分别为84.39%(254/301)、15.28%(46/301)、0.33%(1/301),在慢性乙型肝炎组中分布频率分别为86.04%(857/996)、13.65%(136/996)、0.3%(3/996),两组比较无统计学差异;Tim-3基因tagSNP rs13170556基因型AA、GA、GG在急性乙型肝炎患者中的分布频率分别为68.77%(207/301)、28.57%(86/301)、2.66%(8/301),慢性乙型肝炎组患者中的分布频率分别为68.07%(6...     

Association between the dopamine transporter gene and the inattentive subtype of attention deficit hyperactivity disorder in Taiwan

Attention deficit hyperactivity disorder (ADHD) is a common heritable childhood psychiatric disorder. Since methylphenidate, one of the main drugs used to treat ADHD, targets the dopamine transporter, this study examined the linkage disequilibrium (LD) structure of the dopamine transporter gene (DAT1) and investigated whether the DAT1 gene was associated with ADHD. This Chinese family-based association sample consisted of 273 DSM-IV diagnosed ADHD probands and their family members (n = 906). We screened 15 polymorphisms across the DAT1 gene, including 14 single nucleotide polymorphism (SNP) markers and the variable number of tandem repeat (VNTR) polymorphism in 3′-untranslated region (3′UTR). Calculations of pairwise LD revealed three main haplotype blocks (HBs): HB1 (intron 2 through intron 6), HB2 (intron 8 through intron 11), and HB3 (3′UTR). Family-Based Association Tests showed that no allele was significantly more transmitted than expected to the ADHD children for these 15 markers. Haplotype-Based Association Tests showed that a haplotype rs27048 (C)/rs429699 (T) was significantly associated with the inattentive subtype (P = 0.008). In quantitative analyses, this haplotype also demonstrated significant association with the inattention severity (P = 0.012). Our finding of the haplotype rs27048 (C)/rs429699 (T) as a novel genetic marker in the inattentive ADHD subtype suggests that variation in the DAT1 gene may primarily affect the inattentive subtype of ADHD.     

云南汉族FZD3基因多态性及其单倍型与精神分裂症关联研究

目的 探讨FZD3基因上中下游三位点rs2241802、rs2323019、rs352203在精神分裂症病理生理机制中的可能作用.方法 采用横断面病例-对照研究.患者组为153例云南汉族精神分裂症患者.正常对照组为与患者组性别、年龄、文化程度匹配的100名云南汉族健康人.对患者组用阳性和阴性症状量表(PANSS)评定病情的严重程度.运用PCR-RFLP技术对FZD3基因的三位点进行多态性检测,并运用连锁不平衡分析,用单因素方差分析比较组间差异.结果 患者组的FZD3基因rs2241802、rs2323019、rs352203位点基因型频率和等位基因频率在精神分裂症患者样本中差异无统计学意义(P＞0.05).汉族样本中rs2241802-rs2323019的D'=0.021,r2=0.000;rs2241802-rs352203的D'=0.033,r2=0.001;rs2323019-rs352203的D'=0.057,r2=0.002,且A-A-C单倍型频率在精神分裂症患者组及对照组间差异有统计学意义(P=0.032),G-A-C单倍型频率在精神分裂症患者组及对照组间差异有统计学意义(P=0.024).患者组的FZD3基因rs2241802、rs2323019、rs352203三位点各个基因型在PANSS量表中各项因子分、总分的相关性均无统计学意义(P＞0.05).结论 FZD3基因rs2241802、rs2323019、rs352203 多态性可能与云南汉族精神分裂症无关,而A-A-C单倍型和G-A-C单倍型可能与云南汉族精神分裂症相关.     

The VEGF +405 G>C 5' untranslated region polymorphism and risk of PCOS: a study in the South Indian Women

Purpose

The aim of this study was to investigate the association between two common single nucleotide polymorphisms (SNPs) in the vascular endothelial growth factor (VEGF) gene (−460C/T and +405G/C) and polycystic ovary syndrome (PCOS) risk in south Indian women.

Methods

This study involves clinically confirmed PCOS patients (n = 126) and non-PCOS controls (n = 130) of south Indian origin (Dravidian linguistic group). Genotyping of the VEGF gene −460C/T and +405G/C SNPs were performed by PCR and sequencing analysis. Haplotype frequencies for multiple loci and the standardized disequilibrium coefficient (D'') for pairwise linkage disequilibrium (LD) were assessed by Haploview Software.

Results

The frequencies of +405G/G genotype (P = 0.03) and +405G alleles (P = 0.006) were significantly higher in patients compared to controls. Whereas the genotype and allele frequencies of −460C/T SNP were not significantly different between patients and controls. In addition, LD analysis revealed no significant difference between patients and controls.

Conclusion

Our findings suggest that the VEGF +405G/C polymorphism may constitute an inheritable risk factor for PCOS in south Indian women.     

Relationship between interleukin-6 polymorphism and susceptibility to chronic hepatitis B virus infection

AIM:To identify the relationship between tag single nucleotide polymorphisms(tag SNPs) of interleukin-6(IL-6) gene and susceptibility to chronic hepatitis B virus(HBV) infection in a Han Chinese population.METHODS:We performed a case-control study of501 Chinese patients with chronic HBV infection and301 self-limiting HBV-infected individuals as controls.Genomic DNA was isolated from the whole blood of all subjects using phenol/chloroform with MaXtract highdensity tubes. Tag SNPs were identified using genotype data from the panel(Han Chinese in Beijing) of the phase II HapMap Project. Four tag SNPs in IL-6(rs17147230A/T,rs2066992G/T,rs2069837A/G and rs2069852A/G) were genotyped by the Multiplex Snapshot technique. The genotype and allele frequencies were calculated and analyzed.RESULTS:Five haplotypes were involved in the analysis,with frequencies higher than 0.03. One of the haplotypes,TTAA,was significantly different between the two groups. Overall haplotype P values were:ATAA,P = 0.605,OR(95%CI) = 1.056(0.860-1.297); TGAG,P = 0.385,OR(95%CI) = 1.179(0.813-1.709); TGGG,P = 0.549,OR(95%CI) = 1.087(0.827-1.429); TTAA,P = 0.004,OR(95%CI) = 0.655(0.491-0.873); TTAG,P = 0.266,OR(95%CI) = 1.272(0.832-1.944). However,the four SNPs showed no significant genotype/allele associations with susceptibility to chronic HBV infection. Overall allele P values were:rs17147230,P = 0.696,OR(95%CI) = 1.041(0.850-1.276); rs2066992,P = 0.460,OR(95%CI)= 1.090(0.868-1.369); rs2069837,P = 0.898,OR(95%CI) = 0.983(0.759-1.274); rs2069852,P = 0.165,OR(95%CI) = 0.859(0.693-1.064). Overall genotype P values were:rs17147230,P = 0.625; rs2066992,P= 0.500; rs2069837,P = 0.853; and rs2069852,P =0.380.CONCLUSION:The four tag SNPs of IL-6 gene may be associated with susceptibility to chronic HBV infection in the Han Chinese population.     

HLA-B*07 is a high risk allele for familial cervical cancer

Aim: The purpose of this study was to investigate 50 women from eight families with familial cervical cancer in Wufeng County, Hubei Province, China, a region with a high incidence of cervical cancer. Eighty-nine healthy women, of similar age, location and ethnicity, were selected as a control group. Methods: Blood samples were collected from both groups, and HLA-A, HLA-B, and HLA-DRB1 genotypes were profiled with the Multi-Analyte Profiling system (xMAP) (Luminex HLA-SSO) using a WAKFlow HLA typing kit. Results were analyzed with Luminex HLA typing software and showed good stability, reproducibility and specificity. Results: We found several high risk alleles in women with familial cervical cancer, that associated with the highest risk being HLA-B*07 (OR = 8.7, 95% CI = 1.8-41.1). Conclusions: HLA-B*07 is a high risk allele for cervical cancer, and has strong potential for use as a molecular biomarker.