SNP rs220028和STR HUMARA位点甲基化标记的时空稳定性研究

目的调查印记SNPrs220028和X-STRHUMARA位点甲基化标记的时空稳定性,评估其实用价值。方法采用甲基化敏感性限制酶消化后PCR技术,对SNPrs220028和STRHUMARA位点进行甲基化等位基因特异性分型。实验涉及10例不同年龄男女个体的血液、心、脑、肝、肾等主要组织以及不同程度降解的组织标本。结果SNPrs220028和STRHUMARA的甲基化等位基因特异性分型不受检材年龄、组织种类和一般程度降解的影响。结论SNPrs220028和X-STRHUMARA位点的甲基化标记稳定性良好,有实际应用价值。     

基于飞行时间质谱技术研究手足口病人群IL-22／IL-22RA1基因单核苷酸多态性

目的探讨Th22细胞相关性细胞因子IL-22／IL-22RA1基因单核苷酸多态性（SNP）与手足口病易感性及其转归的关系。方法采用病例-对照研究方法,选取2012年4月至9月深圳市第三人民医院收治并确诊的手足口病住院患者296例为病例组,其中轻症手足口病患者178例,重症患者118例,对照组为同期在该医院健康体检儿童155例。应用飞行时间质谱（timeoffightmassspectrum,TOF—MS）生物芯片技术,检测IL-22／IL-22RAl基因共4个SNP位点基因型（rs2227473、rs2227483、rs3795299、rs34379702）,对SNP进行Hardy．Weiberg平衡检测,并计算各SNP位点在不同人群中等位基因频率,筛选与手足口病易感性、预后相关的SNP位点。结果纳入研究的4个SNP位点的基因型分布均处于遗传平衡状态。人组人群中IL-22的基因rs2227473位点存在GG、GA和AA基因型,重症手足口病组rs222743位点A等位基因频率（13．14％,31／236）显著高于轻症组（6．18％,22／356）,差异有统计学意义（x^2=8．424,P〈0．001,A=2．296,95％CI=1．294—4．074）。对于EV71相关性手足口病而言,重症组A等位基因频率（19．64％,22／112）显著高于轻症组（7．41％,4／54）,差异有统计学意义（x^2=4．129,P=0．042,A=3．056,95％CI=0．997—9．368）。结论IL-22基因rs2227473位点多态性与手足口病转归密切相关,尤其是EV71相关性手足口病。     

G72基因与抑郁症的关联研究

目的探讨抑郁症与G72基因多态性的关系，以及是否有混合家族史的抑郁症其G72基因多态性有无区别。方法应用聚合酶链反应技术分别检测符合《中国精神障碍分类与诊断标准》的100例元混合家族史抑郁症、50例有混合家族史抑郁症、86名正常对照的G72基因的单核苷酸多态性rs947267、rs2181953，并进行关联分析。结果（1）女性无混合家族史抑郁症组与对照组rs947267基因型及等位基因分布频率，差异均有统计学意义（P=0．017、P=0．008），基因型A／A、等位基因A、C的OR值分别为0．300（P=0.010）、0．456（P=0．008）、2．195（P=0．008），而男性差异均无统计学意义（P〉0．05）；（2）不同性别无混合家族史抑郁症组与对照组rs2181953基因型及等位基因分布，差异均无统计学意义（P〉0．05）；（3）不同性别有混合家族史抑郁症组与对照组rs947267、rs2181953基因型及等位基因分布，差异均无统计学意义（P〉0.05）。结论G72基因多态性可能与女性无混合家族史的抑郁症患者存在关联，其中rs947267的C等位基因是危险因子。     

西北地区汉族人群FCAMR基因单核苷酸多态性及单体型分析

为研究西北地区汉族人群IgAIg MFc高亲和力受体(Fc receptor IgAIg Mhigh affinity,FCAMR/Fcα/μR)基因单核苷酸多态性(SNP)及单体型的频率。我们采用聚合酶链反应后直接测序方法,对西北地区79(男45,女34)名没有亲缘关系的汉族健康个体FCAMR基因,T549C(rs1856746),A457G(rs3813952),G421A(rs1340232)和A298G(rs3813950)4个SNP位点进行基因分型。用SHEsis软件分析FCAMR基因的单体型频率。本研究发现西北地区汉族人群中T549C(rs1856746)位点,等位基因频率C是38.6%,T是61.4%;A457G(rs3813952)位点,等位基因频率G是5.7%,A是94.3%;G421A(rs1340232)位点,等位基因频率A是17.1%,G是82.9%,A298G(rs3813950)位点,等位基因频率G是4.4%,A是95.6%。西北地区汉族人群中FCAMR基因T549C(rs1856746)、A457G(rs3813952)、G421A(rs1340232)和A298G(rs3813950)4个位点构成的3种主要单体型率(频率>10%)T/A/G/A是60.5%,C/A/A/A是17.1%和C/A/G/A是16.7%。本研究分析了西北地区汉族人群FCAMR基因T549C(rs1856746)、A457G(rs3813952)、G421A(rs1340232)和A298G(rs3813950)4个SNP位点的基因型频率、等位基因频率和单体型频率,为研究该地区FCAMR基因单核苷酸多态性与免疫反应以及相关疾病如IgA肾病易感性之间的相关性提供研究基础。     

汉族人群一氧化氮合酶基因三个位点单核苷酸多态性与静息心率相关性研究

目的研究汉族人群的一氧化氮合酶（nitric oxide synthase，NOS）基因NOS3-922A／G和NOS3 894G／T以及NOS2-1173C／T3个位点的单核苷酸多态性（single nucleotide polymorphisms，SNP）与静息心率的相关性。方法随机选择自然人群个体211名为研究对象，获取其静脉血白细胞基因组DNA。用等位基因特异性引物PCR技术检测NOS3-922A／G、NOS3 894G／T、NOS2-1173C／T的SNP。结果NOS3-922A／G的AA、AG、GG，NOS3 894G／T的GG、GT和TT与NOS2-1173C／T的CC、CT和TT各基因型频率分布，均符合Hardy-Weinberg平衡（P〉0．05）。NOS3-922A／G各等位基因AA、AG、GG静息心率比较，发现携带从等位基因者静息心率较GG者高，差异有统计学意义（P〈0．01）。NOS3 894G／T各等位基因静息心率比较，发现携带GG等位基因者静息心率较TT者高，差异有统计学意义（P〈0．05）。NOS2-1173C／T各等位基因的静息心率比较，差异均无统计学意义（P〉0．05）。结论NOS3-922A／G与NOS3 894G／TSNP突变型其静息心率较野生型降低，提示上述位点SNP可能与其静息心率有相关性。     

四个E-选择素基因的多态性与哈尼族原发性高血压相关性研究

目的探讨E－选择素基因rs3917408G／T、rs5361A／C、rs5368C／T和rs3917429C／T等4个错义突变与哈尼族原发性高血压的关系。方法采用PCR测序技术，对云南哈尼族172例原发性高血压患者和133例正常对照的E－选择素基因的rs3917408G／T、rs5361A／C、rs5368C／T和rs3917429C／T突变进行检测。结果在哈尼族原发性高血压组，rs3917408T、rs5361C、rs5368T和rs39t7429T等位基因频率分别为2％、7％、28．8％和6．1％，正常对照组相应的等位基因频率分别为4％、4．9％、21．8％和1．1％，其中原发性高血压组rs3917429位点T等位基因频率显著高于正常对照组（P〈0．01），其余突变点两组之间的等位基因频率比较差异均无显著性（P〉0．05）。结论E－选择素基因rs3917429位点T等位基因与哈尼族原发性高血压相关。     

红细胞补体受体1单核苷酸多态性与骨关节结核易感性的关联研究

目的探讨红细胞补体受体1(CR1)单核苷酸多态性(SNP)与骨关节结核(bone and joint tuberculosis)发病的关系。方法收集110例骨关节结核患者(实验组)和104例健康体检者(对照组)的外周血样本,采用单碱基延伸的PCR技术和DNA测序方法对CR1基因3个SNP位点(rs11118167C/T、rs2274567G/A、rs4844600G/A)进行多态性检测,分析2组CR1表达水平、2组CR1基因各SNP位点基因型对于CR1水平差异、CR1基因各SNP位点基因型、等位基因的分布差异及其与骨关节结核患病风险的关系。结果 2组rs4844600G/A基因型和等位基因分布的差异有统计学意义(P0.05)。CR1基因rs4844600G/A位点GG基因型携带者患骨关节结核的风险为非携带者的2.262倍(95%CI:1.275~4.013),其等位基因G携带者患病风险为非携带者的1.565倍(95%CI:1.058~2.314)。rs11118167C/T、rs2274567G/A这2个SNP位点与骨关节结核的患病风险无关(P0.05)。健康对照组CR1的平均荧光前强度为50.87±14.526,高于骨关节结核组的38.95±12.794,差异有统计学意义(t=-6.379,P0.001)。骨关节结核组中,CR1基因rs11118167 C/T、rs2274567 G/A和rs4844600 G/A位点多态性与骨关节结核患者红细胞CR1水平无关(P0.05)。健康对照组中,rs11118167 C/T位点CC、CT基因型携带者的红细胞CR1水平低于TT基因型者;rs2274567G/A位点GG、GA基因型携带者的CR1水平低于AA基因型者(P0.05)。结论骨关节结核患者红细胞免疫功能降低,CR1基因rs4844600G/A位点与骨关节结核发病相关,CR1基因rs4844600G/A位点GG基因型与骨关节结核患者CR1水平低无关。     

单纯性先天性心脏病易感区域12q13内HOXC簇基因单核苷酸多态单倍型分析

目的 在人类单纯性先天性心脏病（congenital heart disease，CHD）易感区12q13内，选取HOXC4、HOXC5、HOXC6基因内4个已知单核苷酸多态（single nucleotide polymorphism，SNP）G7471T、C16476T、A17860G、A36130G，检测其在单纯性CHD患者和正常人群中的分布情况，分析各个SNP位点及所构成单倍型与单纯性CDH的相关性。方法 应用限制性片段长度多态性和变性高效液相色谱法结合测序，分析108例单纯性先天性心脏病患者及200名正常人4个SNP位点基因型；应用列联表法统计分析患者组和对照组各SNP位点基因型及等位基因频率；应用PHASE软件构建单倍型并统计分析患者组及对照组单倍型频率是否存在差异。结果 C16476T未检测到多态；位于HOXC5基因3’侧翼序列的SNP位点A17860G等位基因频率及基因型频率在患者组和对照组中的分布差异有统计学意义，患者组G等位基因频率明显高于对照组（P〈0．05）；单倍型分析可见4种单倍型在患者组和对照中的分布频率有统计学意义（P〈0．01）；G7471／G17860／G36130和G7471／G17860／A36130为人群中常见单倍型，与对照组相比，患者组中G7471／G17860／G36130、G7471／G17860／A36130两种单倍型频率较高。结论 HOXC5基因3’侧翼序列的SNP位点A17860G与单纯性CHD有明显的相关性，具有G等位基因的人发生CHD的危险性相对增高；3个SNP位点所构成的单倍型有一定意义，可能与单纯性CHD易感基因相连锁。     

中国蒙古族人MBL基因启动子区SNP的研究

目的 研究中国蒙古族人群甘露聚糖结合凝集素(MBL)基因启动子区单核苷酸多态性(SNP)。方法 抽提人外周血白细胞基因组DNA，建立SSP-PCR及分子灯塔实时荧光PCR技术，检测MBL基因启动子区SNP位点-550(G／C，称H/L等位基因)、-220(G／C，X／Y等位基因)和 4(C／T，P／Q等位基因)，分析其单倍型及基因型频率。结果 从82人中检出等位基因型LYP／LYP4例(4．9％)，HYP／LYQ5例(6．1％)，LYP／LYQ35例(42．9％)，LXP／LXP1例(1．2％)，LYQ／LYQ11例(13．4％)，LXP／LYQ14例(17．1％)，HYP／LYP2例(2．4％)，HYP／LXP1例(1．2％)，HYP／HYP9例(11．0％)。结论 中国蒙古族人群MBL基因启动子区SNP等位基因型以LYP／LYQ、LXP／LYQ、LYQ／LYQ和HYP／HYP为主。     

中国白族人群MBL基因SNP及其单倍型与基因型的研究

目的：研究中国云南白族人甘露聚糖结合凝集素（MBL）基因单核苷酸多态性（SNP）及其单倍型与基因型。方法：对MBL基因启动子区SNP位点-550G／C（称H／L等位基因）、-221C／G（X／Y）、＋4C／T（P／Q）已明确的白族DNA样本，采用序列特异性引物．多聚酶链反应技术检测结构基因第一外显子点突变CGT52TGT、CCC54GAC和CCA57CAA（分别称为D、B、C等位基因，野生型即A），并分析MBL基因的单倍型与基因型。结果：只检出GGC54GAC点突变，其频率为0．100；检出的5种单倍型及其频率是：HYPA0．250、LXPA0．107、LYQA0．407、LYPA0．135、LYPB0．100；各基因型及其频率为：LYPA／LYPA0．043、LXPA／LYQA0．143、LYPA／LYPB0．014、HYPA／LYQA0．086、LYPA／LYQA0．157、HYPA／LYPA0．014、LYPB／LYQA0．143、HYPA／LYPB0．043、LXPA／LXPA0．014、HYPA／LXPA0．043、LYQA／LYQA0．143、HYPA／HYPA0．157。结论：中国白族人群MBL基因存在GGC54GAC点突变，单倍型以LYQA和HYPA为主，基因型则多见LYPA／LYQA、HYPA／HYPA、LX—PA／LYQA、LYPB／LYQA和LYQA／LYQA。     

Alteration of methylation status in archival DNA samples: A qualitative assessment by methylation specific polymerase chain reaction

DNA methylation is an epigenetic mechanism that regulates gene expression, which also facilitates genomic imprinting. Genomic imprinting is responsible for differential expression of genes based on parent of origin. Altered methylation of parental alleles results in imprinting disorders diagnosed by methylation specific polymerase chain reaction (MS-PCR) technique. With increasing evidence of genes under epigenetic influence, methylation studies are extensively performed on archival samples. To evaluate effect of storage and storage conditions on DNA methylation, a systematic MS-PCR based analysis was planned on an imprinted gene, SNRPN, located on chromosome 15q11.2. It was assessed by MS-PCR on fresh, 4 −20, and −80°C stored DNA samples for different time periods for systematic evaluation of methylation status. Technical factors like type of sample processing, method of DNA isolation, primer region polymorphism, sample heterogeneity were also evaluated. DNA methylation was observed to be altered for SNRPN gene after storage at −80°C from 2 months onwards. Long-term storage of DNA at −80°C results in altered DNA methylation status. This may lead to false MS-PCR diagnosis of imprinting disorders. Our proof of concept study should be followed with quantitative validation since the findings have critical implications in the present era of biobanking.     

Asthma and atopy are associated with chromosome 17q21 markers in Chinese children

Background:  Single-nucleotide polymorphism (SNP)-based genome-wide association study revealed that markers on chromosome 17q21 were linked to childhood asthma but not atopy in Caucasians, with the strongest signal being detected for the SNP rs7216389 in the ORMDL3 gene. Such association was unknown in Chinese. This study delineated the allele and genotype frequencies of 10 SNPs at chromosome 17q21, and investigated the relationship between these SNPs and asthma and plasma IgE in southern Chinese children.
Methods:  Asthmatic children and non-allergic controls were recruited from pediatric clinics. Their plasma total and aeroallergen-specific IgE concentrations were measured by immunoassay. Ten SNPs on 17q21 region were genotyped by multiplex SNaPshot™, and their genotype associations with asthma traits analyzed using multivariate regression.
Results:  315 patients and 192 controls were enrolled. The allele frequency for C allele of rs7216389 varied significantly from 0.232 in our controls, 0.389 in Han Chinese to 0.536 in Caucasians. Asthma diagnosis was associated with rs11650680 and five other SNPs including rs7216389 ( P  =   0.019–0.034), whereas atopy was associated only with rs11650680 ( P  =   0.0004). Linear regression revealed the covariates for plasma total IgE to be significant for rs11650680 ( P  =   0.008–0.0002). Haplotypic associations were found with atopy and increased plasma total IgE, with the respective odds ratios and 95% confidence intervals for TTTCCGTT haplotype to be 0.21 and 0.09–0.52 ( P  =   0.0002) and 0.41 and 0.18–0.90 ( P  =   0.025).
Conclusion:  Childhood asthma and atopy are associated with chromosome 17q21 in Chinese, but such association may involve genes other than ORMDL3 in this region.     

用5′端核酸外切酶法检测基因印迹--编码区单核苷酸多态性

目的 建立一种快速、高效确认人类基因印迹的新方法。方法 以一对荧光标记探针，用5’端核酸外切酶法结合逆转录—PCR，分别在人传代淋巴细胞系基因组DNA和cDNA水平对一已知印迹基因即核内小核糖核蛋白N(small nuclear ribonucleotide protein N，SNRPN)中的一编码区单核苷酸多态性(coding single nucleotide polymorphism，cSNP)位点rs705(C／T)进行SNP分型。结果 等位基因分辨结果显示SNRPN只表达一个等位基因。这一结果通过以逆转录—PCR为基础的限制性片段长度多态性分析，得到了进一步证实。家系分析确认被表达的等位基因均来自父亲，这与以往的报道一致。结论 cSNP是用5’端核酸外切酶法检测基因印迹的理想标记。     

Scavenger Receptor Class B Type 1 Gene rs5888 Single Nucleotide Polymorphism and the Risk of Coronary Artery Disease and Ischemic Stroke: A Case-Control Study

Background: Our previous studies have showed that the rs5888 single nucleotide polymorphism (SNP) in Scavenger receptor class B type 1 (SCARB1) gene is associated with serum lipid levels in the general Chinese populations. The present study was undertaken to detect the associations between rs5888 SNP and the risk of coronary artery disease (CAD) and ischemic stroke (IS).Methods: A total of 1,716 unrelated subjects (CAD, 601; IS, 533; and healthy controls, 582) were included in this study. Genotyping of the rs5888 SNP were determined by polymerase chain reaction and restriction fragment length polymorphism.Results: The genotypic frequencies of SCARB1 rs5888 SNP were different between CAD patients and controls, the subjects with TT genotype had high risk of CAD (OR = 1.76, P = 0.038 for TT vs. CC; and OR = 1.75, P = 0.036 for TT vs. CC/CT). There was no significant association between genotypes and the risk of IS. Further analysis showed that the subjects with TT genotype in the total population had lower levels of high-density lipoprotein cholesterol than the subjects with CC/CT genotypes (P < 0.05), the subjects with TT genotype in controls but not in CAD or IS patients had higher levels of serum LDL-C and ApoB than those with CC genotype (P < 0.05 for each).Conclusions: The present study suggests that the SCARB1 rs5888 SNP influences serum lipid levels, and is associated with the risk of CAD.     

Do mutations in DNMT3A/3B affect global DNA hypomethylation among benzene‐exposed workers in Southeast China?: Effects of mutations in DNMT3A/3B on global DNA hypomethylation

Global DNA hypomethylation is commonly observed in benzene‐exposed workers, but the underlying mechanisms remain unclear. We sought to discover the relationships among reduced white blood cell (WBC) counts, micronuclear (MN) frequency, and global DNA methylation to determine whether there were associations with mutations in DNMT3A/3B. Therefore, we recruited 410 shoe factory workers and 102 controls from Wenzhou in Zhenjiang Province. A Methylated DNA Quantification Kit was used to quantify global DNA methylation, and single nucleotide polymorphisms (SNPs) in DNMT3A (rs36012910, rs1550117, and R882) and DNMT3B (rs1569686, rs2424909, and rs2424913) were identified using the restriction fragment length polymorphism method. A multilinear regression analysis demonstrated that the benzene‐exposed workers experienced significant global DNA hypomethylation compared with the controls (β = −0.51, 95% CI: −0.69 to −0.32, P < 0.001). The DNMT3A R882 mutant allele (R882H and R882C) (β = −0.25, 95% CI: −0.54 to 0.04, P = 0.094) and the DNMT3B rs2424909 GG allele (β = −0.37, 95% CI: −0.70 to −0.03, P = 0.031) were significantly associated with global DNA hypomethylation compared with the wild‐type genotype after adjusting for confounding factors. Furthermore, the MN frequency in the R882 mutant allele (R882H and R882C) (FR = 1.18, 95% CI: 0.99 to 1.40, P = 0.054) was higher than that of the wild‐type. The results imply that hypomethylation occurs due to benzene exposure and that mutations in DNMTs are significantly associated with global DNA methylation, which might have influenced the induction of MN following exposure to benzene. Environ. Mol. Mutagen. 58:678–687, 2017. © 2017 Wiley Periodicals, Inc.     

Association of NKG2D genetic polymorphism with susceptibility to chronic hepatitis B in a Han Chinese population

Natural killer (NK) cells are important antiviral effectors of innate immunity because of their contribution to virus elimination. NK cell‐mediated immunological reaction to hepatitis B virus (HBV) infection depends on a fine balance between inhibitory and activating receptors. The aim of the study was to investigate genetic polymorphisms in NK cell receptors (NKR)—KLRD1 (CD94), KLRK1 (NKG2D), KLRC4 (NKG2F), and KLRC1 (NKG2A)—to evaluate the association of NKR genetic polymorphisms with susceptibility to chronic hepatitis B in a Han Chinese population. Twelve single nucleotide polymorphisms (SNPs), including rs2302489 in CD94; rs2255336, rs2617160, rs7980470, rs 2734565, and rs17513986 in NKG2D; rs2617170, rs17549004, and rs3825295 in NKG2F; rs2734414, rs7301582, and rs2734440 in NKG2A, were selected in the present study. SNP genotyping was undertaken in 500 Han Chinese patients (285 patients with chronic hepatitis B and 215 patients who cleared HBV spontaneously) by a polymerase chain reaction‐restriction fragment length polymorphism (PCR‐RFLP) and by the TaqMan method. Single marker association analysis was conducted and the SNP rs2617160 with a TT genotype in NKG2D was associated significantly with an increased risk of chronic hepatitis B (P = 0.044; OR = 1.49; 95% CI = 1.01–2.19). Haplotype analysis with multiple loci indicated that there was no significant association between the haplotypes of the NKR genes and susceptibility to chronic hepatitis B. The SNP rs2617160 in NKG2D associated with susceptibility to chronic hepatitis B in a Han Chinese population. J. Med. Virol. 82:1501–1507, 2010. © 2010 Wiley‐Liss, Inc.     

Influence of the TNFSF4 rs1234315 polymorphism in the susceptibility to systemic lupus erythematosus and rheumatoid arthritis

ObjectivesThe tumour necrosis factor superfamily 4 (TNFSF4) is a candidate gene for autoimmune diseases. We investigated the relationship of this gene with systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA) in a Chinese Guangxi population.MethodsA total of 294 patients with SLE, 210 with RA, and 282 healthy controls were genotyped for single nucleotide polymorphism (SNP) rs1234315 using the polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP). The potential functional effects of the SNP were predicted by in silico analysis.ResultsStatistically significant associations with SLE and RA were detected at rs1234315, both by allele analysis (odds ratio 1.47, 95% confidence interval 1.17–1.86, p = 0.001; odds ratio 1.49, 95% confidence interval 1.15–1.92, p = 0.002; respectively), and genotype analysis (p = 0.003 and p = 7.000 × 10⁻⁵, respectively). The Akaike’s information criterion (AIC) values indicated that the recessive model may serve as the best-fit model for the SNP for SLE and RA.ConclusionOur results provided support for TNFSF4 rsl234315 as a SLE and RA susceptibility locus in a Chinese Guangxi population.     

GLI3基因与单纯性马蹄内翻足的关联分析及其突变筛查

目的对GLU基因与单纯性马蹄内翻足进行关联分析和突变筛查，探讨GLU基因与单纯性马蹄内翻足的相关性。方法应用限制性片段长度多态性分析技术，分析84个单纯性马蹄内翻足核心家系中GLI3基因内两个单核苷酸多态（single nucleotide polymorphisms, SNP）位点的基因型，并应用ETDT软伯统计分析各SNP位点基因型与单纯性马蹄内翻足的关联；应用变性梯度凝胶电泳技术对103例单纯性马蹄内翻足患者GLI3基因的第9至12外显子进行突变筛查。结果经ETDT分析，位于GLI3基因第4外显子的cSNP rs846266差异无统计学意义（χ^2=3．3582，P〉0．05）；第14外显子的cSNP rs929387差异有统计学意义（χ^2=7．2466，P〈0．05），在单纯性马蹄内翻足核心家系中存在传递不平衡；发现1例患者及其母亲的第9外显子有108（G→A）的同义点突变。结论GLI3基因与单纯性马蹄内翻足相关，其第9至12外显子可能并非该病的突变热点。