精神分裂症与磷脂酶A2基因多态性关系

目的 探讨中国北方汉族人群磷脂酶A2,IVC亚组基因(PLA2G4C基因)多态性与精神分裂症的遗传关联性.方法 采用PCR和连接酶检测反应(LDR)法,在201个精神分裂症患者核心家系中检测PLA2G4C基因上的3个单核苷酸多态性(SNPs)(rs2307279、rs2162886和rs891014),对结果进行单倍型相对风险分析(HRR)、传递不平衡分析(TDT)和与临床症状的关联性分析.结果 各位点在精神分裂症病例组和对照组中基因型分布均符合Hardy-weinberg平衡.HRR和TDT分析表明,检测的3个SNPs位点与精神分裂症关联差异无统计学意义.临床症状关联性分析结果显示,rs2307279等位基因多态性与阳性症状自责自罪妄想相关联(X2=5.755.P:0.016),rs2162886和rs891014等位基因多态性与思维逻辑性障碍和病前人格相关联(X2=6.777,P=0.009;X2=11.113,P=0.001;X2=12.468,P=0.002;X2=9.924,P=0.007);rs2162886等位基因多态性与阳性症状怪异行为相关联(X2=5.409,P=0.020).结论 PLA2G4C基因多态性与精神分裂症阳性临床症状相关联.     

GABRA4基因多态性与儿童孤独症的相关性研究

目的:通过对GABRA4基因上单核苷酸多态性位点rs2229940的检测,探讨GABRA4基因多态性与儿童孤独症的关系。方法:在中国汉族孤独症49个核心家系(孤独症患者49人,父母94人)及正常对照人群(158人)中,应用聚合酶链反应-限制性酶切片段多态性(PCR-RFLP)技术,测定了本位点的等位基因和基因型,进行以核心家系为基础的传递不平衡检验(TDT)及病例对照的关联研究。结果:病例对照关联研究中,rs2229940多态位点等位基因频率(χ2=4.128,P=0.040)及基因型(χ2=9.438,P=0.009)比较均发现差异有统计学意义。结论:提示GABRA4基因可能与孤独症有关联。     

人类13q32精神分裂症易感基因的研究

目的　在中国人群中探讨人类 13q32区域内与精神分裂症相关的易感基因位点。 方法　以中国汉族精神分裂症患者和他们的健康父母双亲组成的 91个核心家系为研究对象。采用聚合酶链式反应 -限制性片段长度多态性 (PCR -RFLP)方法对 13q32区域内分别位于STK2 4位点和GPC6位点上的 2个单核苷酸多态性 (SNPs)rs1886 0 89和rs2 892 6 79进行检测。利用拟合优度卡方检验分析基因型分布频率是否符合Hardy -Weinberg平衡定律 ,单体型相对风险分析 (HRR)和传递不平衡检验 (TDT)用于数据基因型分析。结果　 (1)STK2 4 /GPC6基因型频率分布符合Hardy -Weinberg平衡 (P >0 0 5 ) ;(2 )HRR结果显示 ,rs1886 0 89和rs2 892 6 79两个基因多态性与精神分裂症无关联 (P >0 0 5 )。TDT结果表明 ,父母和受累子女之间不存在显著的传递不平衡 (P >0 0 5 ) ,即杂合父母传递给受累子女的等位基因无差异 ;(3)STK2 4rs1886 0 89等位基因与精神分裂症的两种临床症状真性幻听和情感淡漠相关 (χ2 =6 0 0 5df=1P <0 0 5 ;χ2 =6 0 74df=2P <0 0 5 )。GPC6rs2 892 6 79等位基因与精神分裂症的思维贫乏相关(χ2 =6 0 94df=2P <0 0 5 )。结论　STK2 4rs1886 0 89和GPC6rs2 892 6 79基因多态性与精神分裂症的 3种临床症状相关联     

还原叶酸载体1基因A80G多态性与非综合征型唇腭裂的相关性研究

目的探讨还原叶酸载体(RFC)1基因A80G多态性与非综合症型唇腭裂(NSCL/P)相关性。方法收集97个核心家庭和104个对照家庭,用聚合酶链式反应-限制性片段长度多态性方法,进行RFC1基因A80G位点多态性检测,用人群关联研究分析、NSCL/P核心家庭的TDT、HHRR、FBAT等检验统计分析。结果人群关联研究分析,子代、父亲、母亲病例组和对照组之间基因型和等位基因的分布差异无显著性(P>0.05)。AG基因型相对于AA基因型的比值比OR(95%CI)、P值分别为子代0.87(0.44～1.70)、0.657;父亲1.09(0.54～2.21)、0.788;母亲1.63(0.79～3.36)、0.152。GG基因型相对于AA基因型的OR(95%CI)、P值分别为子代0.48(0.19～1.23)、0.094;父亲0.93(0.38～2.23)、0.850;母亲1.30(0.46～3.67)、0.584。G基因相对于A基因的OR(95%CI)、P值分别为子代1.22(0.78～1.94)、0.386;父亲1.02(0.64～1.61)、0.945;母亲0.91(0.58～1.41)、0.660。携带有突变基因G并不能增加患NSCL/P的危险。NSCL/P核心家庭分析,TDT检验中传递G等位基因给患病子代的为40次,传递A等位基因的为71次,等位基因A比突变等位基因G更易传递给患病子代(χ2=8.658,P<0.05;HHRR检验χ2=10.31,P<0.05;FBAT检验Z=2.942,P<0.05)。结论利用核心家庭资料进行统计分析的结果则认为RFC1基因A80G位点变异存在传递不平衡现象,这与NSCL/P发病危险之间存在有一定的关联关系,等位基因A可能与NSCL/P的高危显性有关系。     

TGFA基因多态性与NSCL/P的遗传易感性

目的:探讨中国汉族人TGFA基因的多态性对非综合征性唇腭裂的遗传易感性的作用。方法:76例核心家庭和60例正常对照儿童的TGFA基因型,采用病例对照研究和传递不平衡检验进行分析。结果:病例对照研究结果表示:(2χ=7.77,P<0.05),TDT(2χ=5.26,P<0.05))。结论:TGFA C2等位基因在NSCL/P中存在连锁不平衡,TGFA基因多态性可能是中国汉族人NSCL/P的遗传易感性因素。     

NLGN4X基因3'UTR区多态性与孤独症关系的家系研究

【目的】 探讨NLGN4X基因与中国汉族儿童孤独症是否存在相关性,查寻中国汉族儿童孤独症的易感基因。 【方法】 选取NLGN4X基因3'UTR区两个多态性位点rs5916269和rs3810686作为遗传标记,采用直接测序法对92个孤独症核心家系的276名成员进行基因型测定,并进行传递不平衡检验(TDT)和单倍型相对危险度(HRR)分析。 【结果】 TDT检验及HRR分析均显示儿童孤独症与rs5916269遗传标记位点不存在传递不平衡(TDT χ²=0.385,P=0.620;HRR χ²=0.345,P=0.557);与rs3810686遗传标记位点存在传递不平衡(TDT χ²=6.368,P=0.015;HRR χ²=5.470,P=0.019)。 【结论】 NLGN4X基因rs5916269位点与中国汉族儿童孤独症无关;rs3810686位点与中国汉族儿童孤独症相关,NLGN4X基因可能是孤独症的易感基因。     

母亲糖代谢基因多态性与胎儿神经管畸形的发病风险

目的 探索母亲糖代谢相关基因的单核苷酸多态性与胎儿神经管畸形发病风险之间的关系.方法 采用病例对照研究方法.病例组为191名生育过无脑畸形、脊柱裂或脑膨出患儿的妇女;对照为按地区和末次月经日期1∶1匹配的健康足月新生儿的母亲.对11个已知的调节体内糖稳态和胰岛素分泌的候选基因共12个多态性位点进行了检测.采用Cochran-Armitage趋势卡方检验和logistic回归,分析母亲基因型与胎儿神经管畸形及其亚型之间的关联.结果 LEPR(rs1137100)在脊柱裂和脑膨出组(A等位基因相较于G等位基因)差异均有统计学意义,其调整后的OR值分别为2.66(95 % CI:1.06~6.64)和6.22(95 % CI:1.37~28.18).未发现其他的位点与神经管畸形发病风险存在关联.结论 LEPR多态性位点rs1137100的变异与胎儿脊柱裂和脑膨出发病风险存在关联.     

神经管畸形儿及其父母还原叶酸载体基因多态性的 FBAT关联研究

目的：探讨神经管畸形（neural tube defects, NTDs）儿及其父母的还原叶酸载体基因（reduced folate carrier gene, RFC1）A80G多态性在NTDs发生危险中的作用,为探讨NTDs遗传易感标记物提供流行病学依据。方法：应用聚合酶链反应-限制性片段长度多态性（PCR?鄄RFLP）技术,检测104例NTDs儿及其父母和100例健康对照儿及其父母的RFC1 A80G多态性,利用病例-父母对照研究中传递/不平衡检验（TDT检验）和以家系为基础的关联检验（FBAT检验）分析NTDs儿的父母RFC1基因A80G多态性与NTDs发生危险的关联,及其在子代中传递的作用强度。结果：患儿父母均为杂合子GA/GA的比例高达36.36%,NTDs患儿成为纯合子GG的概率为25%时具有统计学意义（P＜0.05）,表明患儿接受父母遗传的G等位基因的概率均为25%,并有发生NTDs危险的可能。NTDs的TDT检验结果显示,患儿父母传递等位基因G的危险性是传递等位基因A危险性的1.56 倍（95%CI：1.07~2.28）,认为该基因在亲代和NTDs子代间存在传递失衡现象。FBAT检验中,不论显性模型还是隐性模型,均未发现等位基因G与NTDs的发生危险存在关联,该结果与上述病例-父母对照研究TDT检验结果不一致。结论：虽然TDT检验中G等位基因与NTDs发生危险有关,但FBAT检验未发现G等位基因与NTDs发生危险存在关联,应进一步加大核心家系数量验证该结果。     

注意缺陷多动障碍与多巴胺转运体基因的关联分析

目的 分析多巴胺转运体基因3′端40bp可变数串联重复多态性与注意缺陷多动障碍之间的关系.方法 运用聚合酶连反应和可变数串联重复多态性分析技术对西安地区汉族人群中54例符合美国精神障碍诊断和统计手册第4版诊断标准的注意缺陷多动障碍儿童(n=54)及其父母(n=108)和正常对照组(n=66)进行多巴胺转运体基因3′端40bp可变数串联重复多态性检测,采用病例对照研究和核心家系关联分析(HRR和TDT)等统计方法进行注意缺陷多动障碍与多巴胺转运体基因多态性的关联分析.结果 所测人群中多巴胺转运体的40bp可变数串联重复多态性表现出7～11倍重复的5种等位基因,其中最常见的等位基因为10倍重复的480bp片段,占90.6%.共检出6种基因型,其中最常见的基因型为480bp/480bp,占82.1%.各基因型频率和等位基因频率在注意缺陷多动障碍组与对照组和核心家系中的分布均无显著性差异(均P>0.05).基因型为非480bp/480bp型在Conners-T教师问卷品行、多动、注意分散、多动指数和行为总分均高于基因型480bp/480bp,但无显著性差异(P>0.05).对54个注意缺陷多动障碍核心家系进行HRR和TDT关联分析,未显示注意缺陷多动障碍和多巴胺转运体基因存在关联.结论 在西安地区汉族人群中多巴胺转运体基因与注意缺陷多动障碍之间无显著性关联,多巴胺转运体基因多态性中的10倍重复等位基因可能不是注意缺陷多动障碍的遗传危险因素.     

病例同胞对照设计

目的介绍病例同胞对照设计的研究设计及统计分析方法,并对实际资料进行统计分析.方法以亚甲基四氢叶酸还原酶基因C677T突变与冠心病连锁研究为实例,采用同胞-传递不平衡检验（s-TDT）和同胞组不平衡检验（SDT）等方法进行统计分析.结果采用s-TDT分析,统计量Z=0.27,P〉0.05;采用SDT分析,x^2=0.31,P〉0.05.提示受累子代与非受累子代T等位基因分布差异无统计学意义.结论病例同胞对照设计使用患者同胞作为对照,避免了人群分层现象,可以用来检测基因与疾病之间的关联或连锁.     

胞浆型磷脂酶A2家族基因多态性与精神分裂症的关联性研究

目的 探讨中国北方汉族人群胞浆型磷脂酶A2(cPLA2)家族基因多态性与精神分裂症的遗传关联性.方法 采用聚合酶链反应(PCR)和连接酶检测反应(LDR)方法,在201个精神分裂症患者核心家系中检测cPLA2家族基因上的10个单核苷酸多态性(SNPs),对结果进行单倍型相对风险分析(HRR)、传递不平衡分析(TDT)、单倍型分析和多位点联合分析.结果 各位点在精神分裂症病例组和对照组中基因型分布均符合Hardy-Weinberg平衡.HRR和TDT分析表明,检测的10个SNPs位点与精神分裂症无关联性(P＞0.05).单倍型分析结果显示,由同一染色体上各位点组成的单倍型与精神分裂症均无关联性(P＞0.05).多位点联合作用分析显示,rs2162886与rsl668589,rs891014与rsl668589,rs2307279与rs7542180位点的联合作用与精神分裂症相关联(χ²=6.913,P=0.032;χ²=8.393,P=0.015;χ²=8.447,P=0.038).结论 cPLA2家族基因中存在多个与精神分裂症关联的易感位点.     

还原叶酸载体基因多态性与神经管畸形关联的父母-病例对照研究

目的对神经管畸形（NTDs）发病危险和还原叶酸载体基因（RFC1）A80G多态性进行关联研究，为寻找NTDs的遗传易感标志物提供流行病学依据。方法采用RFLP—PCR方法．对104例NTDs儿及其父母和99名正常儿童及其父母的外周血DNA进行RFC1第80位SNP检测，对核心家庭基因型进行病例对照研究，对NTDs杂合子父母G等位基因进行传递不平衡检验（TOT）。结果NTDs儿G等位基因频率高于对照儿，OR值为1．64（95％CI：1．08～2．49）；GG基因型的患儿发生NTDs危险高于AA基因型（OR=2．56，95％CI：1．04～6．36）；TDT结果显示，RFC1等位基因G与NTDs之间存在关联（x^2=5．2364，P〈0．05），携带G等位基因发生NTDs的危险是非携带者的1．56倍（95％CI：1．07～2．28）。结论发现在中国人群中RFC1基因多态性与NTDs存在关联，初步表明该基因G等位基因可能是NTDs发生的遗传易感基因之一。     

Genomic scanning and the transmission/disequilibrium test: Analysis of error rates

A multi-allelic extension of the transmission/disequilibrium test (TDT) was applied to quantitative data from GAW10 Problem 2A by using thresholds to define affection status. Every one of 367 marker loci was screened. It was found that TDT results at neighboring loci are uncorrelated in these data (where the markers are in linkage equilibrium). It was also found that the chi-square statistics for both tests are larger than they should be so that the probability of false linkage detections is increased. Alternative approaches to the chi-square should be considered for assessing statistical significance. Results at marker D5G15 were strong, probably because of linkage without association. © 1997 Wiley-Liss, Inc.     

Power comparisons between the TDT and two likelihood-based methods

We compare the statistical power of the transmission disequilibrium test (TDT) with that of two likelihood-based linkage tests, the classical LOD score and a modified LOD score in which a linkage disequilibrium (LD) parameter is incorporated into the likelihood (LD-LOD). We hypothesize that, when LD is present, the LD-LOD will have the greatest power of the three tests because the TDT breaks a multiplex pedigree into triads, and the LOD score has previously been shown to have lower power when LD is present but not accounted for. We test this hypothesis using a simulation study in which we generate affected sib-pair (ASP) pedigrees under a range of genetic models, varying the genotypic relative risk (GRR) from 6 to 16. Because the likelihood-based tests require that a genetic model be specified, we compare the tests under two scenarios. First, we assume the true genetic model in the analysis, and second, we compare the tests when the LD-LOD (LOD) is maximized over two wrong genetic models. For the generating models we considered, we find that the LD-LOD has greater power than the TDT even when the genetic models is mis-specified and the results corrected for multiple tests. Extreme differences occur under the multiplicative and dominant models, for which the difference in power is as high as 40% at complete LD. The LOD score provides the lowest power in the presence of LD for the range of GRR considered here.     

A robust TDT-type association test under informative parental missingness

Many family-based association tests rely on the random transmission of alleles from parents to offspring. Among them, the transmission/disequilibrium test (TDT) may be considered to be the most popular statistical test. The TDT statistic and its variations were proposed to evaluate nonrandom transmission of alleles from parents to the diseased children. However, in family studies, parental genotypes may be missing due to parental death, loss, divorce, or other reasons. Under some missingness conditions, nonrandom transmission of alleles may still occur even when the gene and disease are not associated. As a consequence, the usual TDT-type tests would produce excessive false positive conclusions in association studies. In this paper, we propose a novel TDT-type association test which is not only simple in computation but also robust to the joint effect of population stratification and informative parental missingness. Our test is model-free and allows for different mechanisms of parental missingness across subpopulations. We use a simulation study to compare the performance of the new test with TDT and point out the advantage of the new method.     

Informative-transmission disequilibrium test (i-TDT): combined linkage and association mapping that includes unaffected offspring as well as affected offspring

To date, there is no test valid for the composite null hypothesis of no linkage or no association that utilizes transmission information from heterozygous parents to their unaffected offspring as well as the affected offspring from ascertained nuclear families. Since the unaffected siblings also provide information about linkage and association, we introduce a new strategy called the informative-transmission disequilibrium test (i-TDT), which uses transmission information from heterozygous parents to all of the affected and unaffected offspring in ascertained nuclear families and provides a valid chi-square test for both linkage and association. The i-TDT can be used in various study designs and can accommodate all types of independent nuclear families with at least one affected offspring. We show that the transmission/disequilibrium test (TDT) (Spielman et al. [1993] Am. J. Hum. Genet. 52:506-516) is a special case of the i-TDT, if the study sample contains only case-parent trios. If the sample contains only affected and unaffected offspring without parental genotypes, the i-TDT is equivalent to the sibship disequilibrium test (SDT) (Horvath and Laird [1998] Am. J. Hum. Genet. 63:1886-1897. In addition, the test statistic of i-TDT is simple, explicit and can be implemented easily without intensive computing. Through computer simulations, we demonstrate that power of the i-TDT can be higher in many circumstances compared to a method that uses affected offspring only. Applying the i-TDT to the Framingham Heart Study data, we found that the apolipoprotein E (APOE) gene is significantly linked and associated with cross-sectional measures and longitudinal changes in total cholesterol.     

Elementary methods for the analysis of dichotomous outcomes in unselected samples of twins.

This paper presents an elementary statistical method for analyzing dichotomous outcomes in unselected samples of twin pairs using stratified estimators of the odds ratio. The methodology begins by first randomly designating one member of each twin pair as an "index" twin and the other member as the "co-twin." Stratifying on zygosity, odds ratios are used to measure the association between disease in the index twin and disease in the co-twin. From these zygosity-specific tables we calculate the Woolf-Haldane estimator of the common odds ratio (psi F, the weighted average of the zygosity-specific odds ratios), the Mantel-Haenszel test statistic (chi 2M-H) for the common odds ratio, and a test (chi 2G) for the difference in the zygosity-specific odds ratios. In this application, psi F provides an estimate of the familial association for disease and the accompanying chi 2M-H provides a test of the null hypothesis, psi F = 1 (i.e., there is no evidence for a familial influence on disease). The chi 2G is a test of the null hypothesis that psi MZ = psi DZ; a significant value for chi 2G suggests a genetic influence on disease (assuming that the observed odds ratios follow a pattern where psi MZ greater than psi DZ). A new test statistic (chi 2c) is proposed that incorporates the expectation that psi MZ = psi 2DZ under a purely additive genetic model with no common environmental effects. A significant value of chi c2 indicates that the different odds ratios across zygosity are partly due to common environmental influences. Conversely, a nonsignificant value of chi 2c is an indication that the zygosity-specific odds ratios are due solely to additive genetic effects and not to common environment. This basic approach is extended to examine the effects of measured indicators of the specific environment and the assessment of certain forms of gene by environment interaction. All of the methods are easily understood, highly flexible, readily computed using a hand calculator, and incorporate the inherent genetic information contained within twin samples.     

A general framework for robust and efficient association analysis in family‐based designs: quantitative and dichotomous phenotypes

Although transmission disequilibrium tests (TDT) and the FBAT statistic are robust against population substructure, they have reduced statistical power, as compared with fully efficient tests that are not guarded against confounding because of population substructure. This has often limited the application of transmission disequilibrium tests/FBATs to candidate gene analysis, because, in a genome‐wide association study, population substructure can be adjusted by approaches such as genomic control and EIGENSTRAT. Here, we provide new statistical methods for the analysis of quantitative and dichotomous phenotypes in extended families. Although the approach utilizes the polygenic model to maximize the efficiency, it still preserves the robustness to non‐normality and misspecified covariance structures. In addition, the proposed method performs better than the existing methods for dichotomous phenotype, and the new transmission disequilibrium test for candidate gene analysis is more efficient than FBAT statistics. Copyright © 2013 John Wiley & Sons, Ltd.