An extended transmission/disequilibrium test (TDT) for multi-allele marker loci

The transmission/disequilibrium test (TDT) was recently introduced by Spielman et al. (1993) as a test for linkage and linkage disequilibrium. The test is based on the unequal probability of transmission of two different marker alleles from parents to affected offspring, when the marker locus and the hypothetical disease locus are linked and are in linkage disequilibrium. The probabilities of marker allele transmission to affected offspring conditional on parental genotype have been derived by Ott (1989) for a biallelic marker and a recessive disorder with no phenocopies. Here, we derive the transmission probabilities for a multi-allele marker locus and a generalized single locus disease model in a random sample of affected individuals from a randomly mating population. The form of these transmission probabilities suggests an extension of the TDT to multi-allele marker loci, in which the alternative hypothesis is restricted to take account of the likely pattern of unequal transmission when the recombination fraction is near 0. We show how our extended TDT can be implemented by standard software for logistic regression, although we have also written our own program which is available on request. We have evaluated the approximate power of the test under a range of realistic assumptions, and it appears that the test will often have good power when linkage disequilibrium is strong and if the disease is recessive.     

Transmission disequilibrium test (TDT) for case-control studies

Genetic association, case-control studies are becoming a major instrument in the attempt to identify disease susceptibility markers of complex diseases. However, a major drawback of population-based studies of genetic association is the confounding effect of the population subdivision. We developed a statistic named T-value that estimates the differential transmission of marker alleles from heterozygous parents to the affected offspring, based on population data. Our method does not assume Hardy-Weinberg equilibrium and it can be used in very different population structures. A great advantage of this approach is that the genetic structure of the population can be assessed with a few unlinked loci and using classical population genetics theory (i.e. Wright's F-statistics). Four general models, assuming either one population with random mating, or one population without random mating, or several populations with random mating within them, or several populations without random mating within them, were developed to determine the behavior of the T-value under different mating conditions. Although a complete knowledge of the population structure is ideal to choose the best model, the simulations show that for a total inbreeding of 0.30 or less the last three models gave very similar estimates of the T-value. The model that assumed that total departure of Hardy-Weinberg proportions is due to population subdivision was the most robust under different scenarios of population structure. In sum, this study describes a novel procedure that can be used to identify the transmission of disease susceptibility markers in population-based studies.     

Hidden linkage: a comparison of the affected sib pair (ASP) test and transmission/disequilibrium test (TDT)

I compare the transmission/disequilibrium test (TDT) and affected sib pair (ASP) test under a general algebraic model describing a bi-allelic disease locus. Assuming linkage to a bi-allelic marker, I derive two binomial probabilities, one for parental allele 'transmission' (Pt ) which determines the magnitude of the TDT χ² statistic (χ²_tdt), and a second for identity-by-descent (ibd) marker allele 'sharing' ( P _s) which determines the magnitude of the ASP test statistic (χ²_asp). I also consider the ASP test applied to a completely polymorphic marker and demonstrate that the probability of ASP marker allele sharing ( P _s) is identical to P _s observed for a bi-allelic marker in equilibrium with the disease locus. I present a general framework for determining the power of the TDT and ASP test based on expressions for P _t, P _s and the proportion ( H / F ) of ascertained parents who are informative at the marker. Two previous analytic investigations of TDT power based on the work of Ott (1989), and Risch & Merikangas (1996) are shown to be special cases of this general framework. In addition, I show the relationship between the framework I present and a third analytic investigation of TDT power for multi-allelic markers based on the work of Sham & Curtis (1995).     

Family-based transmission disequilibrium test (TDT) and case-control association studies reveal surfactant protein A (SP-A) susceptibility alleles for respiratory distress syndrome (RDS) and possible race differences

A key cause of respiratory distress syndrome (RDS) in the prematurely born infant is deficiency of pulmonary surfactant, a lipoprotein complex. Both low levels of surfactant protein A (SP-A) and SP-A alleles have been associated with RDS. Using the candidate gene approach, we performed family-based linkage studies to discern linkage of SP-A to RDS and identify SP-A susceptibility or protective alleles. Moreover, we performed case-control studies of whites and blacks to detect association between RDS and SP-A alleles. Transmission disequilibrium test (TDT) analysis revealed that the frequency of transmission (from parent to the offspring with RDS) of alleles 6A(2) and 1A(0) and of 1A(0)/6A(2) haplotype in RDS was increased, whereas transmission of alleles 1A(5) and 6A(4) and of haplotype 1A(5)/6A(4) was decreased. Extended TDT analysis further strengthened the observations made. The case-control studies showed that in whites or blacks with RDS the frequencies of specific genotypes, 1A(0) and 6A(2) or 1A(0), were increased, respectively, but the frequency of specific 6A(3) genotypes was increased in certain white subgroups and decreased in blacks. Regression analysis revealed gestational age (GA) and 6A(3) genotypes are significant factors in blacks with RDS. In whites with RDS, GA and antenatal steroids are important factors. The data together indicate linkage between SP-A and RDS; certain SP-A alleles/haplotypes are susceptibility (1A(0), 6A(2), 1A(0)/6A(2)) or protective (1A(5), 6A(4), 1A(5)/6A(4)) factors for RDS. Some differences between blacks and whites with regard to SP-A alleles may exist.     

儿童失神癫痫的病例-对照研究及传递不平衡检验

目的 研究γ－氨基丁酸A型受体亚单位基因GABRA5及GABRB3是否与儿童失神癫痫相关联。方法 以染色体15q11.2-q12区段内2个微卫星DNA GABRA5和GABRB3作为遗传标记，对90例失神癫痫患儿及其父母以及100名正常对照采用微卫星荧光标记半基因分型技术，应用病例－对照研究及传递不平衡检验进行关联分析。结果 微卫星DNA GABRA5和GABRB3在中国正常人群等位基因分布均符合Hardy-Weinberg平衡，多态信息含量分别为0．80和0．66，微卫星DNA GABNRA5的等位基因2及GABRB3等位基因5在病例组的频率显著高于对照组（P＜0．001）。结论 微卫星DNA GABRA5和GABRB3均是多态性较好的遗传标记，γ－氨基丁酸A型受体亚单位基因GABRA5及GABRB3可能是儿童失神癫痫的易感基因或与之存在连锁不平衡。     

Simple approximations for the maximal transmission/disequilibrium test with a multi-allelic marker

Spielman et al . (1993) popularized the transmission/disequilibrium test (TDT) to test for linkage between disease and marker loci that show a population association. Several authors have proposed extensions to the TDT for multi-allelic markers. Many of these approaches exhibit a 'swamping' effect in which a marker with a strong effect is not detected by a global test that includes many markers with no effect. To avoid this effect, Schaid (1996) proposed using the maximum of the bi-allelic TDT statistics computed for each allele versus all others combined. The maximal TDT statistic, however, no longer follows a chi-square distribution. Here, a refinement to Bonferroni's correction for multiple testing provided by Worsley (1982) based on maximal spanning trees is applied to calculate accurate upper bounds for the type I error and p -values for the maximal TDT. In addition, an accurate lower Bonferroni bound is applied to calculate power. This approach does not require any simulation-based analysis and is less conservative than the standard Bonferroni correction. The bounds are given for both the exact probability calculations and for those based on the normal approximation. The results are assessed through simulations.     

Combining the case-control methodology with the small size transmission/disequilibrium test for multiallelic markers

Case-control studies compare marker-allele distributions in affected and unaffected individuals, and significant results may be due to linkage but can also simply reflect population structure. To test for linkage after obtaining a significant case-control finding, within-family analysis can be performed. In a transmission/disequilibrium test (TDT), genotypes of cases are compared to those of their parents to explore whether a specific allele, or marker, at a locus of interest is transmitted to a greater degree than Mendelian inheritance would warrant. For multiallelic markers, several authors have proposed extensions to the TDT. In this article, we propose a TDT test, utilizing the available information of a case-control study in the grouping of alleles for multiallelic markers, and thereby increase the statistical power of a TDT test with a small sample size.     

Combining the transmission disequilibrium test and case-control methodology using generalized logistic regression

To study the role of genetic factors in the etiology, susceptibility, or severity of disease, several methods are available. In a transmission disequilibrium test, genotypes of cases are compared to those of their parents to explore whether a specific allele, or marker, at a locus of interest appears to be transmitted in excess of what is expected on the basis of Mendelian inheritance. Such apparent excess transmission indicates that cases are being selected for that allele, thereby providing evidence that this allele is a risk factor for disease. In case-control studies, genotypes of cases are compared to those of controls from the same population to identify whether a specific allele is associated with disease. If so, either the allele at this locus or one in linkage disequilibrium with it may be causally related to the etiology of the disease. Here, we discuss the problem of combining a transmission disequilibrium test and a case-control comparison, in order to integrate all available information, and thereby increase statistical power. As the same cases are used in both approaches, the two results are not independent. However, parents of cases can be independently compared to controls. Both the issue of testing for a genetic effect and the estimation of relative risks under the multiplicative model using generalized logistic regression are discussed.     

ADRB2 polymorphisms and asthma susceptibility: transmission disequilibrium test and meta-analysis

BACKGROUND: The beta(2)-adrenergic receptor (ADRB2) is the most common adrenergic receptor in the lung, and associations between ADRB2 polymorphisms and intermediate phenotypes of asthma have been reported. Four missense polymorphisms (Arg16Gly, Gln27Glu, Val34Met, and Thr164Ile) and one polymorphism in the 5' leader cistron of the ADRB2 messenger RNA has been identified. In vitro studies have shown that these missense polymorphisms can affect ADRB2 function. METHODS: To examine possible associations of ADRB2 polymorphisms with asthma susceptibility, we performed transmission disequilibrium tests (TDT) of 137 Japanese families identified through children with atopic asthma. RESULTS: We did not find associations between any alleles of the ADRB2 polymorphisms and asthma by TDT (p > 0.1). We also performed a meta-analysis of data from all available studies. The random-effects model showed no significant odds ratio for the Arg16Gln (odds ratio = 1.05, p = 0.53) or Gln27Glu (odds ratio = 1.12, p = 0.22) polymorphism. CONCLUSION: Our data indicate that ADRB2 does not contribute substantially to susceptibility to asthma, but it is possible that these polymorphisms influence disease activity and drug responses in individuals with asthma.     

应用连锁不平衡检验法进行单纯性先天性心脏病易感基因 …

将人类单纯性先天性心脏病（ｃｏｎｇｅｎｉｔａｌｈｅａｒｔｄｅｆｅｃｔ，ＣＨＤ）易感基因初步定位，为进一步对其克隆奠定基础，方法在胚胎心脏发育调控相关基因－ＨＯＸ基因Ａ簇、Ｂ簇所在在的染色体区域７ｐ１４－１５、１７ｑ２１内选择３个微卫星ＤＮＡ标记Ｄ７Ｓ１８０８、Ｄ７Ｓ６７３、Ｄ１７Ｓ７９１，应用荧光标记聚合酶边反应技术扩增微卫星征 段，对３９个单纯性ＣＨＤ核心家系的１１２名成员进行基因型，并进行遗传     

Adaptation of the extended transmission/disequilibrium test to distinguish disease associations of multiple loci: the Conditional Extended Transmission/Disequilibrium Test

Linkage and association studies in complex diseases are used to identify and fine map disease loci. The process of identifying the aetiological polymorphism, the molecular variant responsible for the linkage and association of the chromosome region with disease, is complicated by the low penetrance of the disease variant, the linkage disequilibrium between physically-linked polymorphic markers flanking the disease variant, and the possibility that more than one polymorphism in the most associated region is aetiological. It is important to be able to detect additional disease determinants in a region containing a cluster of genes, such as the major histocompatibility complex (MHC) region on chromosome 6p21. Some methods have been developed for detection of additional variants, such as the Haplotype Method, Marker Association Segregation Chi-squares (MASC) Method, and the Homozygous Parent Test. Here, the Extended Transmission/Disequilibrium Test is adapted to test for association conditional on a previously associated locus. This test is referred to as the Conditional Extended TDT (CETDT). We discuss the advantages of the CETDT compared to existing methods and, using simulated data, investigate the effect of polymorphism, inheritance, and linkage disequilibrium on the CETDT.     

Analysis of the association of HLA-DRB1, TNFalpha promoter and TNFR2 (TNFRSF1B) polymorphisms with SLE using transmission disequilibrium test

A number of studies reported associations of HLA-DRB1, TNFalpha (TNF) promoter and TNF receptor II (TNFR2, TNFRSF1B) polymorphisms with systemic lupus erythematosus (SLE), however, the results have often been inconsistent. Such lack of consistency could partly derive from the population admixture involved in the case-control study. To avoid such a problem, polymorphisms in these genes were analyzed using transmission disequilibrium test (TDT) in Caucasian SLE families. Ninety-one Caucasian SLE family samples recruited in southern California were analyzed for the association with HLA-DRB1, TNF promoter positions at -1031, -863, -857 and -308, and TNFR2-196M/R polymorphisms. Significant transmission was observed for HLA-DRB1*1501, but not for HLA-DRB1*0301, nor for TNF haplotype that codes for -308A. Interestingly, TNF haplotype coding for -1031C, -863A, -857C showed a tendency of preferential nontransmission in the patients without lupus nephritis and in those with malar rash. No transmission distortion was observed for TNFR2-196R allele. These findings confirmed the association of HLA-DRB1*1501, but did not replicate that of the HLA-DRB1*0301, TNFA-308A and TNFR2-196R with SLE in this population. In addition, a possible disease-protective role for TNF haplotype coding for -1031C, -863A, -857C was suggested.     

On Fisher's exact test for detecting gametic disequilibrium between DNA polymorphisms

Nonrandom associations between DNA polymorphisms are commonly tested by Fisher's exact test in spite of it is seriously conservative. Theoretical statistical studies have shown that the exact test with Tocher's correction does not present this problem but Tocher's correction is never used by experimentalists for detecting gametic associations. We have examined the practical consequences of using these two alternative tests for the detection of nonrandom associations in populations. A total of 1566 pairs of RFLPs of eleven gene regions and sixteen populations from previously published human and Drosophila disequilibrium data were examined. The analysis reveals remarkable differences between the two tests for detecting gametic associations. In some gene regions, the exact test with Tocher's correction detects a percentage of significant associations between RFLPS which is twice or three times higher than that detected by the exact test without correction. Therefore, the widely used exact test can be seriously underestimating disequilibrium in populations. In addition, the study shows that the standard chi-square test for independence in 2 × 2 tables detects a similar percentage of significant associations between RFLPs than Tocher's test.     

The synergistic effects of the IL-9 gene and environmental exposures on asthmatic Taiwanese families as determined by the transmission/disequilibrium test

Asthma occurs in genetically susceptible individuals in the presence of environmental factors. The interleukin-9 (IL-9) gene, one of the cytokine genes located on chromosome 5q31, plays an important role in the development of asthmatic syndrome by enhancing both T-cell and mast-cell function. This study investigated GT repeat polymorphism of the IL-9 gene and the gene-environment interactions, which may predispose individuals to asthma and atopy pathogenesis. In this study, we used the transmission/disequilibrium test (TDT) to investigate the relationship between asthma and the IL-9 gene by studying 123 parent-offspring trios and 91 siblings. For allele-specific TDT chi-squared test, allele 122 of the IL-9 gene showed significant association with asthmatics with specific IgE against house dust (HD) (P = 0.038). The additions of covariates to TDT to conduct the synergistic effects between the IL-9 gene and environmental factors into account were estimated by conditional logistic regression models. The odds ratio for transmission of allele 122 of the IL-9 gene was 1.23 (P = 0.28) for all asthmatic probands. There was slight increased interaction effect on asthma between transmission of allele 122 of IL-9 gene to offspring and who were exposed to the fur of pets (OR = 3.33, P = 0.047). We also detected elevated odds of transmission of allele 122 to atopic asthmatic probands (OR = 2.08, P = 0.03) and offspring with very high levels of serum IgE (> or = 800 IU mL(-1)). In conclusion, this study has found that the IL-9 gene was slightly associated with asthmatics who have positive specific IgE against Der p (or Der f) and house dust, when information on environmental factors was incorporated as effect modifiers.     

家族性热性惊厥的染色单体型相对风险和传递不平衡分析

目的　确认家族性热性惊厥是否与染色体６ｑ 或８ｑ 连锁。方法　对核心家系为主的５０ 个家族性热性惊厥家系的热休克蛋白（ ｈｅａｔ ｓｈｏｃｋ ｐｒｏｔｅｉｎ , Ｈ Ｓ Ｐ）７０ 编码区 Ｐｓｔ Ⅰ位点、 Ｈ Ｓ Ｐ７０１ ５′非翻译区、 Ｈ Ｓ Ｐ７０２ ３′非翻译区、微卫星 Ｄ８ Ｓ８４ 和 Ｄ８ Ｓ８５ 等５ 个遗传标志的分型结果,用计算机群体与家系遗传分析系统 Ｐ Ｐ Ａ Ｐ 进行单体型相对风险（ｇｅｎｏｔｙｐｅｂａｓｅｄ ｈａｐｌｏｔｙｐｅ ｒｅｌａｔｉｖｅ ｒｉｓｋ , Ｇ Ｈ Ｒ Ｒ） 和传递不平衡（ｔｒａｎｓｍｉｓｓｉｏｎｄｉｓｅｑｕｉｌｉｂｒｉｕ ｍ ｔｅｓｔ , Ｔ Ｄ Ｔ） 分析。结果　 Ｇ Ｈ Ｒ Ｒ 显示标志 Ｄ８ Ｓ８５ 、 Ｔ Ｄ Ｔ 分析显示 Ｄ８ Ｓ８４ 与家族性热性惊厥有一定关联或存在连锁不平衡。结论　提示家族性热性惊厥可能与染色体８ｑ 连锁。     

The transmission disequilibrium test suggests that HLA-DR4 and DR13 are linked to autism spectrum disorder

We have evaluated possible contributions of HLA-DRB1 alleles to autism spectrum disorder (ASD) in 103 families of Caucasian descent. The DR4 allele occurred more often in probands than controls (0.007), whereas the DR13,14 alleles occurred less often in probands than controls (p = 0.003). The transmission disequilibrium test (TDT) indicated that the ASD probands inherited the DR4 allele more frequently than expected (p = 0.026) from the fathers. The TDT also revealed that fewer DR13 alleles than expected were inherited from the mother by ASD probands (p = 0.006). We conclude that the TDT results suggest that DR4 and DR13 are linked to ASD. Reasons for the parental inheritance of specific alleles are poorly understood but coincide with current genetic research noting possible parent-of-origin effects in autism.     

Evidence for transmission disequilibrium at the DAOA gene locus in a schizophrenia family sample

Recently, the DAOA gene locus on chromosome 13q32–q34 has been implicated in the etiology of schizophrenia. We genotyped three single-nucleotide polymorphisms (SNPs: rs778294, rs779293 and rs3918342) in this region in 126 Chinese family trios. In this study, we have identified statistically significant transmission disequilibrium in two markers rs778293 (P = 0.01) and rs3918342 (P = 0.02), and a highly significant under-transmission between haplotype CAT (P = 0.0005) and schizophrenia. The results provide further evidence to support that DAOA gene locus is involved in conferring susceptibility to schizophrenia.     

Effects of age at onset on the power of the affected sib pair and transmission/disequilibrium tests

Information on the age of a patient at disease onset, an important feature of complex diseases, is often collected in studies designed to map the disease genes. Penetrance-model-free methods, requiring no specification of penetrance functions, have been used extensively for detecting linkage and association between marker and disease loci. In this paper, we conduct an analytical study to examine the effects of incorporation of age at onset information on the power of two commonly used penetrance-model-free methods, the affected sib-pair (ASP) and transmission/disequilibrium tests (TDT). Assuming a Cox model with a major gene effect for the age at onset, we quantify analytically how age at onset affects the identity by descent (IBD) probabilities, the mean IBD values, and the expected numbers of alleles transmitted from heterozygous parents to affected children under various genetic models. We show that the power of the mean IBD test and the TDT can be greatly affected by the ages at onset of affected siblings or children used in the study. Generally, the most powerful test for ASPs is that based on affected sib pairs both having early disease onset and for TDT analyses is that based on trios with early-onset children. Naively combining affected sib pairs with different ages at onset or parent-children trios with different ages at onset of affected children can result in reduced power for detecting linkage or association. These results may be used to guide collection and analysis of sib pairs or families for diseases with variable age at onset.     

5-HT 102T/C多态性与Tourette综合征的病例对照及核心家系关联分析

目的 研究5－羟色胺受体102T／C多态性是否与Tourette综合征（TS）相关联,方法对157个核心家系样本采用病例－对照关联分析,传递不平衡检验方法,聚合酶链反应及RFLP等技术,根据TS与强迫症（obsessive compulsive disorder,OCD)的同病现象,将TS划分亚组进行与5－羟色胺受体102T／C多态性的关联分析。结果 合并OCD的TS与该位点的基因型102C／C（X2＝8．38,P＝0．004）及等位基因102C／（X2＝4．84,P＝0．028）存在关联,进一步采用传递不平衡分析,发现合并（美国精神疾病诊断和统计手册IV》论断标准的OCD的TS与该位点存在关联或连锁不平衡（X2＝5．12,,P＝0．02）,而在TS总体样本及单纯TS样本中未发现与该位点的关联,结论 5－羟色胺受体102T／C多态性与中国人群合并OCD的TS存在关联,合并OCD的TS可能是TS中相对独立的一个亚型。     

On calculating the power of a TDT study – comparison of methods

We show that the methods for calculating the power of the TDT of Risch & Merikangas (1996), McGinnis (1998, 2000), Tu & Whittemore (1999) and Knapp (1999) consist of three distinct approaches. The differences between the methods arise either by treating parental transmissions independently or not, and either conditioning on parental heterozygosity or not. Transmissions are only truly independent when the mode of inheritance of the disease is multiplicative, making this assumption invalid and the methods that assume them (Risch & Merikangas, 1996; McGinnis, 1998, 2000) inappropriate. We demonstrate a basic model that allows analytical comparisons of the methods, and suggest a new method that calculates power at least as accurately as any of the three previously published.