Parent-offspring Trios Research Articles

Abstract 2726: Haplotype Sharing Test as a Tool to Map Genes for Familial Cardiomyopathy

Background: In Mendelian diseases, such as arrhythmogenic right ventricular and dilated cardiomyopathies (ARVC and DCM), chromosomal regions identical-by-descent (IBD) from a common founder can be ascertained both by pedigree analysis and by haplotype-sharing methods. Finding shared haplotypes is greatly facilitated with the currently available high-density SNP arrays. However, determining which of the shared haplotypes is IBD and contains the disease-associated mutation, and which are identical-by-state (IBS) and are shared by chance, is difficult. An additional criterion is needed to indicate the region containing the disease mutation. The probability for shared haplotypes to be IBD rather than IBS increases with an increasing number of SNPs. We hypothesized that the largest shared haplotype is the most likely region to hold the causative disease mutation. Methods: The Haplotype-Sharing Test (HST) was designed, using SNP genotyping data from isolated patients and parent-offspring pairs and trios to identify the largest possibly shared haplotypes between patients that are members of a (large but unobserved) pedigree. We applied the HST to: three distantly related families each with at least one ARVC patient using 10K SNP genotyping arrays, and a large family with 5 DCM patients using 250K SNP arrays. Results: In pedigree A a haplotype run of 118 SNPs spanning 32 MB on chromosome 12p12.3-q13.13 was identified. This haplotype is substantially larger than any other area that is shared due to random effects. Screening of the PKP2 gene, located in this region, revealed a pathogenic splice-site mutation that was segregating with the disease. In family B (DCM) the largest shared haplotype was 178 SNPs, spanning 3.5 MB on chromosome 15. Sequencing of potential candidate genes (including alpha Tropomyosin and Integrin alpha 1) is pending. Conclusions: Our identification of the causative founder mutation in pedigree A in the largest shared region shows that our hypothesis, though heuristic in character, was correct. More importantly, haplotype sharing is a powerful tool for identifying disease-causing genes in single and extended families when an insufficient number of meioses are present to perform classic linkage analysis.

European rational approach for the genetics of diabetic complications EURAGEDIC: patient populations and strategy

Diabetic nephropathy is likely to be a complex genetic trait. To date, most diabetic nephropathy candidate gene studies have tested a limited number of genes and variants in small sized populations, or in populations that were poorly matched or phenotyped. The main objective of the EURAGEDIC study was to address these problems. Single nucleotide polymorphisms (SNPs) in candidate genes were tested for association with overt diabetic nephropathy (persistent albuminuria >300 mg/24 h) in a large (n=2499) Type 1 diabetes case/control study. Testing for transmission disequilibrium in 541 independent parent-offspring trios with or without diabetic nephropathy was applied for validation of consistency. Candidate genes were selected based on previous linkage studies, knowledge of metabolic pathways, and animal models. A comprehensive SNP discovery in more than 100 candidate genes was performed by direct sequencing. In total, 1176 cases with diabetic nephropathy and 1323 diabetic controls with longstanding normoalbuminuria were included from three European populations (Denmark, Finland, France). Data were collected on HbA(1c), blood pressure, urinary albumin excretion rate, kidney function, retinopathy, smoking, medication and cardiovascular disease. To summarize the relevant non-genetic predictors for diabetic nephropathy a baseline phenotypic model fitted to EURAGEDIC data included the covariates: sex, diabetes duration, HbA(1c) and smoking as well as pair-wise interactions. The EURAGEDIC study is designed and powered to identify and validate common alleles as genetic risk factors for diabetic nephropathy in Type 1 diabetic patients.

A study of the PEMT gene in schizophrenia

The phospholipid hypothesis of schizophrenia is becoming popular because of the findings from the niacin flush test, the treatment with polyunsaturated fatty acids (PUFAs), biochemical studies for the phospholipid metabolism pathway and genetic studies of phospholipase A2. The present study attempted to investigate the gene coding for phosphatidylethanolamine N-methyltransferase (PEMT), which is an important enzyme for the synthesis of membrane phospholipids. We recruited 271 Chinese parent-offspring trios of Han descent and detected 3 single nucleotide polymorphisms (SNPs) at the PEMT locus. The transmission disequilibrium test (TDT) showed allelic association for rs464396 (X2=9.4, P=0.002), but not for the other two. The 2-SNP haplotype analysis showed haplotypic association for both the rs936108-rs464396 haplotypes (X2=25.7, d.f.=3, P=0.00001) and the rs464396-rs4244593 haplotypes (X2=17.3, d.f.=3, P=0.0006). The 3-SNP haplotype analysis also showed a haplotypic association (X2=24.4, d.f.=7, P=0.0006). The present results suggest that the PEMT gene may contribute to the etiology of schizophrenia.

Is there an intrauterine influence on obesity? Evidence from parent–child associations in the Avon Longitudinal Study of Parents and Children (ALSPAC)

Background:It has been suggested that increasing obesity levels in young women lead to intrauterine environments that, in turn, stimulate increased obesity among their offspring, generating an intergenerational acceleration of obesity...

Quantitative trait association in parent offspring trios: Extension of case/pseudocontrol method and comparison of prospective and retrospective approaches

The case/pseudocontrol method provides a convenient framework for family-based association analysis of case-parent trios, incorporating several previously proposed methods such as the transmission/disequilibrium test and log-linear modelling of parent-of-origin effects. The method allows genotype and haplotype analysis at an arbitrary number of linked and unlinked multiallelic loci, as well as modelling of more complex effects such as epistasis, parent-of-origin effects, maternal genotype and mother-child interaction effects, and gene-environment interactions. Here we extend the method for analysis of quantitative as opposed to dichotomous (e.g. disease) traits. The resulting method can be thought of as a retrospective approach, modelling genotype given trait value, in contrast to prospective approaches that model trait given genotype. Through simulations and analytical derivations, we examine the power and properties of our proposed approach, and compare it to several previously proposed single-locus methods for quantitative trait association analysis. We investigate the performance of the different methods when extended to allow analysis of haplotype, maternal genotype and parent-of-origin effects. With randomly ascertained families, with or without population stratification, the prospective approach (modeling trait value given genotype) is found to be generally most effective, although the retrospective approach has some advantages with regard to estimation and interpretability of parameter estimates when applied to selected samples. Genet. Epidemiol. 31:833, 2007. © 2007 Wiley-Liss, Inc.

Ascertainment Through Family History of Disease Often Decreases the Power of Family-based Association Studies

Selection of cases with additional affected relatives has been shown to increase the power of the case-control association design. We investigated whether this strategy can also improve the power of family-based association studies that use the transmission disequilibrium test (TDT), while accounting for the effects of residual polygenic and environmental factors on disease liability. Ascertainment of parent-offspring trios conditional on the proband having affected first-degree relatives almost always reduced the power of the TDT. For many disease models, this reduction was quite considerable. In contrast, for the same sample size, designs that analyzed more than one affected offspring per family often improved power when compared to the standard parent-offspring trio design. Together, our results suggest that (1) residual polygenic and environmental influences should be considered when estimating the power of the TDT for studies that ascertain families with multiple affected relatives; (2) if trios are selected conditional on having additional affected offspring, then it is important to genotype and include in the analysis the additional siblings; (3) the ascertainment strategy should be considered when interpreting results from TDT analyses. Our analytic approach to estimate the asymptotic power of the TDT is implemented online at http://pngu.mgh.harvard.edu/ ~purcell/gpc/.

A method for haplotype inference in general pedigrees without recombination

The abundance of single nucleotide polymorphisms (SNPs) makes the haplotype-based method instead of single-maker-oriented method the main approach to association studies on QTL mapping. The key problem in haploptype-based method is how to reconstruct haplotypes from genotype data. Directly assaying haplotypes in diploid individuals by experimental methods is too expensive, therefore the in silico haplotyping-determination methods are the major choice at the present. This paper presents a rapid and reliable algorithm for haplotype reconstruction for tightly linked SNPs in general pedigrees. It is based on six rules and consists of three steps. First, the parental origins of alleles in offspring are assigned conditional on genotypes in parent-offspring trios; second, the redundant haplotypes are eliminated based on the six rules; and finally, the most likely haplotype combinations are chosen via maximum likelihood method. Our method was verified and compared with PEDPHASE by simulated data with different pedigree sizes, numbers of loci, and proportions of missing genotypes. The result shows that our algorithm was superior to PEDPHASE in terms of computing time and accuracy of haplotype estimation. The computing time for 100 runs was 10–15 times less and the accuracy was 4%–10% higher than PEDPHASE. The result also indicates that our method was very robust and was hardly affected by pedigree size, number of loci, and proportion of missing genotypes.

Genetic variations of the CDC2L2 gene are associated with type 2 diabetes in a Han Chinese cohort

The purpose of the present study was to study the potential association of CDC2L2 variations with type 2 diabetes (T2D). SNPs (single nucleotide polymorphisms) were extensively screened across the CDC2L2 gene by the site-specific PCR method ARMS (Amplification Refractory Mutation System). The identified novel polymorphisms were further evaluated in a Han Chinese cohort comprising of 467 patients with diabetes and 569 nondiabetic controls. In addition, 76 parent-offspring trios were also included in this association study. The case-control and TDT/sibTDT studies are applied for association analysis in this study. Seven loci (rs1059831, SNP33, rs7528782, SNP11, SNP36, rs11488590 and SNP30) were shown to be significantly associated with T2D in unrelated individuals (p < 0.05). When individuals were stratified by age, sex and body mass index (BMI), the SNP11 was shown to be strongly associated with female patients with T2D, patients whose age was over 45 years and individuals whose BMI was less than 23 (p = 0.018, 0.011 and 0.0089, respectively). However, it was not replicated in the family-based TDT/sibTDT analysis (p = 0.085, OR = 0.63 (CI 95% 0.34-1.06)). Our data suggested that the CDC2L2 gene may contribute to the susceptibility of type 2 diabetes in the northern Han Chinese population, but further studies are needed to replicate these findings.

Evidence of linkage and association on 18p11.2 for psychosis

The genetic basis of bipolar disorder (BPD) and schizophrenia (SCZ) has been established through numerous clinical and molecular studies. Although often considered separate nosological entities, evidence now suggests that the two syndromes may share some genetic liability. Recent studies have used a composite phenotype (psychosis) that includes BPD, SCZ, psychosis not otherwise specified, and schizoaffective disorder, to identify shared susceptibility loci. Several chromosomal regions are reported to be shared between these syndromes (18p, 6q, 10p, 13q, 22q). As a part of our endeavor to scan these regions, we report a positive linkage and association finding at 18p11.2 for psychosis. Two-point linkage analysis performed on a series of 52 multiplex pedigrees with 23 polymorphic markers yielded a LOD score of 2.02 at D18S37. An independent set of 159 parent offspring trios was used to confirm this suggestive finding. The TDT analysis yielded support for association between the marker D18S453 and the disease allele (chi2 = 4.829, P < 0.028). This region has been implicated by several studies on BPD [Sjoholt et al. (2004); Mol Psychiatry 9(6):621-629; Washizuka et al. (2004); Biol Psychiatry 56(7):483-489; Pickard et al. (2005); Psychiatr Genet 15(1):37-44], SCZ [Kikuchi et al. (2003); J Med Dent Sci 50(3):225-229; Babovic-Vuksanovic et al. (2004); Am J Med Genet 124(3):318-322] and also as a shared region between the two diseases [Ishiguro et al. (2001); J Neural Transm 108(7):849-854; Reyes et al. (2002); Mol Psychiatry 7(4):337-339; Craddock et al. (2005); J Med Genet 42(3):193-204]. Our findings provide an independent validation of the above reports, and suggest the presence of susceptibility loci for psychoses in this region.

Epidemiologic Evidence for the Fetal Overnutrition Hypothesis: Findings from the Mater-University Study of Pregnancy and Its Outcomes

The fetal overnutrition hypothesis proposes that greater maternal adiposity results in increased obesity throughout life in the offspring. The authors examined the associations between parental prepregnancy body mass index (BMI; weight (kg)/height (m)(2)), based on height and weight reported by the mother at her first antenatal clinic visit, and offspring BMI (height and weight measured at age 14 years) in 3,340 parent-offspring trios from a birth cohort based in Brisbane, Australia (mothers were recruited in 1981-1984). The maternal-offspring BMI association was stronger than the paternal-offspring BMI association. In the fully adjusted model, the increase in standardized offspring BMI at age 14 for a one-standard-deviation (SD) increase in maternal BMI was 0.362 SD (95% confidence interval: 0.323, 0.402), and the corresponding result for a one-SD increase in paternal BMI was 0.239 SD (95% confidence interval: 0.197, 0.282). There was statistical support for a difference in the magnitude of the association between maternal-offspring BMI and paternal-offspring BMI in all confounder-adjusted models tested (all p's < 0.0001). In sensitivity analyses taking account of different plausible levels of nonpaternity (up to 15%), the greater maternal effect remained. These findings provide some support for the fetal overnutrition hypothesis.

Analysis of the type 2 diabetes gene, TCF7L2, in 13,795 type 1 diabetes cases and control subjects

To the Editor: The two most common forms of diabetes that have been classified are type 1 diabetes and type 2 diabetes. Type 1 diabetes is characterised by infiltration of the pancreas by autoreactive T cells and autoimmune destruction of pancreatic beta cells, leading to a complete loss of insulin production, whereas type 2 diabetes is associated with the gradual increase of insulin insensitivity in tissues leading to hyperglycaemia and beta cell failure. However, it has been suggested that type 1 diabetes and type 2 diabetes may share a common genetic aetiology [1]. For example, the accelerator hypothesis suggests that type 1 diabetes and type 2 diabetes are the same disease of hyperglycaemiainduced beta cell damage but that type 1 diabetes has the added effect of autoimmunity [1]. One way of testing the hypothesis that there is a common causal pathway between type 1 and type 2 diabetes is to analyse a type 2 diabetes gene with a large effect in a large type 1 diabetes sample. Until very recently [2] this has not been possible, as no such locus has emerged from type 2 diabetes genetics studies. Recently, however, the transcription-factor-7-like 2 (TCF7L2) gene region on chromosome 10q25.2 has been found to contribute substantially to the risk of type 2 diabetes with convincing statistical support (relative risk [RR]=0.67; p=2.1×10 for the 0 allele of the microsatellite marker DG10S478) [2]. This study was carried out in three different populations: Icelandic, Danish and white American. Two single nucleotide polymorphisms (SNPs) were also genotyped in this study: rs12255372 (G>T, minor allele frequency [MAF] 0.36 in control subjects) and rs7903146 (C>T, MAF=0.28 in control subjects). rs12255372 was found to be in high linkage disequilibrium (LD) with DG10S478 (r=0.95 for the major G allele of the SNP with the 0 allele of the microsatellite marker). rs7903146 was in lower LD with the DG10S478 (r=0.75): for the minor allele (T) of this SNP the authors obtained odds ratios (ORs) of 1.41–1.71 in the three populations and p values from 0.0018 to 1.6×10 [2]. These results were independently replicated in 2,158 white UK type 2 diabetic subjects, 2,574 geographically matched white control subjects and 388 parent–offspring trios [3]. In this population it was found that the T allele of rs7903146 was the most associated with type 2 diabetes susceptibility (OR=1.36, 95% CI=1.24–1.48 and p=3.6× 10, MAF=0.31 in control subjects), but that the T allele of rs12255372 was also associated (OR=1.29, 95% CI= 1.18–1.41; p=2.2×10, MAF=0.30 in control subjects) [3]. These results have also been confirmed by other studies in Finnish and US populations [4, 5]. A study on type 2 diabetes progression suggests that TCF7L2 may be associated with insulin secretion [6]. Therefore, as TCF7L2 is a major gene in type 2 diabetes we can now test if it affects type 1 diabetes susceptibility. We analysed the two SNPs, rs12255372 and rs7903146, in 6,199 white UK type 1 diabetic subjects (5,872 from the Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory’s Genetic Resource Diabetologia (2007) 50:212–213 DOI 10.1007/s00125-006-0506-y

IGF1, growth pathway polymorphisms and schizophrenia: A pooling study

It has been hypothesized that insulin-like growth factors (IGFs) and components of the growth-hormone (GH)-IGF axis may underlie reported associations of poor fetal and childhood growth with schizophrenia. We have investigated the association of schizophrenia with 16 SNPs spanning the IGF1 gene with an inter-marker distance of approximately 2-3 kb. We also examined associations with four common functional polymorphisms of genes involved in aspects of the GH-IGF system--the IGF1 receptor (IGF1R), insulin receptor substrate (IRS1), growth hormone (GH1), and IGF binding protein-3 (IGFBP3). The study was based on an analysis of pooled DNA samples from 648 UK and Irish cases of schizophrenia and 712 blood donor controls and of 297 Bulgarian parent offspring trios. In replicated pool analyses, none of the 16 SNPs in IGF1 nor the 4 key SNPs in the other growth pathway genes were associated with schizophrenia. SNP coverage of IGF1 was extensive, so our findings do not support a major role for IGF-I in the aetiology of schizophrenia.

No evidence for association between NOTCH4 and schizophrenia in a large family-based and case–control association analysis

An analysis of 80 British parent-offspring trios by Wei and Hemmings in 2000 revealed thre1e out of five markers within the NOTCH4 locus to be strongly associated with schizophrenia. In our present study, we have examined NOTCH4 markers in large samples of German and Palestinian-Arab origin. Our study population comprised a German case-control sample (n=512 schizophrenia patients and n=232 controls) and two independent parent-offspring trio samples of German (n=159 trios) and Palestinian-Arab (n=208 trios) descent. We examined a total of ten single nucleotide polymorphisms within the NOTCH4 locus and the adjacent loci, spanning a region of approximately 100 kb. Neither single marker nor haplotype analyses showed association with schizophrenia. In addition, analyses of the German case-control and trio samples revealed no significant association between NOTCH4 polymorphisms and early-onset schizophrenia. Our results suggest that NOTCH4 is unlikely to play a major role in the genetic predisposition to schizophrenia in the German or the Palestinian-Arab population.

Association Analysis of 6,736 U.K. Subjects Provides Replication and Confirms TCF7L2 as a Type 2 Diabetes Susceptibility Gene With a Substantial Effect on Individual Risk

Recent data suggest that common variation in the transcription factor 7-like 2 (TCF7L2) gene is associated with type 2 diabetes. Evaluation of such associations in independent samples provides necessary replication and a robust assessment of effect size. Using four TCF7L2 single nucleotide polymorphisms (SNPs; including the two most associated in the previous study), we conducted a case-control study in 2,158 type 2 diabetic subjects and 2,574 control subjects and a family-based association analysis in 388 parent-offspring trios all from the U.K. All SNPs showed powerful associations with diabetes in the case-control analysis, with strongest effects at rs7903146 (allele-wise relative risk 1.36 [95% CI 1.24-1.48], P = 1.3 x 10(-11)). Data were consistent with a multiplicative model. The family-based analyses provided independent evidence for association at all loci (e.g., rs4506565, 62% transmission, P = 7 x 10(-5)) with no parent-of-origin effects. The frequency of diabetes-associated TCF7L2 genotypes was greater in cases ascertained for positive family history and early onset (rs4606565, P = 0.02); the population-attributable risk, estimated from the least-selected cases, is approximately 16%. The overall evidence for association for these variants (P = 4.4 x 10(-14) combining case-control and family-based analyses for rs4506565) exceeds genome-wide significance criteria and clearly establishes TCF7L2 as a type 2 diabetes susceptibility gene of substantial importance.

Analysis of ProDH, COMT and ZDHHC8 risk variants does not support individual or interactive effects on schizophrenia susceptibility

Synergistic interaction between genes on chromosome 22q11 recently has been proposed as a possible mechanism which could confer increased risk for schizophrenia. Based on this hypothesis, our study aimed to explore main, cis- and trans-interacting effects of three candidate genes on 22q11, ProDH, COMT and ZDHHC8. We selected four putative risk variants, residing within these genes, ProDH 1945, ProDH 2026, COMT ValMet and ZDHHC8 rs175174, and studied these in a large family-based schizophrenia association sample of European origin (488 Bulgarian parent–offspring trios). The presence of interaction between the variants was tested by conditional logistic regression analysis based on a case–pseudocontrol design. Our study did not find statistical evidence for allelic (investigation of ProDH markers only), genotypic, haplotypic, or interactive effects between ProDH, COMT and ZDHHC8. Our data do not support the hypothesis that an interaction between these genes influences susceptibility to schizophrenia.

Increased Support for Linkage of a Novel Locus on Chromosome 5q13 for Essential Hypertension in the British Genetics of Hypertension Study

Human hypertension arises from a combination of genetic factors and lifestyle influences. With cardiovascular disease set to become the number 1 cause of death worldwide, it is important to understand the etiologic mechanisms for hypertension, because these might provide new routes to improved treatment. The British Genetics of Hypertension Study has recently published a primary genome screen that identified 4 chromosomal regions of interest. We have now genotyped additional markers to confirm the most promising regions for follow-up studies. Thirty-four additional microsatellites were genotyped in our severely hypertensive affected sibling pair resource (now 1635 families with 2142 affected sibling pairs), leading to a substantial increase in information content in the regions of interest. We found increased support for linkage of chromosome 5q13 to human hypertension (multipoint logarithm of odds=2.50) with 3 adjacent markers yielding single point logarithm of odds scores of 3.22, 2.84, and 2.51. The placement of additional markers on 2q, 6q, and 9q diminished support for linkage in these regions. However, the addition of new data and families identified novel regions of interest on chromosomes 1q and 11q. The 3 positive markers in the chromosome 5 region were also genotyped in 712 distinct parent-offspring trios with the same severe phenotype to replicate linkage and association. Borderline support for replication was found (P=0.07). We found increased evidence for linkage and borderline-significant evidence for association for a hypertension susceptibility locus on chromosome 5q13 that is worthy of detailed fine mapping and assessment of candidate genes.

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.

Tests in a Case–control Design Including Relatives

Abstract. We present a new approach to handle dependencies within the general framework of case–control designs, illustrating our approach by a particular application from the field of genetic epidemiology. The method is derived for parent–offspring trios, which will later be relaxed to more general family structures. For applications in genetic epidemiology we consider tests on equality of allele frequencies among cases and controls utilizing well‐known risk measures to test for independence of phenotype and genotype at the observed locus. These test statistics are derived as functions of the entries in the associated contingency table containing the numbers of the alleles under consideration in the case and the control group. We find the joint asymptotic distribution of these entries, which enables us to derive critical values for any test constructed on this basis. A simulation study reveals the finite sample behaviour of our test statistics.

Association analysis between affective disorder and polymorphism in the 3' untranslated region of serotonin transporter gene

目的 探讨5-羟色胺转运体(5-HTT)基因3'端非编码区UTRG/T与心境障碍之间的分子遗传学联系.方法在中国汉族人群中,以心境障碍核心家系作为研究对象,根据哈佛大学提供的遗传学研究用诊断性检查表(DIGS)自编家系调查表,采用DSM-IV诊断标准并结合一些心理测评工具,以达到表型一致.在72个情感性精神障碍核心家系,232个家系成员(其中双相障碍56例,重性抑郁症34例)中,应用聚合酶链反应(PCR)和限制性片段长度多态性方法,对5-HTT基因3'端非编码区UTRG/T与心境障碍之间的分子遗传学联系进行了以家系为基础的连锁不平衡分析.结果 (1)5-HTT3'UTRG/T位点PCR产物经MseI酶切后,检测出800bp等位基因G片断和745bp及55bp等位基因T片断,等位基因频率分别为88%和12%,等位片断G的频率占明显优势.(2)基因型和等位基因频率在心境障碍患病组和父母对照组之间差异无显著性.GHRR和HHRR分析以及多等位基因ETDT统计分析也没有发现存在连锁不平衡.结论 5-HTT3'UTRG/T位点多态性在心境障碍的发病中可能不起重要作用。

A high-resolution survey of deletion polymorphism in the human genome

Recent work has shown that copy number polymorphism is an important class of genetic variation in human genomes. Here we report a new method that uses SNP genotype data from parent-offspring trios to identify polymorphic deletions. We applied this method to data from the International HapMap Project to produce the first high-resolution population surveys of deletion polymorphism. Approximately 100 of these deletions have been experimentally validated using comparative genome hybridization on tiling-resolution oligonucleotide microarrays. Our analysis identifies a total of 586 distinct regions that harbor deletion polymorphisms in one or more of the families. Notably, we estimate that typical individuals are hemizygous for roughly 30-50 deletions larger than 5 kb, totaling around 550-750 kb of euchromatic sequence across their genomes. The detected deletions span a total of 267 known and predicted genes. Overall, however, the deleted regions are relatively gene-poor, consistent with the action of purifying selection against deletions. Deletion polymorphisms may well have an important role in the genetics of complex traits; however, they are not directly observed in most current gene mapping studies. Our new method will permit the identification of deletion polymorphisms in high-density SNP surveys of trio or other family data.