The weighted rank pairwise correlation statistic for linkage analysis: Simulation study and application to Alzheimer's disease

The weighted rank pairwise correlation (WRPC) statistic has been proposed as a robust test of genetic linkage, particularly adapted to the analysis of large and complex pedigrees and for age-dependent and heterogeneous diseases. In this paper a simulation study is presented. Validity and power of the WRPC test are studied and compared to the Haseman-Elston sibpair method for various types of problems. The power of the WRPC test is slightly lower than the Haseman-Elston method for analyzing a large number of small randomly chosen pedigrees. It is higher however in presence of genetic heterogeneity or for analyzing large individual pedigrees. Recently, evidence of linkage of Alzheimer's disease with a locus on chromosome 14, D14s43, has been obtained by the Lod-score method. We reanalyze these data using the WRPC test, essentially confirming the results of the Lod-score method. The WRPC test statistic is higher than the equivalent Lod-score statistic for the two pedigrees which show strong evidence of linkage with the two methods. The global WRPC test statistic is slightly lower than the Lod-score test statistic. The WRPC test, however, makes no hypothesis of a specific genetic transmission model and can be computed very quickly; in addition, an exact P-value can be computed by simulation for individual pedigrees. © 1994 Wiley-Liss, Inc.     

东方人苯丙酮尿症的分子遗传学—苯丙氨酸羟化酶基因中一终止突变与单体型4的连锁不平衡性

应用聚合酶链反应(PCR)方法扩增苯丙氨酸羟化酶(PAH)基因的每个外显子及其侧翼的内含子,并克隆到M 13载体中进行序列分析。发现中国人苯丙酮尿症(Phenylketonuria,PKU)患者的PAH基因外显子3中有1个Arg~(111)→Ter~(111)的点突变,此突变与东方人最常见的突变单体型4呈连锁不平衡。此突变占中国人PAH等位基因的10％左右,但不存在于高加索人群中,表明在种族分化过程中PAH基因位点发生了互不相关的突变事件。     

云芝糖肽的结构组成分析

目的:对云芝糖肽的结构与组成进行研究.方法:采用还原衍生化气相色谱,紫外、核磁、高碘酸氧化、Smith降解、琼脂糖凝胶电泳等方法.结果:云芝糖肽由葡萄糖、半乳糖、岩藻糖、甘露糖、木糖和鼠李糖组成,具有α,β型糖苷键,连接方式有(1→4)、(1→6)两种,含有结合态蛋白,糖肽键类型初步确定为N-连接.结论:首次对云芝糖肽的化学结构与组成进行了较为细致的研究.     

Extended HLA profile of an inbred isolate: The Schmiedeleut Hutterites of South Dakota

HLA-A, -B, -C, -DR, and -DQ typings of the Schmiedeleut Hutterites of South Dakota were collected as part of an ongoing genetic-epidemiologic study of HLA and fertility. A total of 1,082 individuals, including 852 married adults representative of the reproductive population of this isolate, were characterized for five-locus HLA haplotypes. HLA-A1, A2, A3, and A24 accounted for 75% of observed HLA-A alleles and HLA-B27, B35, B51, and B62 accounted for 55% of observed HLA-B alleles. S-leut Hutterites are derived from 68 or fewer ancestors. However, only 48 ancestral HLA haplotypes were observed and nine of these accounted for over 52% of the observed haplotypes. Measures of two-locus linkage disequilibrium derived from these haplotypes indicated that one-third to half of the observed HLA-A/B, B/DR, and A/DR allele combinations exhibited highly statistically significant linkage disequilibrium. Allele and haplotype frequencies did not differ between males and females. Recombination rates of 0.004% and 0.005% between HLA-A and -C and between HLA-B and -DR, respectively, were observed. This HLA profile points out a paucity of HLA alleles and haplotypes in this population and marked linkage disequilibrium among the HLA alleles that are present. © Wiley-Liss, Inc.     

Fine mapping of X-linked clasped thumb and mental retardation (MASA syndrome) in Xq28

The MASA syndrome is an X-linked disorder with mental retardation, spastic paraparesis, and adducted thumbs as the most characteristic features. We performed linkage analysis, using Xq28 markers, on a large MASA syndrome family. The maximum lodscore was 6.37 at 0 recombination for DXS52 and 5.99 at 0 recombination for DXS305. Crossovers were demonstrated between the disorder and DXS455. Clinical and linkage data from this family further support the hypothesis that the MASA syndrome and X-linked hydrocephalus are allelic disorders.     

Statistical properties of the allelic and genotypic transmission/disequilibrium test for multiallelic markers

The transmission/disequilibrium test (TDT) is extended in two ways for a multiallelic marker: (1) to compare transmitted and nontransmitted alleles from a single heterozygous parent and (2) to compare genotypes formed by the two transmitted alleles and genotypes formed by the two nontransmitted alleles using the information on both parents, heterozygous or not, simultaneously. © 1995 Wiley-Liss, Inc.     

Association and linkage with quantitative traits

This paper examines two approaches for the analysis of quantitative traits: (1) association studies and (2) linkage studies. The trait studied was Q1 from simulated Problem 2 data set in Genetic Analysis Workshop 9. Our purpose was to evaluate associations present in the data, to identify nongenetic and genetic predictors of the trait, and to explore the simulated genome for linkage. Through the association study, we found evidence for the primary major gene associated with this trait. The linkage study found evidence of residual genetic effect acting through other traits. Adjustments of Q1 for Q2 and Q3 led to a failure to find significant effects of MG2 and MG3. This supports the suggestion that adjustment for genetically influenced traits for effects of other genetic traits can reduce the power to detect major gene effects. In summary, we detected the major gene directly associated with the trait of interest through association studies. Linkage analysis detected evidence for two other genes associated to a lesser degree with the trait. © 1995 Wiley-Liss, Inc.     

Attempted suicide in bipolar disorder pedigrees: evidence for linkage to 2p12.

BACKGROUND: We are interested in identifying susceptibility genes that predispose subjects to attempted suicide. METHODS: We conducted a secondary analysis of genome-wide linkage data from 162 bipolar pedigrees that incorporated attempted suicide as a clinical covariate. RESULTS: The strongest covariate-based linkage signal was seen on 2p12 at marker D2S1777. The logarithm of odds (LOD) score at marker D2S1777 rose from 1.56 to 3.82 after inclusion of the suicide covariate, resulting in significant chromosome-wide empirically derived p-values for the overall linkage finding (p = .01) and for the change in LOD score after the inclusion of the covariate (p = .02). CONCLUSIONS: The finding on chromosome 2 replicates results from two previous studies of attempted suicide in pedigrees with alcohol dependence and in pedigrees with recurrent early-onset depression. Combined, these three studies provide compelling evidence for a locus influencing attempted suicide on 2p12.     

The ordered transmission disequilibrium test: detection of modifier genes

We consider the problem of detection of modifier genes that lead to variations in a disease‐related continuous variable (DRCV), such as the age of onset or a measure of disease severity, in a strategy of candidate genes. We propose a novel method, the ordered transmission disequilibrium test (OTDT), to test for a relation between the clinical heterogeneity expressed by a DRCV and marker genotypes of a candidate gene. The OTDT applies to trio families with one patients and his parents, all three genotyped at a bi‐allelic marker M. The OTDT aims to find a critical value of the DRCV which separates the sample of families in two subsamples in which the transmission rates are significantly different. We investigate the power of the method by simulations under various genetic models and covariate distributions and compare it with a linear regression analysis. Genet. Epidemiol. 2008. ©2008 Wiley‐Liss, Inc.     

Characterization of an arabinogalactan protein from the pressed juice of <Emphasis Type="Italic">Echinacea purpurea</Emphasis>: investigations into the type of linkage between the protein and polysaccharide moieties

A high molecular weight arabinogalactan protein (AGP) from the pressed juice of Echinacea purpurea, known to exhibit immunomodulatory properties in vitro, was characterized. Alkaline hydrolysis was carried out, leading to degradation of the protein core and to carbohydrate moieties linked to the amino acid responsible for binding. Gel permeation chromatography of these AG subunits gave one peak with a molecular weight of 30 × 10³ Da. Hydroxyproline (42.9% w/w) was detected as the dominant amino acid after alkaline hydrolysis and was thus identified as the major amino acid responsible for the binding between the protein and the AG subunits via an O-glycosidic linkage. Large amounts of glutamine/glutamic acid (24.5% w/w) and asparagine/aspartic acid (17.3% w/w) were also found. Polyclonal antibodies raised against the intact AGP were shown to bind to the AG subunits too, indicating that the epitopes responsible for such interactions are localized in the polysaccharide moiety of the AGP.