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A test for linkage and association in general pedigrees 一种在一般家谱中检测连锁和关联的测试
GeneScreen Pub Date : 2008-06-28 DOI: 10.1046/j.1466-9218.2000.00023.x
Norman L. Kaplan, Stephanie A. Monks, Eden R. Martin
{"title":"A test for linkage and association in general pedigrees","authors":"Norman L. Kaplan,&nbsp;Stephanie A. Monks,&nbsp;Eden R. Martin","doi":"10.1046/j.1466-9218.2000.00023.x","DOIUrl":"10.1046/j.1466-9218.2000.00023.x","url":null,"abstract":"<p>Family-based tests of linkage disequilibrium are usually based on nuclear family data including affected individuals and their parents or their unaffected siblings. A problem with these tests is that they are not valid tests of association when data from related nuclear families from larger pedigrees are used. One way to ensure validity when testing for association is to select a single nuclear family from each extended pedigree in the sample. When data are available for larger pedigrees, it would be desirable to have a valid test of linkage disequilibrium that can use all potentially informative data. In this paper we present such a test: the Pedigree Disequilibrium Test (PDT). The PDT can use data from related nuclear families from extended pedigrees and remains valid when there is population substructure. Power simulations demonstrate that, when extended pedigree data are available, gains in power can be obtained by using the PDT rather than existing methods that only use a subset of the data. The PDT can also be more powerful than current methods when the data consist of a sample of independent nuclear families or sibships.</p>","PeriodicalId":100575,"journal":{"name":"GeneScreen","volume":"1 2","pages":"65-67"},"PeriodicalIF":0.0,"publicationDate":"2008-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1046/j.1466-9218.2000.00023.x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"57739868","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 463
The use of Mx for association and linkage analysis 使用Mx进行关联和连锁分析
GeneScreen Pub Date : 2008-06-28 DOI: 10.1046/j.1466-9218.2000.00032.x
Michael C. Neale
{"title":"The use of Mx for association and linkage analysis","authors":"Michael C. Neale","doi":"10.1046/j.1466-9218.2000.00032.x","DOIUrl":"10.1046/j.1466-9218.2000.00032.x","url":null,"abstract":"<p>Evidence for genetic linkage, obtained from a correlation between phenotypic similarity and genetic similarity at a specific chromosomal location typically yields a broad genomic region in which a candidate locus might be found. Evidence for association is usually gathered from case control studies and is subject to false positives from phenomena such as population stratification. Data from relatives may be used to distinguish population stratification from genuine allelic effects in an association context. Of special interest is joint linkage and association which may be used for fine mapping because evidence for linkage will be reduced in the presence of evidence for association. This article describes the implementation of these methods using Mx, in both path diagram and script formats, and discusses a number of possible extensions to the model.</p>","PeriodicalId":100575,"journal":{"name":"GeneScreen","volume":"1 2","pages":"107-111"},"PeriodicalIF":0.0,"publicationDate":"2008-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1046/j.1466-9218.2000.00032.x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77438526","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 12
Sib-TDT analysis of human TGF-β1 gene single nucleotide polymorphisms in female twins: evidence for linkage and association with blood pressure at the codon 263 polymorphism 女性双胞胎中人类TGF-β1基因单核苷酸多态性的Sib-TDT分析:密码子263多态性与血压相关的证据
GeneScreen Pub Date : 2008-06-28 DOI: 10.1046/j.1466-9218.2000.00019.x
H. Snieder, Ejcg Van Den Oord, M. Chiano, Aj MacGregor,  Td Spector
{"title":"Sib-TDT analysis of human TGF-β1 gene single nucleotide polymorphisms in female twins: evidence for linkage and association with blood pressure at the codon 263 polymorphism","authors":"H. Snieder,&nbsp;Ejcg Van Den Oord,&nbsp;M. Chiano,&nbsp;Aj MacGregor,&nbsp; Td Spector","doi":"10.1046/j.1466-9218.2000.00019.x","DOIUrl":"10.1046/j.1466-9218.2000.00019.x","url":null,"abstract":"<p>We illustrate the use of a quantitative trait locus (QTL) association test with data on blood pressure and six single nucleotide polymorphisms (SNPs) within the transforming growth factor-β1(<i>TGF-β1</i>) gene in a large sample of dizygotic (DZ) twins. The test was specified within the framework of structural equation modelling and allows for population stratification and easily incorporates confounders. Results showed linkage in the presence of association between the <i>TGF-β1 263</i> polymorphism and blood pressure levels, with carriers showing a clinically significant increase of 6 and 4 mm Hg in systolic and diastolic blood pressure, respectively. The described association test offers an easy and flexible way to analyse QTL data in sib or DZ twin pairs while controlling for population stratification by making use of within-family controls.</p>","PeriodicalId":100575,"journal":{"name":"GeneScreen","volume":"1 2","pages":"89-91"},"PeriodicalIF":0.0,"publicationDate":"2008-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1046/j.1466-9218.2000.00019.x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82239927","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 7
Fine-scale mapping of disease loci 疾病位点的精细制图
GeneScreen Pub Date : 2008-06-28 DOI: 10.1046/j.1466-9218.2000.00030.x
J. C. Whittaker, A. P. Morris, D. J. Balding
{"title":"Fine-scale mapping of disease loci","authors":"J. C. Whittaker,&nbsp;A. P. Morris,&nbsp;D. J. Balding","doi":"10.1046/j.1466-9218.2000.00030.x","DOIUrl":"10.1046/j.1466-9218.2000.00030.x","url":null,"abstract":"<p>We review the issues involved in the fine-scale mapping of disease loci via allelic association. We argue that it is vital to properly account for uncertainty about the genealogy of the disease locus and founding haplotypes at the surrounding markers: we sketch how this might be done in a Bayesian framework using Markov chain Monte Carlo tecniques, and show that this works well for the much analysed data on the location of the Δ508 mutation for cystic fibrosis.</p>","PeriodicalId":100575,"journal":{"name":"GeneScreen","volume":"1 2","pages":"101-102"},"PeriodicalIF":0.0,"publicationDate":"2008-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1046/j.1466-9218.2000.00030.x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86394360","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
A new test for linkage in affected sib pairs 一种检测受影响兄弟姐妹连锁的新方法
GeneScreen Pub Date : 2008-06-28 DOI: 10.1111/j.1466-9218.2000.00026.pp.x
Sanjay S. Shete, Christopher I. Amos
{"title":"A new test for linkage in affected sib pairs","authors":"Sanjay S. Shete,&nbsp;Christopher I. Amos","doi":"10.1111/j.1466-9218.2000.00026.pp.x","DOIUrl":"10.1111/j.1466-9218.2000.00026.pp.x","url":null,"abstract":"<p>In affected sib pair linkage methods the mean proportion of marker alleles shared identical by descent (ibd) among affected sib pairs has been shown to be a powerful test for detecting linkage compared with other tests for most situations. However, it is not always possible to estimate identity by descent sharing between sibs unambiguously, even when the parental genotypes are known. Here we define a measure of informativity for scoring ibd sharing based on the parental mating and sib pair genotypes. This measure reflects the precision with which one can obtain the ibd sharing information between sibs based on family data. Then we define a new weighted mean proportion of alleles shared ibd by sib pairs test statistics. In this study we assign precision for estimating the ibd sharing as weights to the proportion of alleles shared ibd by affected sib pairs. However, the simulation results showed that there is no significant gain in power using the weighted mean proportion test. Implications of this observation are discussed.</p>","PeriodicalId":100575,"journal":{"name":"GeneScreen","volume":"1 2","pages":"53-54"},"PeriodicalIF":0.0,"publicationDate":"2008-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1111/j.1466-9218.2000.00026.pp.x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91496298","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Power of the TDT to detect association: effect of linkage disequilibrium between genetic markers and an unobserved disease mutation TDT检测关联的能力:遗传标记与未观察到的疾病突变之间连锁不平衡的影响
GeneScreen Pub Date : 2008-06-28 DOI: 10.1046/j.1466-9218.2000.00022.x
Cathryn M. Lewis, Sheila A. Fisher
{"title":"Power of the TDT to detect association: effect of linkage disequilibrium between genetic markers and an unobserved disease mutation","authors":"Cathryn M. Lewis,&nbsp;Sheila A. Fisher","doi":"10.1046/j.1466-9218.2000.00022.x","DOIUrl":"10.1046/j.1466-9218.2000.00022.x","url":null,"abstract":"<p>The transmission disequilibrium test (TDT) is widely used to test for association in families. Many previous papers have shown sample size calculations where the true disease mutation is tested. When a neighbouring marker is used in place of the mutation, the power to detect association depends on the linkage disequilibrium between the loci. A difference in frequency between the mutation and the tested allele, or a reduction in linkage disequilibrium will substantially increase the required sample size. If a study design includes reasonable assumptions regarding linkage disequilibrium, using the TDT with anonymous nonfunctional markers may not be feasible.</p>","PeriodicalId":100575,"journal":{"name":"GeneScreen","volume":"1 2","pages":"69-71"},"PeriodicalIF":0.0,"publicationDate":"2008-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1046/j.1466-9218.2000.00022.x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78763425","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
Uses of twins in studying the genetics of complex traits 利用双胞胎研究复杂性状的遗传学
GeneScreen Pub Date : 2008-06-28 DOI: 10.1046/j.1466-9218.2000.00020.x
Tim D. Spector, Alex J. MacGregor, Harold Snieder
{"title":"Uses of twins in studying the genetics of complex traits","authors":"Tim D. Spector,&nbsp;Alex J. MacGregor,&nbsp;Harold Snieder","doi":"10.1046/j.1466-9218.2000.00020.x","DOIUrl":"10.1046/j.1466-9218.2000.00020.x","url":null,"abstract":"Twins provide a useful and powerful tool for identifying genes, by acting as ideally matched sib-pairs, but are also uniquely placed to measure the extent of their action, their expression and the nature of their interaction with the environment. Classical twin studies have provided insight into the relative genetic and environmental contribution to characteristics and diseases in human populations. The search for a more detailed understanding of genetic mechanisms through linkage and association has, however, traditionally been regarded as the province of other family designs. The last few years have seen a resurgence of interest in twin research following an increasing awareness that the study of twins can also provide an important contribution to localizing and understanding the function of specific genes.1 In this brief overview, we focus on these newer developments that are currently being applied in the search to uncover the genetic basis of disease.","PeriodicalId":100575,"journal":{"name":"GeneScreen","volume":"1 2","pages":"93-95"},"PeriodicalIF":0.0,"publicationDate":"2008-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1046/j.1466-9218.2000.00020.x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88115242","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
Challenges for genetic analysis in the 21st century: localizing and characterizing genes for common complex diseases and their quantitative risk factors 21世纪遗传分析的挑战:定位和表征常见复杂疾病的基因及其定量风险因素
GeneScreen Pub Date : 2008-06-28 DOI: 10.1046/j.1466-9218.2000.00033.x
L. Almasy, J. Blangero
{"title":"Challenges for genetic analysis in the 21st century: localizing and characterizing genes for common complex diseases and their quantitative risk factors","authors":"L. Almasy,&nbsp;J. Blangero","doi":"10.1046/j.1466-9218.2000.00033.x","DOIUrl":"10.1046/j.1466-9218.2000.00033.x","url":null,"abstract":"<p>The optimal study design and method of analysis for genetic studies of complex traits have received much attention of late. Most previous works on this topic have assumed that investigators will study a single focal disease trait. In this paper, we approach the question of study design from the perspective of the inherently multivariate study which includes a variety of quantitative risk factors as well as one or more common complex disease traits. We conclude that a sample of randomly ascertained extended pedigrees provides both analytical power and flexibility, permitting profitable investigation of numerous traits using both linkage and linkage-disequilibrium based methods.</p>","PeriodicalId":100575,"journal":{"name":"GeneScreen","volume":"1 2","pages":"113-116"},"PeriodicalIF":0.0,"publicationDate":"2008-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1046/j.1466-9218.2000.00033.x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78380365","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
Linkage disequilibrium in maps of SNPs and other markers snp和其他标记图谱中的连锁不平衡
GeneScreen Pub Date : 2008-06-28 DOI: 10.1111/j.1466-9218.2000.00024.pp.x
Andrew Collins
{"title":"Linkage disequilibrium in maps of SNPs and other markers","authors":"Andrew Collins","doi":"10.1111/j.1466-9218.2000.00024.pp.x","DOIUrl":"10.1111/j.1466-9218.2000.00024.pp.x","url":null,"abstract":"<p>One strategy for detection of disease genes is to exploit linkage disequilibrium in the hope that in candidate regions there will be detectable association between disease and marker alleles. Maps of single nucleotide polymorphisms (SNPs) will be used for this purpose but a recent simulation suggests that a useful level of linkage disequilibrium is unlikely to extend beyond an average distance of 3 Kb in the general population. This implies that very high marker densities will be required to detect disease: SNP associations. The evidence from published data comprising 877 SNP pairs is presented. For comparison, associations between other pairs of markers, principally microsatellites, are examined in a large sample of haplotypes from the fragile X (FRAX) region in Xq27–28.</p><p>Association ρ is estimated from haplotype frequencies and the decline in linkage disequilibrium with distance is described using the model originally described by Malecot. The evidence from SNP pairs suggest that linkage disequilibrium extends to at least 263 Kb in random haplotypes, but with a considerable amount of variation particularly at small distances. For microsatellites in the FRAX region disequilibrium extends to at least 435 Kb. This suggests that a genome scan with markers spaced every 100 Kb would be powerful (30 000 markers per genome). Higher densities might be required in some genomic regions and presumably will be required to determine causal SNPs.</p>","PeriodicalId":100575,"journal":{"name":"GeneScreen","volume":"1 2","pages":"59-61"},"PeriodicalIF":0.0,"publicationDate":"2008-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1111/j.1466-9218.2000.00024.pp.x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75961352","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The genetic characteristics of the osteoporosis phenotype 骨质疏松症表型的遗传特征
GeneScreen Pub Date : 2008-06-28 DOI: 10.1046/j.1466-9218.2000.00016.x
A. J. MacGregor
{"title":"The genetic characteristics of the osteoporosis phenotype","authors":"A. J. MacGregor","doi":"10.1046/j.1466-9218.2000.00016.x","DOIUrl":"10.1046/j.1466-9218.2000.00016.x","url":null,"abstract":"<p>Osteoporosis fits well into the category of complex disease with multiple genes and environmental factors likely to be involved in its development. The osteoporosis phenotype itself comprises a number of component parts, aspects of which are captured differently by a range of different clinical and laboratory measurements. This review discusses the nature of the genetic factors that underlie this complex phenotype and considers approaches that take into account this complexity in modelling the effects of specific genes.</p>","PeriodicalId":100575,"journal":{"name":"GeneScreen","volume":"1 2","pages":"73-76"},"PeriodicalIF":0.0,"publicationDate":"2008-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1046/j.1466-9218.2000.00016.x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83538544","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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