GeneScreen最新文献_第3页

Distinct differences in a cyclin D1 single nucleotide polymorphism between ethnic groups 不同种族间细胞周期蛋白D1单核苷酸多态性的显著差异

GeneScreen Pub Date : 2002-01-25 DOI: 10.1046/j.1466-9218.2001.00014.x

Judith A. McKay, Jessie Githang’a, Anne Indalo, Tao Li, Xiehe Liu, Margaret-Mary Ameyaw, David Ofori-Adjei, Howard L. McLeod

引用次数: 6

Efficient SNP-based tests of association for quantitative phenotypes using pooled DNA 使用混合DNA进行定量表型关联的高效snp检测

GeneScreen Pub Date : 2002-01-25 DOI: 10.1046/j.1466-920x.2001.00036.x

Joel S. Bader, Aruna Bansal, Pak Sham

{"title":"Efficient SNP-based tests of association for quantitative phenotypes using pooled DNA","authors":"Joel S. Bader, Aruna Bansal, Pak Sham","doi":"10.1046/j.1466-920x.2001.00036.x","DOIUrl":"10.1046/j.1466-920x.2001.00036.x","url":null,"abstract":"Introduction Genetic factors underlying complex diseases are difficult to identify: many polymorphisms may contribute, each having a small effect and low penetrance. These factors may be identified by association studies of large populations, an alternative to family-based linkage studies. Allele frequency measurements of pooled DNA selected from population-level DNA repositories can reduce the costs of these studies. We provide guidance for selecting unrelated individuals for pooling and for comparing the power of studies based on pooled measurements to the power of individual genotyping, particularly for studies using single-nucleotide polymorphism (SNP) markers.Materials and methods We used exact numerical calculations to set pooling criteria that maximized the power to detect association as a function of marker frequency, inheritance mode, and additive variance. Analytical approximations are also provided.Results and discussion Power estimates are provided for two pooled DNA designs: the classification of individuals as affected or unaffected, analogous to a case-control design, and the optimized selection of individuals with extreme phenotypic values. Optimized selection is approximately fourfold more efficient than affected/unaffected classification. The optimal design for most markers is to pool the top and bottom 27% of individuals. Neglecting experimental measurement error, this design requires a population only 1.24-fold larger than that required for individual genotyping. When measurement error is included, the pooled DNA association test serves better as a pre-screen to identify candidate markers which then proceed to individual genotyping. This strategy can still provide a 100-fold savings over individual genotyping.","PeriodicalId":100575,"journal":{"name":"GeneScreen","volume":"1 3","pages":"143-150"},"PeriodicalIF":0.0,"publicationDate":"2002-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1046/j.1466-920x.2001.00036.x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75226573","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: 29

Simulation of a putative susceptibility risk factor to explain the findings of the Heart and Estrogen/progestin Replacement Study (HERS) 模拟一个假定的易感性风险因素来解释心脏和雌激素/黄体酮替代研究(HERS)的发现

GeneScreen Pub Date : 2002-01-25 DOI: 10.1046/j.1466-920x.2001.00035.x

Bruce M. Psaty, Mary Cushman, Frits R. Rosendaal

引用次数: 0

Identifying and characterizing a five-gene cluster of ATP-binding cassette transporters mapping to human chromosome 17q24: a new subgroup within the ABCA subfamily 鉴定和表征一个映射到人类染色体17q24的atp结合盒转运蛋白的五基因簇:ABCA亚家族中的一个新亚群

GeneScreen Pub Date : 2002-01-25 DOI: 10.1046/j.1466-920x.2001.00038.x

Isabelle Arnould, Lynn M. Schriml, Catherine Prades, Marcia Lachtermacher-Triunfol, Thomas Schneider, Christelle Maintoux, Cendrine Lemoine, Delphine Debono, Catherine Devaud, Laurent Naudin, Stéphanie Bauché, Mélanie Annat, Tarmo Annilo, Rando Allikmets, Bert Gold, Patrice Denèfle, Marie Rosier, Michael Dean

{"title":"Identifying and characterizing a five-gene cluster of ATP-binding cassette transporters mapping to human chromosome 17q24: a new subgroup within the ABCA subfamily","authors":"Isabelle Arnould, Lynn M. Schriml, Catherine Prades, Marcia Lachtermacher-Triunfol,  Thomas Schneider, Christelle Maintoux, Cendrine Lemoine, Delphine Debono, Catherine Devaud, Laurent Naudin, Stéphanie Bauché, Mélanie Annat, Tarmo Annilo, Rando Allikmets, Bert Gold, Patrice Denèfle, Marie Rosier, Michael Dean","doi":"10.1046/j.1466-920x.2001.00038.x","DOIUrl":"10.1046/j.1466-920x.2001.00038.x","url":null,"abstract":"<div>\u0000 \u0000 <section>\u0000 \u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Introduction</h3>\u0000 \u0000 The ATP-binding cassette (ABC) gene superfamily encodes a series of transporter proteins that move a wide variety of substances across extra- and intracellular membranes. Forty-eight known human ABC genes can be divided into seven phylogenetically distinct subfamilies. The ABCA gene subfamily is found exclusively in multicellular eukaryotes.\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 We report here on a unique tandem array of five ABCA genes on chromosome 17q24 defining a phylogenetically distinct group. This is the largest cluster of mammalian ABC genes described to date. They are arranged head-to-tail and have similar intron/exon organization in both mouse and human. Northern analysis reveals a heterogeneous pattern of expression in human tissues, with ABCA5 and ABCA10 expressed in skeletal muscle, ABCA6 in the liver, ABCA9 in the heart, and ABCA8 in ovaries. This suggests that these proteins have distinct functions.\u0000 </section>\u0000 </div>","PeriodicalId":100575,"journal":{"name":"GeneScreen","volume":"1 3","pages":"157-164"},"PeriodicalIF":0.0,"publicationDate":"2002-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1046/j.1466-920x.2001.00038.x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89212958","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: 20

Partial 2qter trisomy and partial 9pter monosomy associated with Charcot–Marie–Tooth disease Type 2 (CMT2) 与2型Charcot-Marie-Tooth病(CMT2)相关的部分2 / 4三体和部分9 / 4单体

GeneScreen Pub Date : 2002-01-25 DOI: 10.1046/j.1466-9218.2001.00010.x

引用次数: 0

Contamination of human genome sequence? The story of a fourth peroxisomal human acyl-CoA oxidase 人类基因组序列污染?第四个过氧化物酶体人类酰基辅酶a氧化酶的故事

GeneScreen Pub Date : 2002-01-25 DOI: 10.1046/j.1466-9218.2001.00034.x

引用次数: 0

Physical mapping of the MEGF1 gene, human homologue of the Drosophila tumour suppressor gene fat, to the critical region of the 5q-syndrome MEGF1基因的物理定位，果蝇肿瘤抑制基因脂肪的人类同源物，到5q综合征的关键区域

GeneScreen Pub Date : 2002-01-25 DOI: 10.1046/j.1466-9218.2001.00015.x

Carrie Fidler, Manabu Nakayama, Ethylin Wang Jabs, Jan-Fang Cheng, Amanda Strickson, Osamu Ohara, James S. Wainscoat, Jacqueline Boultwood

{"title":"Physical mapping of the MEGF1 gene, human homologue of the Drosophila tumour suppressor gene fat, to the critical region of the 5q-syndrome","authors":"Carrie Fidler, Manabu Nakayama, Ethylin Wang Jabs, Jan-Fang Cheng, Amanda Strickson, Osamu Ohara,  James S. Wainscoat, Jacqueline Boultwood","doi":"10.1046/j.1466-9218.2001.00015.x","DOIUrl":"10.1046/j.1466-9218.2001.00015.x","url":null,"abstract":"Introduction The 5q-syndrome is a myelodysplastic syndrome with the 5q deletion as the sole karyotypic abnormality. The MEGF1 gene is the human homologue of the Drosophilafat tumour suppressor gene.Results We have mapped this gene to the 3 Mb critical region of the 5q-syndrome within 5q31–32, using gene dosage analysis. Fine physical mapping of the MEGF1 gene within this genomic interval was then performed by screening YAC and BAC contigs spanning the critical region using PCR amplification. The MEGF1 gene maps between the genes for SPARC and Annexin-6 at 5q32, and is flanked by the genetic markers D5S2146 and D5S2077. We have demonstrated the expression of MEGF1 in a range of haematological tissues using RT-PCR analysis.Discussion Genomic localization, expression and predicted function would suggest that the MEGF1 gene represents a candidate gene for the 5q-syndrome.","PeriodicalId":100575,"journal":{"name":"GeneScreen","volume":"1 3","pages":"165-167"},"PeriodicalIF":0.0,"publicationDate":"2002-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1046/j.1466-9218.2001.00015.x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74566837","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

Precise mapping of the fragile site FRA12A on chromosome 12q13.1 染色体12q13.1上脆性位点FRA12A的精确定位

GeneScreen Pub Date : 2002-01-25 DOI: 10.1046/j.1466-9218.2001.00013.x

Birgitta Winnepenninckx, Edwin Reyniers, Paul Bossuyt, Arie Smits, Jan Wauters, R. Frank Kooy

{"title":"Precise mapping of the fragile site FRA12A on chromosome 12q13.1","authors":"Birgitta Winnepenninckx, Edwin Reyniers, Paul Bossuyt, Arie Smits, Jan Wauters, R. Frank Kooy","doi":"10.1046/j.1466-9218.2001.00013.x","DOIUrl":"10.1046/j.1466-9218.2001.00013.x","url":null,"abstract":"Introduction A causative relationship has been reported between fragile site expression and disease for FRA12A, a rare, folate-sensitive fragile site on chromosome 12q13.1. FRA12A expression has been described in a number of patients with mental retardation, sometimes in combination with clinical abnormalities. In correspondence to the molecular mechanism of previously cloned, rare, fragile sites, it may be expected that FRA12A is caused by repeat expansion, affecting the expression of genes in the region. To identify the repeat and the associated gene, this paper reports the precise mapping of FRA12A on chromosome 12q12–13.Methods Fluorescence in situ hybridization (FISH) techniques were used to map YAC and PAC clones in the neighbourhood of FRA12A. PAC DNA pools and PAC filters were screened to find additional PAC clones spanning the candidate region. Markers in the region were obtained via web searches and used to construct both PAC and YAC contigs.Results and Discussion A single YAC clone that overspans the fragile site was identified and a complete YAC and PAC contig for the FRA12A region was constructed. The region contains several candidate genes, including a calcium ion channel (CACNLB3), a GTP-binding factor (ARF3), a gene involved in brain development (INT1) and two other genes involved in developmental processes (WNT10B and ALR). The FXR1 gene, a homologue of the FMR1 gene, that is associated with fragile X syndrome and that maps to chromosome 12q12–13, was ruled out as a possible candidate gene for the FRA12A site.","PeriodicalId":100575,"journal":{"name":"GeneScreen","volume":"1 3","pages":"131-137"},"PeriodicalIF":0.0,"publicationDate":"2002-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1046/j.1466-9218.2001.00013.x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79095414","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: 1

Robustness of the maximum-likelihood-binomial approach for linkage analysis of quantitative trait loci with non-normal phenotypic data 最大似然二项法对非正常表型数量性状位点连锁分析的稳健性

GeneScreen Pub Date : 2001-12-25 DOI: 10.1046/j.1466-9218.2000.00003.x

Alexandre Alcaïs, Laurent Abel

{"title":"Robustness of the maximum-likelihood-binomial approach for linkage analysis of quantitative trait loci with non-normal phenotypic data","authors":"Alexandre Alcaïs, Laurent Abel","doi":"10.1046/j.1466-9218.2000.00003.x","DOIUrl":"10.1046/j.1466-9218.2000.00003.x","url":null,"abstract":"Introduction Model-free linkage studies are increasingly used to investigate the genetic factors implicated in complex quantitative traits because they do not require any specification of the underlying genetic model. However, the term model-free does not imply that no assumption is introduced by the corresponding statistical methods. In particular, the widely used variance components approaches assume multivariate normality of the phenotypic distribution and it has been shown that violation of this normality hypothesis could lead to large inflation of the type I error. In this paper, we assess the robustness of the recently developed sibship-oriented Maximum-Likelihood-Binomial (MLB) method for genetic model-free linkage analysis in the context of several types of non-normal phenotypic data using a large simulation study.Simulation study Under the hypothesis of no linkage at the marker locus under study, 20 000 replicates of family samples including 100 or 500 independent sib-pairs were simulated considering four different designs that lead to non-normal phenotypic data: (1) presence of a major gene not linked to the studied marker, (2) gene–environment interaction, (3) analysis of a binary phenotype, and (4) extreme sampling. Further, three levels of residual sib–sib correlation were considered.Results and discussion For each simulation design the empirical type I errors were consistent with their asymptotic expectations showing that the MLB approach is insensitive to non-normal phenotypic distribution whatever the mechanism underlying this non-normality. Therefore, the MLB method should be an attractive alternative method for model-free linkage analysis of QTL, especially for investigators who do not want to worry about the validity of asymptotic thresholds when performing their analyses.","PeriodicalId":100575,"journal":{"name":"GeneScreen","volume":"1 1","pages":"47-50"},"PeriodicalIF":0.0,"publicationDate":"2001-12-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1046/j.1466-9218.2000.00003.x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84723396","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: 4

Observation of null alleles of microsatellite markers in a Chinese population 中国人群微卫星标记零等位基因的观察

GeneScreen Pub Date : 2001-12-25 DOI: 10.1046/j.1466-9218.2000.00007.x

Zhaoxi Wang, Tianhua Niu, K. L. Lunetta, Xin Xu, Zhian Fang, Xiping Xu

{"title":"Observation of null alleles of microsatellite markers in a Chinese population","authors":"Zhaoxi Wang, Tianhua Niu, K. L. Lunetta, Xin Xu, Zhian Fang, Xiping Xu","doi":"10.1046/j.1466-9218.2000.00007.x","DOIUrl":"10.1046/j.1466-9218.2000.00007.x","url":null,"abstract":"Introduction Genotyping of a set of microsatellite markers is often necessary to map genes for complex human diseases by linkage analysis. Presence of null alleles (such as a mutation in the primer-binding sequence) can lead to pseudo-deficiency of heterozygosity.Materials and methods We completed a genomic scan using 367 autosomal markers on 1477 Chinese subjects in a total of 337 nuclear families. Two markers with apparent non-Mendelian inheritance patterns were further investigated: marker GGAA15B08 results were re-scored, and marker GATA29A01 was re-genotyped using redesigned primers.Results The GGAA15B08 marker was found to contain a relatively frequent (24.4%) 185-bp allele in the Chinese that was previously treated as a ‘null allele’. Marker GATA29A01 contained a null allele due to a mutation within the annealing region of its reverse primer. With a pair of redesigned PCR primers, the null allele diminished. In this study, we have a power > 82% to detect null alleles of frequency 0.04 or greater.Discussion The presence of GATA29A01 null alleles in this population was quite common (31.4%). Identification of markers with null alleles in our study has great implications in paternity testing, linkage analysis and forensic DNA testing. Particular care should be taken in analysing microsatellite genotype results to avoid this problem.","PeriodicalId":100575,"journal":{"name":"GeneScreen","volume":"1 1","pages":"41-45"},"PeriodicalIF":0.0,"publicationDate":"2001-12-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1046/j.1466-9218.2000.00007.x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73399670","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: 1