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SHEsis,a powerful software platform for analyses of linkage disequilibrium,haplotype construction,and genetic association at polymorphism loci

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Cell Research 2005年第2期15卷 97-98页

作者： Yong Yong SHI1,2, Lin HE2,3,*1Bio-X Life Science Research Center, Shanghai Jiao Tong University, Shanghai, China 2Institute for Nutritional Sciences, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai,China 3NHGG, Bio-X Center, Shanghai Jiao Tong University, Shanghai, China Bio-X Life Science Research Center Shanghai Jiao Tong University Shanghai China Institute for Nutritional Sciences Shanghai Institute of Biological Sciences Chinese Academy of Sciences Shanghai China NHGG Bio-X Center Shanghai Jiao Tong University Shanghai China

In multiloci-based genetic association studies of complex diseases, a powerful and high efficient tool for analyses oflinkage disequilibrium (LD) between markers, haplotype distributions and many chi-square/p values with a large numberof samples has been sought for long. In order to achieve the goal of obtaining meaningful results directly from raw data,we developed a robust and user-friendly software platform with a series of tools for analysis in association study withhigh efficiency. The platform has been well evaluated by several sets of real data.

关键词： software linkage disequilibrium haplotype analysis genetic association study.

Haplotype phasing after joint estimation of recombination and linkage disequilibrium in breeding populations

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Journal of Animal Science and Biotechnology 2014年第1期5卷 38-52页

作者： Luis Gomez-Raya Amanda M Hulse David Thain Wendy M Rauw Departamento de Mejora Genética Animal Instituto Nacional deInvestigación y Tecnología Agraria y Alimentaria (INIA) Interdisciplinary Program in Genetics Texas A&M University College Station Department of Animal Biotechnology University of Nevada

A novel method for haplotype phasing in families after joint estimation of recombination fraction and linkage disequilibrium is developed. Results from Monte Carlo computer simulations show that the newly developed E.M. algorithm is accurate if true recombination fraction is 0 even for single families of relatively small sizes. Estimates of recombination fraction and linkage disequilibrium were 0.00 （SD 0.00） and 0.19 （SD 0.03） for simulated recombination fraction and linkage disequilibrium of 0.00 and 0.20, respectively. A genome fragmentation phasing strategy was developed and used for phasing haplotypes in a sire and 36 progeny using the 50 k Illumina BeadChip by： a） estimation of the recombination fraction and LD in consecutive SNPs using family information, b） linkage analyses between fragments, c） phasing of haplotypes in parents and progeny and in following generations. Homozygous SNPs in progeny allowed determination of paternal fragment inheritance, and deduction of SNP sequence information of haplotypes from dams. The strategy also allowed detection of genotyping errors. A total of 613 recombination events were detected after linkage analysis was carried out between fragments. Hot and cold spots were identified at the individual （sire level）. SNPs for which the sire and calf were heterozygotes became informative （over 90%） after the phasing of haplotypes. Average of regions of identity between half-sibs when comparing its maternal inherited haplotypes （with at least 20 SNP） in common was 0.11 with a maximum of 0.29 and a minimum of 0.05. A Monte-Carlo simulation of BTA1 with the same linkage disequilibrium structure and genetic linkage as the cattle family yielded a 99.98 and 99.94% of correct phases for informative SNPs in sire and calves, respectively.

关键词： Breeding Haplotype phasing linkage disequilibrium SNP

Distribution Characteristics and linkage disequilibrium of TIM4 Promoter Polymorphisms in Asthma Patients of Chinese Han Population

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Journal of Huazhong University of Science and Technology(Medical Sciences) 2008年第4期28卷 447-450页

作者：蔡鹏程武其文王琳熊娟陈凤花胡丽华 Department of Clinical Laboratory Union Hospital Huazhong University of Science and Technology

To investigate the distribution characteristics and linkage disequilibrium of T cell immunoglobulin domain and mucin domain protein 4 （TIM4） promoter polymorphisms in asthma patients of Chinese Han population, the promoter region of TIM4 was re-sequenced by PCR-sequencing, and linkage disequilibrium was analyzed by SHEsis software. Four single nucleotide polymor- phisms （SNPs） in the promoter region of TIM4 were detected, including two new SNPs （at positions -1609, -153） and two reported SNPs （rs6874202, rs6882076）. The frequency distribution of rs6882076 was different among different races （P〈0.05）. In addition, linkage disequilibrium among the SNPs of the promoter region of TIM4 was found and GGTG was the predominant haplotype. There were four SNPs in the promoter region of TIM4 in asthma patients of Chinese Han population, which were in linkage disequilibrium.

关键词： asthma T cell immunoglobulin domain and mucin domain protein 4 single nucleotidepolymorphism linkage disequilibrium

Identification of Single Nucleotide Polymorphisms and Analysis of linkage disequilibrium in Different Bamboo Species Using the Candidate Gene Approach

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Phyton-International Journal of Experimental Botany 2021年第6期90卷 1697-1709页

作者： Xihua Liu Min Luo Xiaofei Chen Changjun Ding Fujian Provincial Key Laboratory of Resources and Environment Monitoring&Sustainable Management and Utilization Sanming UniversitySanming36504China Research Institute of Forestry Chinese Academy of ForestryKey Laboratory of Tree Breeding and CultivationState Forestry AdministrationBeijing100091China

Bamboos are one of the most beautiful and useful plants on Earth.The genetic background and population structure of bamboos are well known,which helps accelerate the process of artificial domestication of bamboo.Partial sequences of six genes involved in nitrogen use efficiency in 32 different bamboo species were analyzed for occurrence of single nucleotide polymorphisms(SNPs).The nucleotide diversityθw and total nucleotide polymorphismsπT of the sequenced DNA regions was 0.05137 and 0.03332,respectively.Bothπnonsyn/πsyn and Ka/Ks values were0.1.Estimation and analysis of linkage disequilibrium of five genes revealed that with the increase in nucleotide sequence length,the degree of SNP linkage disequilibrium decreased rapidly.We inferred the population genetic structure of 32 bamboo species based on the SNP loci of six genes with frequencies>18%.32 bamboo species were divided into five categories,which indicated that the combined population of all bamboo species had obvious multivariate characteristics and was heterogeneous;red(Group 1)and green(Group 2)were the main groups.

关键词： Bamboo nitrogen use efficiency single nucleotide polymorphism linkage disequilibrium

Testing for Homogeneity of linkage disequilibrium Across Strata

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Northeastern Mathematical Journal 2007年第4期23卷 311-320页

作者：郝立柱阴小林 Institute of Mathematics Jilin University Changehun 130012 Key Laboratory for Applied Statistics of MOE and School of Mathematics and Statistics Northeast Normal University Changchun 130024

In this article, using the likelihood score theory extended to nuisance parameters we derive a new homogeneity score test for comparing linkage disequilibrium across several strata. Power and sample size formulae are... 详细信息

关键词： linkage disequilibrium homogeneity score test

ezQTL:A Web Platform for Interactive Visualization and Colocalization of QTLs and GWAS Loci

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Genomics, Proteomics & Bioinformatics 2022年第3期20卷 541-548页

作者： Tongwu Zhang Alyssa Klein Jian Sang Jiyeon Choi Kevin M.Brown Division of Cancer Epidemiology and Genetics National Cancer InstituteBethesdaMD 20892USA

Genome-wide association studies(GWAS)have identified thousands of genomic loci associated with complex diseases and traits,including cancer.The vast majority of common traitassociated variants identified via GWAS fall in non-coding regions of the genome,posing a challenge in elucidating the causal variants,genes,and mechanisms involved.Expression quantitative trait locus(eQTL)and other molecular QTL studies have been valuable resources in identifying candidate causal genes from GWAS loci through statistical colocalization methods.While QTL colocalization is becoming a standard analysis in post-GWAS investigation,an easy web tool for users to perform formal colocalization analyses with either user-provided or public GWAS and eQTL datasets has been lacking.Here,we present ezQTL,a web-based bioinformatic application to interactively visualize and analyze genetic association data such as GWAS loci and molecular QTLs under different linkage disequilibrium(LD)patterns(1000 Genomes Project,UK Biobank,or user-provided data).This application allows users to perform data quality control for variants matched between different datasets,LD visualization,and two-trait colocalization analyses using two state-of-the-art methodologies(eCAVIAR and HyPrColoc),including batch processing.ezQTL is a free and publicly available cross-platform web tool,which can be accessed online at https://analysistools.***.gov/ezqtl.

关键词： Genome-wide association study Expression quantitative trait locus Colocalization linkage disequilibrium Visualization

Identification of genomic regions distorting population structure inference in diverse continental groups

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Quantitative Biology 2022年第3期10卷 287-298页

作者： Qiuxuan Liu Degang Wu Chaolong Wang Department of Epidemiology and Biostatistics Ministry of Education Key Laboratory of Environment and Health and State Key Laboratory of Environmental Health(Incubating)School of Public HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhan 430030China

Background:Inference of population structure is crucial for studies of human evolutionary history and genome-wide association studies.While several genomic regions have been reported to distort population structure analysis of European populations,no systematic analysis has been performed on non-European continental groups and with the latest human genome assembly.Methods:Using the 1000 Genomes Project high coverage whole-genome sequencing data from four major continental groups(Europe,East Asia,South Asia,and Africa),we developed a statistical framework and systematically detected genomic regions with unusual contributions to the inference of population structure for each of the continental groups.Results:We identified and characterized 27 unusual genomic regions mapped to GRCh38,including 13 regions around centromeres,2 with chromosomal inversions,8 under natural selection,and 4 with unknown causes.Excluding these regions would result in a more interpretable population structure inferred by principal components analysis and ADMIXTURE analysis.Conclusions:Unusual genomic patterns in certain regions can distort the inference of population structure.Our compiled list of these unusual regions will be useful for many population-genetic studies,including those from non-European populations.Availability:The code to reproduce our results is available at the website of Github(/dwuab/UnRegFinder).

关键词： population genetics population structure linkage disequilibrium principal component analysis natural selection

Bivariate association analysis for quantitative traits using generalized estimation equation

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Journal of Genetics and Genomics 2009年第12期36卷 733-743页

作者： Fang Yang Zihui Tang Hongwen Deng Laboratory of Molecular and Statistical Genetics College of Life Sciences Hunan Normal University Changsha 410081 China Center of Systematic Biomedical Research Shanghai University of Science and Technology Shanghai 200093 China Departments of Orthopedic Surgery and Basic Medical Sciences University of Missouri-Kansas City Kansas City MO 64108 USA

Quantitative traits often underlie risk for complex diseases. Many studies collect multiple correlated quantitative phenotypes and perform univariate analyses on each of them respectively. However, this strategy may not be powerful and has limitations to detect plei- otropic genes that may underlie correlated quantitative traits. In addition, testing multiple traits individually will exacerbate perplexing problem of multiple testing. In this study, generalized estimating equation 2 （GEE2） is applied to association mapping of two correlated quantitative traits. We suppose that a quantitative trait locus is located in a chromosome region that exerts pleiotropic effects on multiple quantitative traits. In that region, multiple SNPs are genotyped. Genotypes of these SNPs and the two quantitative traits affected by a causal SNP were simulated under various parameter values： residual correlation coefficient between two traits, causal SNP heritability, minor allele frequency of the causal SNP, extent of linkage disequilibrium with the causal SNP, and the test sample size. By power ana- lytical analyses, it is showed that the bivariate method is generally more powerful than the univariate method. This method is robust and yields false-positive rates close to the pre-set nominal significance level. Our real data analyses attested to the usefulness of the method.

关键词： general estimating equation bivariate quantitative trait linkage disequilibrium

Association of USP26 haplotypes in men in Taiwan, China with severe spermatogenic defect

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Asian Journal of Andrology 2008年第6期10卷 896-904页

作者： I-Wen Lee Long-Ching Kuan Chien-Hung Lin Hsien-An Pan Chao-Chin Hsu Yung-Chieh Tsai Pao-Lin Kuo Yen-Ni Teng Department of Obstetrics ＆ Gynecology National Cheng Kung University College of Medicine Tainan 701 Taiwan China Department of Obstetrics and Gynecology Kuo General Hospital Tainan 700 Taiwan China Institute of Basic Sciences National Cheng Kung University College of Medicine Tainan 701 Taiwan China Department of Obstetrics and Gynecology China Medical University Taichung 404 Taiwan China Department of Obstetrics and Gynecology Chi-Mei Medical Center Tainan 710 Taiwan China Department of Biotechnology Chia Nan University of Pharmacy and Science Tainan 717 Taiwan China

Aim： To complete comprehensive haplotype analysis of USP26 for both fertile and infertile men. Methods： Two hundred infertile men with severe oligospermia or non-obstructive azoospermia were subjected to sequence analysis for the entire coding sequences of the USP26 gene. Two hundred men with proven fertility were genotyped by primer extension methods. Allele/genotype frequencies, linkage disequilibrium （LD） characteristics and haplotypes of fertile men were compared with infertile men. Results： The allele frequencies of five single nucleotide polymor- phisms （370-37 linsACA, 494T〉C, 576G〉A, ss6202791C〉T, 1737G〉A） were significantly higher in infertile patients than control subjects. The major haplotypes in infertile men were TACCGA （28% of the population）, TGCCGA （15%）, TACCAA （8%）, TGCCAA （6%）, TATCAA （5%） and CATCAA （5%）. The major haplotypes for the control subjects were TACCGA （58% of the population）, CACCGA （7%）, CATCGA （6%） and TGCCGA （5%）. Haplotypes TGCCGA, TATCAA, CATCAA, CATCGC, TACCAA and TGCCAA were over-transmitted in patients with spermato- genic defect, whereas haplotypes TACCGA, CACCGA, and CATCGA were under-transmitted in these patients. Conclusion： Some USP26 alleles and haplotypes are associated with spermatogenic defect in the Han nationality in Taiwan, China.

关键词： single nucleotide polymorphism USP26 gene spermatogenic defect linkage disequilibrium