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Bivariate association analysis for quantitative traits using generalized estimation equation

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

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Paleotopographic controls on facies development in various types of braid-delta depositional systems in lacustrine basins in China

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Geoscience Frontiers 2015年第4期6卷 579-591页

作者： Dong Feng hongwen deng Zhan Zhou Xiaopeng Gao Longtao Cui School of Energy Resources China University of Geosciences (Beijing) Zhanjiang Branch of China National Offshore Oil Corporation Ltd SINOPEC Exploration and Production Research Institute

Braid-delta depositional systems are widely developed in most continental basins in China. Research indicates that, for different types of braid delta, the facies sequence and association, which are critical to the prediction of the distribution of reservoirs, differ greatly. This study illustrates the differences in braid-delta depositional systems in terms of sedimentary characteristics, associated systems and reser- voir distributions using three typical paleodeltas in western China： the Zhenbei delta of the upper Triassic Yanchang Formation in the Ordos Basin, the Yuanba delta of the upper Triassic Xujiahe Formation in the Sichuan Basin and the Jimsar delta of the upper Permian Wutonggou Formation in the Junggar Basin. A stratigraphic framework was established using seismic data, logs and cores by choosing stable mud sections as regional correlation markers and, topographies of these deltas were reconstructed based on the decompaction and paleobathymetric corrections. Based on both the paleotopography of these deltas and the differences of their sedimentary facies, these braided deltas can be classified into two systems： steep-gradient braid-delta-turbidite system and low-gradient braid-delta-lacustrine system. Moreover, the low-gradient braid-delta-lacustrine system can be further divided into interfingered and sharp contact sub-types according to the contact relation between the delta sands and lacustrine muds. This study shows that the paleotopography of basin margins strongly controls the accommodation as braid deltas prograde into lacustrine basins and, influences the location of the shoreline in response to changes in the lake level. Furthermore, paleotopography plays a significant role in facies and reservoir distribution which is important for petroleum exploration and development.

关键词： Paleotopography Braid deltas Facies Basin margin Lacustrine basins

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Bivariate whole-genome linkage scan for bone geometry and total body fat mass

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Journal of Genetics and Genomics 2009年第2期36卷 89-97页

作者： Shufeng Lei Feiyan deng Peng Xiao Kai Zhong Hongyi deng Robert R. Recker hongwen deng Laboratory of Molecular and Statistical Genetics College of Life Sciences Hunan Normal University Changsha 410081 China Osteoporosis Research Center and Department of Biomedical Sciences Creighton University Medical Center Omaha NE 68131 USA Departments of Orthopedic Surgery and Basic Medical Sciences University of Missouri-Kansas City Kansas City Missouri 64108-2792 USA

To quantify the genetic correlations between total body fat mass （TBFM） and femoral neck geometric parameters （FNGPs） and, if pos- sible, to detect the specific genomic regions shared by them, bivariate genetic analysis and bivariate whole-genome linkage scan were carried out in a large Caucasian population. All the phenotypes studied were significantly controlled by genetic factors （P 〈 0.001） with the heritabilities ranging from 0.45 to 0.68. Significantly genetic correlations were found between TBFM and CSA （cross-section area）, W （sub-periosteal diameter）, Z （section modulus） and CT （cortical thickness） except between TBFM and BR （buckling ratio）. The peak bivariate LOD scores were 3.23 （20q12）, 2.47 （20p11）, 3.19 （6q27）, 1.68 （20p12）, and 2.47 （7q11） for the five pairs of TBFM and BR, CSA, CT, W, and Z in the entire sample, respectively. Gender-specific bivariate linkage evidences were also found for the five pairs. 6p25 had complete pleiotropic effects on the variations of TBFM ＆ Z in the female sub-population, and 6q27 and 17q11 had coincident link- ages for TBFM ＆ CSA and TBFM ＆ Z in the entire population. We identified moderate genetic correlations and several shared genomic regions between TBFM and FNGPs in a large Caucasian population.

关键词： bivariate whole-genome linkage scan total body fat mass bone geometry genetic correlation

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Bivariate genome-wide association study suggests that the DARC gene influences lean body mass and age at menarche

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Science China(Life Sciences) 2012年第6期55卷 516-520页

作者： HAI Rong ZHANG Lei PEI YuFang ZHAO LanJuan RAN Shu HAN YingYing ZHU XueZhen SHEN Hui TIAN Qing deng hongwen Center of System Biomedical Sciences University of Shanghai for Science and Technology Shanghai 200093 China The Affiliated Hospital of lnner Mongolia Medical College Huhhot 010050. China Department of Biostatistics Tulane University. New Orleans LA 70112 USA

Lean body mass （LBM） and age at menarche （AAM） are two important complex traits for human health. The aim of this study was to identify pleiotropic genes for both traits using a powerful bivariate genome-wide association study （GWAS）. Two stud- ies, a discovery study and a replication study, were performed. In the discovery study, 909622 single nucleotide polymor- phisms （SNPs） were genotyped in 801 unrelated female Han Chinese subjects using the Affymetrix human genome-wide SNP array 6.0 platform. Then, a bivariate GWAS was performed to identify the SNPs that may be important for LBM and AAM. In the replication study, significant findings from the discovery study were validated in 1692 unrelated Caucasian female subjects One SNP rs3027009 that was bivafiately associated with left arm lean mass and AAM in the discovery samples （P=7.26x10-6） and in the replication samples （P=0.005） was identified. The SNP is located at the upstream of DARC （Duffy antigen receptor for chemokines） gene, suggesting that DARC may play an important role in regulating the metabolisms of both LBM and AAM.

关键词： bivariate genome-wide association study age at menarche lean body mass DARC gene

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Shear mechanical properties and fracturing responses of layered rough jointed rock-like materials

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International Journal of Minerals, Metallurgy and Materials 2024年第11期31卷 2417-2434页

作者： Nie, Xinxin Yin, Qian He, Manchao Wang, Qi Jing, hongwen Zheng, Bowen Meng, Bo deng, Tianci Jiang, Zheng Wu, Jiangyu State Key Laboratory for Geomechanics & Deep Underground Engineering China University of Mining and Technology Xuzhou China State Key Laboratory for Geomechanics & Deep Underground Engineering China University of Mining and Technology (Beijing) Beijing China Key Laboratory of Shale Gas and Geoengineering Institute of Geology and Geophysics Chinese Academy of Sciences Beijing China Department of Materials University of Oxford Oxford UK

This study aims to investigate mechanical properties and failure mechanisms of layered rock with rough joint surfaces under direct shear loading. Cubic layered samples with dimensions of 100 mm × 100 mm × 100 mm were casted using rock-like materials, with anisotropic angle (α) and joint roughness coefficient (JRC) ranging from 15° to 75° and 2–20, respectively. The direct shear tests were conducted under the application of initial normal stress (σn) ranging from 1–4 MPa. The test results indicate significant differences in mechanical properties, acoustic emission (AE) responses, maximum principal strain fields, and ultimate failure modes of layered samples under different test conditions. The peak stress increases with the increasing α and achieves a maximum value at α = 60° or 75°. As σn increases, the peak stress shows an increasing trend, with correlation coefficients R2 ranging from 0.918 to 0.995 for the linear least squares fitting. As JRC increases from 2–4 to 18–20, the cohesion increases by 86.32% when α = 15°, while the cohesion decreases by 27.93% when α = 75°. The differences in roughness characteristics of shear failure surface induced by α result in anisotropic post-peak AE responses, which is characterized by active AE signals when α is small and quiet AE signals for a large α. For a given JRC = 6–8 and σn = 1 MPa, as α increases, the accumulative AE counts increase by 224.31% (α increased from 15° to 60°), and then decrease by 14.68% (α increased from 60° to 75°). The shear failure surface is formed along the weak interlayer when α = 15° and penetrates the layered matrix when α = 60°. When α = 15°, as σn increases, the adjacent weak interlayer induces a change in the direction of tensile cracks propagation, resulting in a stepped pattern of cracks distribution. The increase in JRC intensifies roughness characteristics of shear failure surface for a small α, however, it is not pronounced for a large α. The findings will contribute to a better understa

关键词： layered samples anisotropic angle joint roughness coefficient mechanical properties acoustic emission response fracturing evolution failure modes

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An Entropy-based Index for Fine-scale Mapping of Disease Genes

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Journal of Genetics and Genomics 2007年第7期34卷 661-668页

作者：李玉梅向阳邓红文孙振球中南大学公共卫生学院中南大学数学学院湖南师大分子与统计遗传实验室

By comparing the entropy and the conditional entropy in a marker, an entropy-based index has been presented for fine-scale linkage disequilibrium gene mapping using high-density marker maps for human disease genes. The index can quantify the level of linkage disequilibrium （LD） between the marker and the disease susceptibility locus （DSL） of genes. The advantage of using the index is attributed to the fact that it does not depend on marker allele frequencies across loci. Moreover, it is parallel to Hardy-Weinberg disequilibrium （HWD） measure for DSL fine mapping. Through various simulations, the fine mapping perform- ances of the proposed entropy-based index was extensively investigated under various genetic parameters. The results show that the index presented is both robust and powerful for DSL mapping in genes.

关键词： entropy entropy-based index fine mapping

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高分辨率层序地层学应用中的问题探析

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古地理学报 2009年第5期11卷 471-480页

作者：邓宏文中国地质大学(北京)能源学院北京100083

高分辨率层序地层学自诞生以来,由于其基本原理和分析技术的广泛适用性、可行性、高精度和可预测性,得到了广大石油地质工作者的认可并在油气勘探与开发研究中得到了广泛的应用,对中国油气勘探与油田开发挖潜起着至关重要的作用。但在... 详细信息

高分辨率层序地层学自诞生以来,由于其基本原理和分析技术的广泛适用性、可行性、高精度和可预测性,得到了广大石油地质工作者的认可并在油气勘探与开发研究中得到了广泛的应用,对中国油气勘探与油田开发挖潜起着至关重要的作用。但在应用过程中,还存在一些对概念理解的偏差以及模糊不清的认识,须要更深入的探讨以加深认识。作者主要从概念和方法上分析探讨了高分辨率层序地层学在储集层规模的地层划分与对比中存在的一些问题,包括基准面旋回与准层序概念的差异性;基准面旋回的级次划分;基准面旋回的界面识别与基准面旋回对比等,旨在通过对这些问题的分析,与运用该理论和方法的学者达成一定的共识并提供一些思考。

关键词：高分辨率层序地层学级次基准面旋回界面识别与对比

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A genome wide association study between copy number variation (CNV) and human height in Chinese population

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Journal of Genetics and Genomics 2010年第12期37卷 779-785页

作者： Xi Li Lijun Tan Xiaogang Liu Shufeng Lei Tielin Yang Xiangding Chen Fang Zhang Yue Fang Yan Guo Liang Zhang Han Yan Feng Pan Zhixin Zhang Yumei Peng Qi Zhou Lina He Xuezhen Zhu Jing Cheng Lishu Zhang Yaozhong Liu Qing Tian hongwen deng Laboratory of Molecular and Statistical Genetics College of Life Sciences Hunan Normal University Changsha 410081 China The Key Laboratory of Biomedical Information Engineering of Ministry of Education and Institute of Molecular Genetics School of Life Science and Technology Xi'an Jiaotong University Xi'an 710049 China National Engineering Research Center for Beijing Biochip Technology Beijing 102206 China Department of Basic Medical Science and Orthopedic Surgery School of Medicine University of Missouri - Kansas City Kansas City MO 64108 USA College of Life Sciences and Bioengineering Beijing Jiaotong University Beijing 100044 China

Copy number variation （CNV） is a type of genetic variation which may have important roles in phenotypic variability and disease susceptibility. To hunt for genetic variants underlying human height variation, we performed a genome wide CNV association study for human height in 618 Chinese unrelated subjects using Affymetrix 500K array set. After adjusting for age and sex, we found that four CNVs at 6p21.3, 8p23.3-23.2, 9p23 and 16p12.1 were associated with human height （with borderline significant p value： 0.013, 0.011, 0.024, 0.049; respectively）. However, after multiple tests correction, none of them was associated with human height. We observed that the gain of copy number （more than 2 copies） at 8p23.3-23.2 was associated with lower height （normal copy number vs. gain of copy number： 161.2 cm vs. 153.7 cm, p = 0.011）, which accounted for 0.9% of height variation. Loss of copy number （less than 2 copies） at 6p21.3 was associated with 0.8% lower height （loss of copy number vs. normal copy number： 154.5 cm vs. 161.1 cm, p = 0.013）. Since no important genes influencing height located in CNVs at loci of 8p23.3-23.2 and 6p21.3, the two CNVs may cause the structural rear- rangements of neighbored important candidate genes, thus regulates the variation of height. Our results expand our knowledge of the genetic factors underlying height variation and the biological regulation of human height.

关键词： CNV human height GWAS Affymetrix 500K array

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Shear mechanical properties and fracturing responses of layered rough jointed rock-like materials

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International Journal of Minerals,Metallurgy and Materials 2024年第11期 2417-2434页

作者： Xinxin Nie Qian Yin Manchao He Qi Wang hongwen Jing Bowen Zheng Bo Meng Tianci deng Zheng Jiang Jiangyu Wu State Key Laboratory for Geomechanics & Deep Underground Engineering China University of Mining and Technology State Key Laboratory for Geomechanics & Deep Underground Engineering China University of Mining and Technology (Beijing) Key Laboratory of Shale Gas and Geoengineering Institute of Geology and GeophysicsChinese Academy of Sciences Department of Materials University of Oxford

This study aims to investigate mechanical properties and failure mechanisms of layered rock with rough joint surfaces under direct shear loading. Cubic layered samples with dimensions of 100 mm × 100 mm × 100 mm were casted using rock-like materials, with anisotropic angle（α） and joint roughness coefficient（JRC） ranging from 15° to 75° and 2–20, respectively. The direct shear tests were conducted under the application of initial normal stress（σn） ranging from 1–4 MPa. The test results indicate significant differences in mechanical properties, acoustic emission（AE） responses, maximum principal strain fields, and ultimate failure modes of layered samples under different test conditions. The peak stress increases with the increasing α and achieves a maximum value at α = 60° or 75°. As σn increases, the peak stress shows an increasing trend, with correlation coefficients R2ranging from 0.918 to 0.995 for the linear least squares fitting. As JRC increases from 2–4 to 18–20, the cohesion increases by 86.32% when α = 15°, while the cohesion decreases by 27.93%when α = 75°. The differences in roughness characteristics of shear failure surface induced by α result in anisotropic post-peak AE responses, which is characterized by active AE signals when α is small and quiet AE signals for a large α. For a given JRC = 6–8 and σn =1 MPa, as α increases, the accumulative AE counts increase by 224.31%（α increased from 15° to 60°）, and then decrease by 14.68%（αincreased from 60° to 75°）. The shear failure surface is formed along the weak interlayer when α = 15° and penetrates the layered matrix when α = 60°. When α = 15°, as σn increases, the adjacent weak interlayer induces a change in the direction of tensile cracks propagation,resulting in a stepped pattern of cracks distribution. The increase in JRC intensifies roughness characteristics of shear failure surface for a small α, however, it is not pronounced for a large α. The findings will contribute to a better understanding of th

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地层切片技术在中新统刚果扇中的应用

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大庆石油地质与开发 2013年第6期32卷 135-140页

作者：谢清惠邓宏文中国地质大学能源学院

地层切片比时间切片、沿层切片更接近等时界面，能够提供更加真实的地质信息。以中新统刚果扇为例，在三级层序格架基础上内插得到一系列地层切片并提取了均方根属性，进而研究三级层序的沉积相展布、高频层序划分、水道发育期次及其充... 详细信息

地层切片比时间切片、沿层切片更接近等时界面，能够提供更加真实的地质信息。以中新统刚果扇为例，在三级层序格架基础上内插得到一系列地层切片并提取了均方根属性，进而研究三级层序的沉积相展布、高频层序划分、水道发育期次及其充填结构、演化特征。研究结果表明：三级层序内部由多个具有相似沉积规律的高频沉积旋回构成；高频层序界面是沉积界面的组合，富砂的沉积组合面是高频层序界面的底，富泥的沉积组合面为高频层序界面的顶；水道复合体通常由多期次的一级水道构成，后期水道叠置在前期水道之上或不同程度地切割水道；水道演化主要经历初期侵蚀、侵蚀一充填、加积充填和废弃4个阶段，水道弯度逐渐变大。

关键词：地层切片均方根属性充填结构沉积相层序界面深水水道

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