Research Topics
Genomes and GenesSpecies | Xiaofeng ZhuSummaryAffiliation: Case Western Reserve University Country: USA Publications
Research Grants
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Detail Information
Publications
Combined admixture mapping and association analysis identifies a novel blood pressure genetic locus on 5p13: contributions from the CARe consortiumXiaofeng Zhu
Department of Epidemiology and Biostatistics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
Hum Mol Genet 20:2285-95. 2011..Our study highlights that admixture mapping analysis can help identify genetic variants missed by genome-wide association studies because of drastically reduced number of tests in the whole genome...- Genome-wide searching of rare genetic variants in WTCCC dataTao Feng
Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106, USA
Hum Genet 128:269-80. 2010.... - Two-marker association tests yield new disease associations for coronary artery disease and hypertensionThomas P Slavin
Department of Genetics, Center for Human Genetics, University Hospitals of Cleveland and Case Western Reserve University, 10524 Euclid Avenue, Cleveland, OH, USA
Hum Genet 130:725-33. 2011..We have shown that novel, multiple-marker, statistical methods can be of use in finding variants in GWAS. We describe many new, associated variants for both CAD and HTN and describe their known genetic mechanisms... - Admixture mapping of quantitative trait loci for BMI in African Americans: evidence for loci on chromosomes 3q, 5q, and 15qAnalabha Basu
Institute for Human Genetics, Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
Obesity (Silver Spring) 17:1226-31. 2009..These results suggest that these regions may harbor genes influencing BMI in the AA population... - Improving power in contrasting linkage-disequilibrium patterns between cases and controlsTao Wang
Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106, USA
Am J Hum Genet 80:911-20. 2007..Finally, we illustrate our new method by applying it to real data from the International Collaborative Study on Hypertension in Blacks... - Power comparison of admixture mapping and direct association analysis in genome-wide association studiesHuaizhen Qin
Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
Genet Epidemiol 36:235-43. 2012..Surprisingly, our study also suggests that power can be improved when we use less strict criteria to define the candidate regions at stage 1... - Detecting rare variants for complex traits using family and unrelated dataXiaofeng Zhu
Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio 44106, USA
Genet Epidemiol 34:171-87. 2010..These results suggest that searching for rare genetic variants is feasible and can be fruitful in current GWAS, candidate gene studies or resequencing studies... - Detecting rare and common variants for complex traits: sibpair and odds ratio weighted sum statistics (SPWSS, ORWSS)Tao Feng
Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106, USA
Genet Epidemiol 35:398-409. 2011..We demonstrated that family data are extremely informative in searching for rare variants underlying complex traits, and the odds ratio weighted sum statistic is more efficient than currently existing methods... - Admixture mapping provides evidence of association of the VNN1 gene with hypertensionXiaofeng Zhu
Department of Epidemiology and Biostatistics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
PLoS ONE 2:e1244. 2007..Despite these encouraging results, susceptibility loci for hypertension have been exceptionally difficult to localize and confirmation by independent studies will be necessary to establish these findings... - A unified association analysis approach for family and unrelated samples correcting for stratificationXiaofeng Zhu
Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106, USA
Am J Hum Genet 82:352-65. 2008..This property is demonstrated in both a variety of simulation models and empirical data. The proposed approach can be equally applied to the analysis of both qualitative and quantitative traits... - Variants in CXADR and F2RL1 are associated with blood pressure and obesity in African-Americans in regions identified through admixture mappingPriya B Shetty
Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
J Hypertens 30:1970-6. 2012..Genetic variants in 296 genes in regions identified through admixture mapping of hypertension, BMI, and lipids were assessed for association with hypertension, blood pressure (BP), BMI, and high-density lipoprotein cholesterol (HDL-C)... - Testing gene-environment interactions in gene-based association studiesXuefeng Wang
Department of Epidemiology and Biostatistics, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106 7281, USA
BMC Proc 5:S26. 2011..We demonstrate through a genome scan of the quantitative phenotype Q1 that the simulated gene-environment interaction effect in the data can be detected with reasonable power by using the least-squares kernel machine method... - Estimating heritability using family and unrelated individuals dataPriya B Shetty
Case Western Reserve University School of Medicine, 2103 Cornell Road, Cleveland, OH 44106, USA
BMC Proc 5:S34. 2011..462 ± 0.1, and the calibrated restricted maximum-likelihood method yielded an average of 0.535 ± 0.121. Our results demonstrate discrepancies in heritability estimates using the family data and the unrelated individuals data... - Capability of common SNPs to tag rare variantsXiangqing Sun
Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106, USA
BMC Proc 5:S88. 2011..Our results indicate that common SNPs can, to some extent, tag the presence of rare alleles and that including SNPs in strong linkage disequilibrium with each other among the tagging SNPs helps to detect rare alleles... - Comparison of a unified analysis approach for family and unrelated samples with the transmission-disequilibrium test to study associations of hypertension in the Framingham Heart StudyXiangqing Sun
Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio 44106, USA
BMC Proc 3:S22. 2009..We discuss the reasons for this inconsistency. After correcting for multiple tests, we did not detect any significant single-nucleotide polymorphisms by either FamCC or the TDT... - Genome-wide association of anthropometric traits in African- and African-derived populationsSun J Kang
Department of Biostatistics and Epidemiology, Case Western Reserve University, Cleveland, OH 44106, USA
Hum Mol Genet 19:2725-38. 2010..Meta-analysis of this data set with additional studies in African-ancestry populations will be helpful to improve power to detect novel associations... - Interrogating local population structure for fine mapping in genome-wide association studiesHuaizhen Qin
Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA
Bioinformatics 26:2961-8. 2010..Current association methods for correcting population stratification usually involve adjustment of global ancestry between study subjects... - Gene, pathway and network frameworks to identify epistatic interactions of single nucleotide polymorphisms derived from GWAS dataYu Liu
Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH, USA
BMC Syst Biol 6:S15. 2012.... - A novel method to detect rare variants using both family and unrelated case-control dataTao Feng
Department of Epidemiology and Biostatistics, School of Medicine, Case Western Reserve University, Wolstein Research Building, 2103 Cornell Road, Cleveland, OH 44106, USA
BMC Proc 5:S80. 2011..We applied the proposed method to the simulated sequencing data in Genetic Analysis Workshop 17 and identified two genes associated with the disease... - Interrogating population structure and its impact on association testsHuaizhen Qin
Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
BMC Proc 5:S25. 2011..Adjusting for the principal components appeared more effective than did adjusting for ethnicity in terms of preventing false discoveries. This analysis was performed with knowledge of the causal loci... 
Detecting rare variantsTao Feng
Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
Methods Mol Biol 850:453-64. 2012..In this chapter, we introduce these methods as well as their applications in practice...- Analysis of exome sequences with and without incorporating prior biological knowledgeJunghyun Namkung
Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106, USA
Genet Epidemiol 35:S48-55. 2011..Another work group suggested that modeling local rather than global ancestry may be beneficial when controlling the effect of population structure in rare variant association analysis... - A method to correct for population structure using a segregation modelQingfu Feng
Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio 44106 USA
BMC Proc 3:S104. 2009.... - Assessing the impact of global versus local ancestry in association studiesSun Jung Kang
Department of Epidemiology and Biostatistics, Division of Genetic and Molecular Epidemiology, Case Western Reserve University School of Medicine, Wolstein Research Building, 2103 Cornell Road, Cleveland, Ohio 44106 USA
BMC Proc 3:S107. 2009.... - Rare variant density across the genome and across populationsPaola Raska
Department of Epidemiology and Biostatistics, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106, USA
BMC Proc 5:S39. 2011..This may suggest that differences between populations should be considered when delimiting genomic regions according to functionality and that these differences can create potential for disease heterogeneity... - Evaluation of a LASSO regression approach on the unrelated samples of Genetic Analysis Workshop 17Wei Guo
Department of Epidemiology and Biostatistics, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106, USA
BMC Proc 5:S12. 2011..If a rare causal SNP is in strong linkage disequilibrium with a common marker in the same gene, power will be much improved... - The analysis of ethnic mixturesXiaofeng Zhu
Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
Methods Mol Biol 850:465-81. 2012..Therefore, admixture mapping can be more powerful because of the smaller penalty due to multiple tests. In this chapter, I introduce the theory behind admixture mapping and how we conduct the analysis in practice... - Allowing for population stratification in association analysisHuaizhen Qin
Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
Methods Mol Biol 850:399-409. 2012..With an acceptable computation burden, the proposed algorithm successfully eliminates the known spurious association between SNPs in the LCT gene and height due to the population structure in European Americans... - The meaning of interactionXuefeng Wang
Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106 7281, USA
Hum Hered 70:269-77. 2010.... - Admixture mapping and the role of population structure for localizing disease genesXiaofeng Zhu
Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106, USA
Adv Genet 60:547-69. 2008..In this chapter, we describe the recent methodology and software development, review successful applications, and comment on the future of this approach...
Research Grants
- Statistical methods for analyzing high-throughput genotype dataXiaofeng Zhu; Fiscal Year: 2010..We will develop the statistical methods of detecting rare variants, controlling population stratification, performing the joint analysis of admixture mapping and association and developing new software. ..
- Fine Mapping of Hypertension Genes Detected by Admixture Mapping in the FBPPXiaofeng Zhu; Fiscal Year: 2007..Overall, our multi-stage design is likely to achieve greater power and higher resolution compared to a single-stage design. ..
- LD Mapping Using Haplotype Block: Methods & ApplicationXiaofeng Zhu; Fiscal Year: 2007..The results of this project would therefore provide a bridge between high throughput genotyping and efforts by genetic epidemiologists to localize informative SNPs. ..
- Defining an Obesity QTL on Chromosome 3qXiaofeng Zhu; Fiscal Year: 2006..The methodologies applied have been used successfully to identify unique sequence variants in linkage peaks and to conduct fine mapping with specific physiologic candidate genes. ..
- LD Mapping Using Haplotype Block: Methods & ApplicationXiaofeng Zhu; Fiscal Year: 2006..The results of this project would therefore provide a bridge between high throughput genotyping and efforts by genetic epidemiologists to localize informative SNPs. ..
- Fine Mapping of Hypertension Genes Detected by Admixture Mapping in the FBPPXiaofeng Zhu; Fiscal Year: 2010..Overall, our multi-stage design is likely to achieve greater power and higher resolution compared to a single-stage design. ..