Research Topics
Genomes and Genes
Species | Mingyao LiSummaryAffiliation: University of Pennsylvania Country: USA Publications
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Detail Information
Publications
Genome-wide linkage and association analysis of rheumatoid arthritis in a Canadian populationZhi Wei
Genomics and Computational Biology Graduate Group, University of Pennsylvania School of Medicine, 1401 Blockley Hall, 423 Guardian Drive, Philadelphia, Pennsylvania 19104, USA
BMC Proc 1:S19. 2007..We could not replicate association with HLA-DRB1 and PTPN22. Our results indicate that high coverage and sufficient sample size are crucial for the success of genome-wide association studies...- ATOM: a powerful gene-based association test by combining optimally weighted markersMingyao Li
Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, The Children s Hospital of Philadelphia, Philadelphia, PA 19104, USA
Bioinformatics 25:497-503. 2009..One particularly challenging yet important question is how to best use all genetic information to test whether a gene or a region is associated with the trait of interest... - Assessing departure from Hardy-Weinberg equilibrium in the presence of disease associationMingyao Li
Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
Genet Epidemiol 32:589-99. 2008..For case-parents trios, our test is more powerful than the traditional HWE test that uses parents only... - Evaluation of coverage variation of SNP chips for genome-wide association studiesMingyao Li
Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
Eur J Hum Genet 16:635-43. 2008..These evaluations can reveal the degree of variation of each SNP chip in covering the genome and can facilitate SNP chip comparisons at a finer scale... - Examination of all type 2 diabetes GWAS loci reveals HHEX-IDE as a locus influencing pediatric BMIJianhua Zhao
Division of Human Genetics, The Children s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
Diabetes 59:751-5. 2010..Our goal was to investigate if any type 2 diabetes variants uncovered through genome-wide association studies (GWAS) impact BMI in childhood... - Novel variants in the PRDX6 Gene and the risk of Acute Lung Injury following major traumaMelanie Rushefski
Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Pennsylvania School of Medicine, 3600 Spruce Street, Philadelphia, USA
BMC Med Genet 12:77. 2011..Little is known about genetic variation within the PRDX6 gene and its association with acute lung injury (ALI). In this study we sequenced the PRDX6 gene to uncover common variants, and tested association with ALI following major trauma... - BMD-associated variation at the Osterix locus is correlated with childhood obesity in femalesJianhua Zhao
Division of Human Genetics, The Children s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
Obesity (Silver Spring) 19:1311-4. 2011..In conclusion, these findings indicate that a well established variant at the Osterix locus associated with increased BMD is also associated with childhood obesity primarily in females... - The role of obesity-associated loci identified in genome-wide association studies in the determination of pediatric BMIJianhua Zhao
Division of Human Genetics, The Children s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
Obesity (Silver Spring) 17:2254-7. 2009..We conclude that among 13 loci that have been reported to associate with adult BMI, at least nine also contribute to the determination of BMI in childhood as demonstrated by their associations in our pediatric cohort... - Modeling genetic inheritance of copy number variationsKai Wang
Department of Genetics, Division of Human Genetics, Center for Applied Genomics, The Children s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA 19104, USA
Nucleic Acids Res 36:e138. 2008..In conclusion, our method produces accurate CNV calls, gives probabilistic estimates of CNV transmission and builds a solid foundation for the development of linkage and association tests utilizing CNVs... - The role of height-associated loci identified in genome wide association studies in the determination of pediatric statureJianhua Zhao
Division of Human Genetics, The Children s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
BMC Med Genet 11:96. 2010..Despite environmental influences, genetic factors are known to play an important role in stature determination. A number of genetic determinants of adult height have already been established through genome wide association studies... - Investigation of the locus near MC4R with childhood obesity in Americans of European and African ancestryStruan F A Grant
Center for Applied Genomics, Abramson Research Center, The Children s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
Obesity (Silver Spring) 17:1461-5. 2009..As such, variants 3' to the MC4R locus present on the genotyping platform utilized confer a similar magnitude of risk of obesity in white children as to their adult white counterparts but this observation did not extend to AAs... - Gene-based interaction analysis by incorporating external linkage disequilibrium informationJing He
Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
Eur J Hum Genet 19:164-72. 2011..As our method operates at the gene level, it can be applied to a genome-wide association setting and used as a screening tool to detect gene-gene interactions... - Mining the LIPG allelic spectrum reveals the contribution of rare and common regulatory variants to HDL cholesterolSumeet A Khetarpal
Institute for Translational Medicine and Therapeutics, Institute for Diabetes, Obesity, and Metabolism, and Cardiovascular Institute, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
PLoS Genet 7:e1002393. 2011..Taken together, the findings show that both rare and common noncoding regulatory variants are important contributors to the allelic spectrum in complex trait loci... - A second independent locus within DMRT1 is associated with testicular germ cell tumor susceptibilityPeter A Kanetsky
Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
Hum Mol Genet 20:3109-17. 2011..Our findings continue to corroborate that genes influencing male germ cell development and differentiation have emerged as the major players in inherited TGCT susceptibility... - Examination of type 2 diabetes loci implicates CDKAL1 as a birth weight geneJianhua Zhao
Division of Human Genetics, The Children s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
Diabetes 58:2414-8. 2009..In order to investigate whether type 2 diabetes risk-conferring alleles associate with low birth weight in our Caucasian childhood cohort, we examined the effects of 20 such loci on this trait... - Dense genotyping of candidate gene loci identifies variants associated with high-density lipoprotein cholesterolAndrew C Edmondson
Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104 6160, USA
Circ Cardiovasc Genet 4:145-55. 2011..SNP selection was based on tagging SNPs and included low-frequency nonsynonymous SNPs... - Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platformsSharon J Diskin
Center for Childhood Cancer Research, Children s Hospital of Philadelphia, Philadelphia, PA 19104, USA
Nucleic Acids Res 36:e126. 2008..With the wide application of whole-genome SNP genotyping techniques, our wave adjustment method will be important for taking full advantage of genotyped samples for CNV analysis... - A genome-wide study reveals copy number variants exclusive to childhood obesity casesJoseph T Glessner
Abramson Research Center, The Children s Hospital of Philadelphia, Philadelphia, 19104, USA
Am J Hum Genet 87:661-6. 2010..Although these variants may be individually rare, our results indicate that CNVs contribute to the genetic susceptibility of common childhood obesity in subjects of both European and African ancestry... - Loss-of-function DNA sequence variant in the CLCNKA chloride channel implicates the cardio-renal axis in interindividual heart failure risk variationThomas P Cappola
Penn Cardiovascular Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
Proc Natl Acad Sci U S A 108:2456-61. 2011..The variant CLCNKA risk allele, telegraphed by linked variants in the adjacent HSPB7 gene, uncovers a previously overlooked genetic mechanism affecting the cardio-renal axis... - Adjustment for local ancestry in genetic association analysis of admixed populationsXuexia Wang
Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
Bioinformatics 27:670-7. 2011.... - Role of BMI-Associated Loci Identified in GWAS Meta-Analyses in the Context of Common Childhood Obesity in European AmericansJianhua Zhao
Division of Human Genetics, The Children s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
Obesity (Silver Spring) 19:2436-9. 2011.... - Translational studies of lipoprotein-associated phospholipase A? in inflammation and atherosclerosisJane F Ferguson
Cardiovascular Institute, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104 6160, USA
J Am Coll Cardiol 59:764-72. 2012..This study sought to examine the role of lipoprotein-associated phospholipase A? (Lp-PLA?/PLA2G7) in human inflammation and coronary atherosclerosis... - Common variants in HSPB7 and FRMD4B associated with advanced heart failureThomas P Cappola
Penn Cardiovascular Institute, University of Pennsylvania School of Medicine, Philadelphia, USA
Circ Cardiovasc Genet 3:147-54. 2010..We tested the hypothesis that inherited variation in genes of known importance to cardiovascular biology would thus contribute to heart failure risk... - PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping dataKai Wang
Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
Genome Res 17:1665-74. 2007..3%. Our results demonstrate the feasibility of whole-genome fine-mapping of CNVs via high-density SNP genotyping... - A naturally occurring variant of endothelial lipase associated with elevated HDL exhibits impaired synthesisRobert J Brown
Department of Medicine and Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104
J Lipid Res 50:1910-6. 2009..Thus, this N-terminal variant results in reduced secretion of EL protein, plausibly leading to increased HDL-C levels... - Efficient study designs for test of genetic association using sibship data and unrelated cases and controlsMingyao Li
Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
Am J Hum Genet 78:778-92. 2006..Our findings will be helpful for researchers designing and analyzing complex disease-association studies and will facilitate genotyping resource allocation... - Widespread RNA and DNA sequence differences in the human transcriptomeMingyao Li
Department of Biostatistics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
Science 333:53-8. 2011..These widespread RNA-DNA differences in the human transcriptome provide a yet unexplored aspect of genome variation... - Fractalkine is a novel human adipochemokine associated with type 2 diabetesRachana Shah
Division of Pediatric Endocrinology, Children s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
Diabetes 60:1512-8. 2011..Fractalkine (CX3CL1) and its receptor (CX3CR1) comprise a chemokine system involved in leukocyte recruitment and adhesion in atherosclerosis, but its role in adipose inflammation and type 2 diabetes is unknown... - Quantitative trait linkage analysis using Gaussian copulasMingyao Li
Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia 19104, USA
Genetics 173:2317-27. 2006.... - Association analysis of the FTO gene with obesity in children of Caucasian and African ancestry reveals a common tagging SNPStruan F A Grant
Center for Applied Genomics, Abramson Research Center, The Children s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
PLoS ONE 3:e1746. 2008..As such, variants in the FTO gene confer a similar magnitude of risk of obesity to children as to their adult counterparts and appear to have a global impact... - Pathway-based approaches for analysis of genomewide association studiesKai Wang
Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
Am J Hum Genet 81:1278-83. 2007.... - Analysing biological pathways in genome-wide association studiesKai Wang
Center for Applied Genomics, The Childrens Hospital of Philadelphia, Pennsylvania 19104, USA
Nat Rev Genet 11:843-54. 2010..Here we review the development of pathway-based approaches for GWA studies, discuss their practical use and caveats, and suggest that pathway-based approaches may also be useful for future GWA studies with sequencing data... - Concept, design and implementation of a cardiovascular gene-centric 50 k SNP array for large-scale genomic association studiesBrendan J Keating
The Institute for Translational Medicine and Therapeutics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvannia, USA
PLoS ONE 3:e3583. 2008..These datasets will also facilitate more robust secondary analyses, such as explorations with alternative genetic models, epistasis and gene-environment interactions... - Diverse genome-wide association studies associate the IL12/IL23 pathway with Crohn DiseaseKai Wang
Center for Applied Genomics, Children s Hospital of Philadelphia, Philadelphia, PA 19104, USA
Am J Hum Genet 84:399-405. 2009..Our study suggests that examination beyond individual SNP hits, by focusing on genetic networks and pathways, is important to unleashing the true power of GWA studies... - Identification of ADAMTS7 as a novel locus for coronary atherosclerosis and association of ABO with myocardial infarction in the presence of coronary atherosclerosis: two genome-wide association studiesMuredach P Reilly
Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA 19104 6160, USA
Lancet 377:383-92. 2011..We tested whether genetic factors distinctly contribute to either development of coronary atherosclerosis or, specifically, to myocardial infarction in existing coronary atherosclerosis... - ANNOVAR: functional annotation of genetic variants from high-throughput sequencing dataKai Wang
Center for Applied Genomics, Children s Hospital of Philadelphia, PA 19104, USA
Nucleic Acids Res 38:e164. 2010..7?million variants, making it practical to handle hundreds of human genomes in a day. ANNOVAR is freely available at http://www.openbioinformatics.org/annovar/... - A review of family-based tests for linkage disequilibrium between a quantitative trait and a genetic markerWarren J Ewens
Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
PLoS Genet 4:e1000180. 2008..Finally, we comment on power considerations in the choice of the test to be used. We hope this brief review will shed light on the similarities and differences of the various quantitative TDTs... - The novel atherosclerosis locus at 10q11 regulates plasma CXCL12 levelsNehal N Mehta
Penn Cardiovascular Institute, University of Pennsylvania School of Medicine, Penn Tower, 6th Floor, 3400 Civic Center Blvd, Philadelphia, PA 19104, USA
Eur Heart J 32:963-71. 2011..Therefore, we examined the relationship between these two SNPs and plasma CXCL12 levels... - Correcting population stratification in genetic association studies using a phylogenetic approachMingyao Li
Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
Bioinformatics 26:798-806. 2010.... - ANGPT2 genetic variant is associated with trauma-associated acute lung injury and altered plasma angiopoietin-2 isoform ratioNuala J Meyer
Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
Am J Respir Crit Care Med 183:1344-53. 2011..Acute lung injury (ALI) acts as a complex genetic trait, yet its genetic risk factors remain incompletely understood. Large-scale genotyping has not previously been reported for ALI... - Common variation in KITLG and at 5q31.3 predisposes to testicular germ cell cancerPeter A Kanetsky
Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
Nat Genet 41:811-5. 2009..All of the genotypes were associated with both seminoma and nonseminoma TGCT subtypes. These results demonstrate that common genetic variants affect TGCT risk and implicate KITLG and SPRY4 as genes involved in TGCT susceptibility... - Variation in the myosin light chain kinase gene is associated with development of acute lung injury after major traumaJason D Christie
Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
Crit Care Med 36:2794-800. 2008..We tested the association of MYLK gene variation in the development of acute lung injury in major trauma patients... - Genome wide association identifies PPFIA1 as a candidate gene for acute lung injury risk following major traumaJason D Christie
Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
PLoS ONE 7:e28268. 2012..This study supports the feasibility of future multi-center GWA investigations of ALI risk, and identifies PPFIA1 as a potential functional candidate ALI risk gene for future research... - RNA-sequence analysis of human B-cellsJonathan M Toung
Genomics and Computational Biology Program, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
Genome Res 21:991-8. 2011..Results from this project are available on the UCSC Genome Browser to allow readers to study the expression and structure of genes in human B-cells... - GENIE: a software package for gene-gene interaction analysis in genetic association studies using multiple GPU or CPU coresSatish Chikkagoudar
Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
BMC Res Notes 4:158. 2011..abstract:.. - Loss-of-function variants in endothelial lipase are a cause of elevated HDL cholesterol in humansAndrew C Edmondson
Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104 6160, USA
J Clin Invest 119:1042-50. 2009..Our results establish that loss-of-function mutations in LIPG lead to increased HDL-C levels and support the idea that inhibition of endothelial lipase may be an effective mechanism to raise HDL-C... - Joint modeling of linkage and association: identifying SNPs responsible for a linkage signalMingyao Li
Department of Biostatistics, School of Public Health, and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109 2029, USA
Am J Hum Genet 76:934-49. 2005..Our method provides a new tool for detecting linkage and association and can be extended to study designs that include unaffected family members... - Strong association of the Y402H variant in complement factor H at 1q32 with susceptibility to age-related macular degenerationSepideh Zareparsi
Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI, USA
Am J Hum Genet 77:149-53. 2005..39 (95% confidence interval 0.36-0.42) and the genotype relative risk to be 2.44 (95% confidence interval 2.08-2.83) for TC heterozygotes and 5.93 (95% confidence interval 4.33-8.02) for CC homozygotes... - Prioritized subset analysis: improving power in genome-wide association studiesChun Li
Department of Biostatistics, Center for Human Genetics Research, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
Hum Hered 65:129-41. 2008..Traditional approaches for assessing the overall statistical significance of GWAS results ignore such information by inherently treating all markers equally... - GWAsimulator: a rapid whole-genome simulation programChun Li
Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
Bioinformatics 24:140-2. 2008..AVAILABILITY: The C++ source code, executables for Linux, Windows and MacOS, manual, example data sets and analysis program are available at http://biostat.mc.vanderbilt.edu/GWAsimulator.. - Evaluating cost efficiency of SNP chips in genome-wide association studiesChun Li
Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
Genet Epidemiol 32:387-95. 2008..We illustrate these approaches using five currently available whole genome SNP chips... - U-statistics-based tests for multiple genes in genetic association studiesZhi Wei
Department of Computer Science, New Jersey Institute of Technology, University Heights, Newark, NJ 07102, USA
Ann Hum Genet 72:821-33. 2008..Finally, potential applications of the proposed tests to genome-wide association studies are also discussed... - CFH haplotypes without the Y402H coding variant show strong association with susceptibility to age-related macular degenerationMingyao Li
Department of Biostatistics, 1420 Washington Heights, University of Michigan, Ann Arbor, Michigan 48109, USA
Nat Genet 38:1049-54. 2006..Our results suggest that there are multiple disease susceptibility alleles in the region and that noncoding CFH variants play a role in disease susceptibility... - Comments on the entropy-based transmission/disequilibrium testWarren Ewens
Hum Genet 123:97-100. 2008..We show that the incorrect claim arises because of inappropriate assumptions, and also show that the entropy-based statistic has various undesirable properties... - Genetic association with rheumatoid arthritis-Genetic Analysis Workshop 15: summary of contributions from Group 2Marsha A Wilcox
i3 Drug Safety, 950 Winter Street, Waltham, MA 02451, USA
Genet Epidemiol 31:S12-21. 2007..Generally, models that considered haplotypes or multiple markers showed stronger evidence for association than did single marker analyses... - Toll-like receptor 4 variant D299G is associated with susceptibility to age-related macular degenerationSepideh Zareparsi
Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI 48105, USA
Hum Mol Genet 14:1449-55. 2005..Our data provide evidence of a link between multiple diverse mechanisms underlying AMD pathogenesis...