Mingyao Li

Summary

Affiliation: University of Pennsylvania
Country: USA

Publications

  1. ncbi request reprint GWAsimulator: a rapid whole-genome simulation program
    Chun Li
    Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
    Bioinformatics 24:140-2. 2008
  2. pmc Efficient study designs for test of genetic association using sibship data and unrelated cases and controls
    Mingyao 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
  3. pmc Quantitative trait linkage analysis using Gaussian copulas
    Mingyao Li
    Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia 19104, USA
    Genetics 173:2317-27. 2006
  4. pmc Examination of all type 2 diabetes GWAS loci reveals HHEX-IDE as a locus influencing pediatric BMI
    Jianhua Zhao
    Division of Human Genetics, The Children s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
    Diabetes 59:751-5. 2010
  5. pmc Novel variants in the PRDX6 Gene and the risk of Acute Lung Injury following major trauma
    Melanie 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
  6. doi request reprint BMD-associated variation at the Osterix locus is correlated with childhood obesity in females
    Jianhua Zhao
    Division of Human Genetics, The Children s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
    Obesity (Silver Spring) 19:1311-4. 2011
  7. pmc The role of obesity-associated loci identified in genome-wide association studies in the determination of pediatric BMI
    Jianhua Zhao
    Division of Human Genetics, The Children s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
    Obesity (Silver Spring) 17:2254-7. 2009
  8. pmc Modeling genetic inheritance of copy number variations
    Kai 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
  9. doi request reprint Role of BMI-associated loci identified in GWAS meta-analyses in the context of common childhood obesity in European Americans
    Jianhua Zhao
    Division of Human Genetics, The Children s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
    Obesity (Silver Spring) 19:2436-9. 2011
  10. pmc The role of height-associated loci identified in genome wide association studies in the determination of pediatric stature
    Jianhua Zhao
    Division of Human Genetics, The Children s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
    BMC Med Genet 11:96. 2010

Collaborators

Detail Information

Publications65

  1. ncbi request reprint GWAsimulator: a rapid whole-genome simulation program
    Chun Li
    Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
    Bioinformatics 24:140-2. 2008
    ..As genome-wide association (GWA) studies become increasingly popular and new GWA data analysis methods are being developed, we anticipate that GWAsimulator will be an important tool for evaluating performance of new GWA analysis methods...
  2. pmc Efficient study designs for test of genetic association using sibship data and unrelated cases and controls
    Mingyao 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...
  3. pmc Quantitative trait linkage analysis using Gaussian copulas
    Mingyao Li
    Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia 19104, USA
    Genetics 173:2317-27. 2006
    ....
  4. pmc Examination of all type 2 diabetes GWAS loci reveals HHEX-IDE as a locus influencing pediatric BMI
    Jianhua 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...
  5. pmc Novel variants in the PRDX6 Gene and the risk of Acute Lung Injury following major trauma
    Melanie 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...
  6. doi request reprint BMD-associated variation at the Osterix locus is correlated with childhood obesity in females
    Jianhua 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...
  7. pmc The role of obesity-associated loci identified in genome-wide association studies in the determination of pediatric BMI
    Jianhua 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...
  8. pmc Modeling genetic inheritance of copy number variations
    Kai 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...
  9. doi request reprint Role of BMI-associated loci identified in GWAS meta-analyses in the context of common childhood obesity in European Americans
    Jianhua Zhao
    Division of Human Genetics, The Children s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
    Obesity (Silver Spring) 19:2436-9. 2011
    ....
  10. pmc The role of height-associated loci identified in genome wide association studies in the determination of pediatric stature
    Jianhua 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...
  11. pmc Gene-based interaction analysis by incorporating external linkage disequilibrium information
    Jing 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...
  12. pmc IL1RN coding variant is associated with lower risk of acute respiratory distress syndrome and increased plasma IL-1 receptor antagonist
    Nuala J Meyer
    Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
    Am J Respir Crit Care Med 187:950-9. 2013
    ..Acute respiratory distress syndrome (ARDS) behaves as a complex genetic trait, yet knowledge of genetic susceptibility factors remains incomplete...
  13. pmc Mining the LIPG allelic spectrum reveals the contribution of rare and common regulatory variants to HDL cholesterol
    Sumeet 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...
  14. pmc Examination of type 2 diabetes loci implicates CDKAL1 as a birth weight gene
    Jianhua 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...
  15. pmc A second independent locus within DMRT1 is associated with testicular germ cell tumor susceptibility
    Peter 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...
  16. pmc Dense genotyping of candidate gene loci identifies variants associated with high-density lipoprotein cholesterol
    Andrew 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...
  17. doi request reprint Assessing departure from Hardy-Weinberg equilibrium in the presence of disease association
    Mingyao 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...
  18. pmc ATOM: a powerful gene-based association test by combining optimally weighted markers
    Mingyao 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...
  19. pmc PennSeq: accurate isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution
    Yu Hu
    Department of Biostatistics and Epidemiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA and Cardiovascular Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
    Nucleic Acids Res 42:e20. 2014
    ..Our results indicate superior performance of PennSeq over existing methods, particularly for isoforms demonstrating severe non-uniformity. PennSeq is freely available for download at http://sourceforge.net/projects/pennseq. ..
  20. pmc Translational studies of lipoprotein-associated phospholipase A₂ in inflammation and atherosclerosis
    Jane 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 A₂ (Lp-PLA₂/PLA2G7) in human inflammation and coronary atherosclerosis...
  21. pmc Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms
    Sharon 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...
  22. pmc Loss-of-function DNA sequence variant in the CLCNKA chloride channel implicates the cardio-renal axis in interindividual heart failure risk variation
    Thomas 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...
  23. pmc A genome-wide study reveals copy number variants exclusive to childhood obesity cases
    Joseph 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...
  24. pmc Adjustment for local ancestry in genetic association analysis of admixed populations
    Xuexia Wang
    Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
    Bioinformatics 27:670-7. 2011
    ..However, association analysis in such populations is challenging because population stratification may lead to association with loci unlinked to the disease locus...
  25. pmc MetaDiff: differential isoform expression analysis using random-effects meta-regression
    Cheng Jia
    Department of Biostatistics and Epidemiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
    BMC Bioinformatics 16:208. 2015
    ..It is desirable to have a method that can account for these issues and is flexible enough to allow adjustment for covariates...
  26. pmc 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 studies
    Muredach 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...
  27. pmc Testing genetic association with rare variants in admixed populations
    Xianyun Mao
    Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
    Genet Epidemiol 37:38-47. 2013
    ..Our results suggest that it is important to appropriately control for potential population stratification induced by local ancestry difference in the analysis of rare variants in admixed populations...
  28. pmc Widespread RNA and DNA sequence differences in the human transcriptome
    Mingyao 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...
  29. pmc Investigation of the locus near MC4R with childhood obesity in Americans of European and African ancestry
    Struan 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...
  30. pmc A naturally occurring variant of endothelial lipase associated with elevated HDL exhibits impaired synthesis
    Robert 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...
  31. pmc Common variants in HSPB7 and FRMD4B associated with advanced heart failure
    Thomas 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...
  32. pmc Genome wide association identifies PPFIA1 as a candidate gene for acute lung injury risk following major trauma
    Jason 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...
  33. pmc Fractalkine is a novel human adipochemokine associated with type 2 diabetes
    Rachana 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...
  34. pmc Diverse genome-wide association studies associate the IL12/IL23 pathway with Crohn Disease
    Kai 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...
  35. pmc Pathway-based approaches for analysis of genomewide association studies
    Kai Wang
    Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
    Am J Hum Genet 81:1278-83. 2007
    ....
  36. pmc Evaluating the impact of sequencing depth on transcriptome profiling in human adipose
    Yichuan Liu
    Department of Biostatistics and Epidemiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
    PLoS ONE 8:e66883. 2013
    ..Our results suggest that a much higher sequencing depth is needed to reliably identify DAS events than for DE genes. ..
  37. pmc Plasma HDL cholesterol and risk of myocardial infarction: a mendelian randomisation study
    Benjamin F Voight
    Department of Pharmacology, University of Pennsylvania, Philadelphia, PA, USA
    Lancet 380:572-80. 2012
    ....
  38. pmc A Gaussian copula approach for the analysis of secondary phenotypes in case-control genetic association studies
    Jing He
    Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
    Biostatistics 13:497-508. 2012
    ..Our results suggest that to avoid false-positive associations, it is important to appropriately model secondary phenotypes in case-control genetic association studies...
  39. pmc ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data
    Kai 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/...
  40. pmc Concept, design and implementation of a cardiovascular gene-centric 50 k SNP array for large-scale genomic association studies
    Brendan 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...
  41. pmc A genome-wide association meta-analysis identifies new childhood obesity loci
    Jonathan P Bradfield
    Center for Applied Genomics, Abramson Research Center, The Children s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
    Nat Genet 44:526-31. 2012
    ..These two loci also yielded directionally consistent associations in a previous meta-analysis of adult BMI(1)...
  42. pmc Common variation in KITLG and at 5q31.3 predisposes to testicular germ cell cancer
    Peter 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...
  43. pmc The novel atherosclerosis locus at 10q11 regulates plasma CXCL12 levels
    Nehal 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...
  44. pmc ANGPT2 genetic variant is associated with trauma-associated acute lung injury and altered plasma angiopoietin-2 isoform ratio
    Nuala 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...
  45. pmc A review of family-based tests for linkage disequilibrium between a quantitative trait and a genetic marker
    Warren 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...
  46. pmc Correcting population stratification in genetic association studies using a phylogenetic approach
    Mingyao Li
    Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
    Bioinformatics 26:798-806. 2010
    ....
  47. pmc Genome-wide linkage and association analysis of rheumatoid arthritis in a Canadian population
    Zhi 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...
  48. pmc RNA-Seq identifies novel myocardial gene expression signatures of heart failure
    Yichuan Liu
    Department of Biostatistics and Epidemiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, United States Electronic address
    Genomics 105:83-9. 2015
    ..Our results indicate that it is possible to use RNA-Seq to classify disease status for complex diseases such as heart failure using an extremely small training dataset. ..
  49. doi request reprint Evaluation of coverage variation of SNP chips for genome-wide association studies
    Mingyao 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...
  50. ncbi request reprint Variation in the myosin light chain kinase gene is associated with development of acute lung injury after major trauma
    Jason 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...
  51. doi request reprint Association of schizophrenia with the phenylthiocarbamide taste receptor haplotype on chromosome 7q
    Paul J Moberg
    Neuropsychiatry Section, Schizophrenia Research Center, Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
    Psychiatr Genet 22:286-9. 2012
    ..The PTC nontaster haplotype is a genetic marker that may be used to identify subsets of schizophrenia patients who potentially harbor vulnerability genes in this region of chromosome 7q...
  52. pmc GENIE: a software package for gene-gene interaction analysis in genetic association studies using multiple GPU or CPU cores
    Satish Chikkagoudar
    Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
    BMC Res Notes 4:158. 2011
    ..However, currently there are no genetic analysis software packages that allow users to fully utilize the computing power of these multi-core devices for genetic interaction analysis for binary traits...
  53. pmc Loss-of-function variants in endothelial lipase are a cause of elevated HDL cholesterol in humans
    Andrew 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...
  54. pmc PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data
    Kai 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...
  55. pmc RNA-sequence analysis of human B-cells
    Jonathan 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...
  56. pmc Prioritized subset analysis: improving power in genome-wide association studies
    Chun 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...
  57. pmc Evaluating cost efficiency of SNP chips in genome-wide association studies
    Chun 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...
  58. pmc Joint modeling of linkage and association: identifying SNPs responsible for a linkage signal
    Mingyao 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...
  59. pmc Strong association of the Y402H variant in complement factor H at 1q32 with susceptibility to age-related macular degeneration
    Sepideh 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...
  60. pmc CFH haplotypes without the Y402H coding variant show strong association with susceptibility to age-related macular degeneration
    Mingyao 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...
  61. pmc U-statistics-based tests for multiple genes in genetic association studies
    Zhi 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...
  62. pmc Association analysis of the FTO gene with obesity in children of Caucasian and African ancestry reveals a common tagging SNP
    Struan 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...
  63. ncbi request reprint Comments on the entropy-based transmission/disequilibrium test
    Warren 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...
  64. ncbi request reprint Genetic association with rheumatoid arthritis-Genetic Analysis Workshop 15: summary of contributions from Group 2
    Marsha 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...
  65. ncbi request reprint Toll-like receptor 4 variant D299G is associated with susceptibility to age-related macular degeneration
    Sepideh 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...