Goncalo R Abecasis

Summary

Affiliation: University of Michigan
Country: USA

Publications

  1. ncbi request reprint Merlin--rapid analysis of dense genetic maps using sparse gene flow trees
    Goncalo R Abecasis
    The Wellcome Trust Center for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
    Nat Genet 30:97-101. 2002
  2. pmc A variant of mitochondrial protein LOC387715/ARMS2, not HTRA1, is strongly associated with age-related macular degeneration
    Atsuhiro Kanda
    Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI 48105, USA
    Proc Natl Acad Sci U S A 104:16227-32. 2007
  3. pmc Genotype-based matching to correct for population stratification in large-scale case-control genetic association studies
    Weihua Guan
    Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109 2029, USA
    Genet Epidemiol 33:508-17. 2009
  4. pmc METAL: fast and efficient meta-analysis of genomewide association scans
    Cristen J Willer
    Department of Biostatistics, University of Michigan, 1420 Washington Heights, Ann Arbor, Michigan 48109, USA
    Bioinformatics 26:2190-1. 2010
  5. pmc Seven new loci associated with age-related macular degeneration
    Lars G Fritsche
    Institute of Human Genetics, University of Regensburg, Regensburg, Germany
    Nat Genet 45:433-9, 439e1-2. 2013
  6. pmc Exome sequencing and complex disease: practical aspects of rare variant association studies
    Ron Do
    Center for Human Genetic Research and Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
    Hum Mol Genet 21:R1-9. 2012
  7. pmc Fine mapping of five loci associated with low-density lipoprotein cholesterol detects variants that double the explained heritability
    Serena Sanna
    Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche CNR, Monserrato, Italy
    PLoS Genet 7:e1002198. 2011
  8. pmc Genome-wide association scan meta-analysis identifies three Loci influencing adiposity and fat distribution
    Cecilia M Lindgren
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
    PLoS Genet 5:e1000508. 2009
  9. pmc Enhanced genetic maps from family-based disease studies: population-specific comparisons
    Chunsheng He
    Department of Genetics, Rutgers University, Piscataway, NJ, USA
    BMC Med Genet 12:15. 2011
  10. pmc Handling marker-marker linkage disequilibrium: pedigree analysis with clustered markers
    Goncalo R Abecasis
    Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
    Am J Hum Genet 77:754-67. 2005

Collaborators

Detail Information

Publications76

  1. ncbi request reprint Merlin--rapid analysis of dense genetic maps using sparse gene flow trees
    Goncalo R Abecasis
    The Wellcome Trust Center for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
    Nat Genet 30:97-101. 2002
    ....
  2. pmc A variant of mitochondrial protein LOC387715/ARMS2, not HTRA1, is strongly associated with age-related macular degeneration
    Atsuhiro Kanda
    Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI 48105, USA
    Proc Natl Acad Sci U S A 104:16227-32. 2007
    ..We propose that rs10490924 represents a major susceptibility variant for AMD at 10q26. A likely biological mechanism is that the A69S change in the LOC387715/ARMS2 protein affects its presumptive function in mitochondria...
  3. pmc Genotype-based matching to correct for population stratification in large-scale case-control genetic association studies
    Weihua Guan
    Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109 2029, USA
    Genet Epidemiol 33:508-17. 2009
    ..We suggest that initial matching of cases and controls prior to genotyping combined with careful re-matching after genotyping is a method of choice for genome-wide association studies...
  4. pmc METAL: fast and efficient meta-analysis of genomewide association scans
    Cristen J Willer
    Department of Biostatistics, University of Michigan, 1420 Washington Heights, Ann Arbor, Michigan 48109, USA
    Bioinformatics 26:2190-1. 2010
    ..METAL provides a rich scripting interface and implements efficient memory management to allow analyses of very large data sets and to support a variety of input file formats...
  5. pmc Seven new loci associated with age-related macular degeneration
    Lars G Fritsche
    Institute of Human Genetics, University of Regensburg, Regensburg, Germany
    Nat Genet 45:433-9, 439e1-2. 2013
    ..A genetic risk score combining SNP genotypes from all loci showed similar ability to distinguish cases and controls in all samples examined. Our findings provide new directions for biological, genetic and therapeutic studies of AMD...
  6. pmc Exome sequencing and complex disease: practical aspects of rare variant association studies
    Ron Do
    Center for Human Genetic Research and Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
    Hum Mol Genet 21:R1-9. 2012
    ..Here, we provide practical guidance in the design and analysis of complex trait association studies focused on rare, coding variants...
  7. pmc Fine mapping of five loci associated with low-density lipoprotein cholesterol detects variants that double the explained heritability
    Serena Sanna
    Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche CNR, Monserrato, Italy
    PLoS Genet 7:e1002198. 2011
    ..Further, our results suggest that, as prelude to large-scale sequencing efforts, targeted re-sequencing efforts paired with large-scale genotyping will increase estimates of complex trait heritability explained by known loci...
  8. pmc Genome-wide association scan meta-analysis identifies three Loci influencing adiposity and fat distribution
    Cecilia M Lindgren
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
    PLoS Genet 5:e1000508. 2009
    ..By focusing on anthropometric measures of central obesity and fat distribution, we have identified three loci implicated in the regulation of human adiposity...
  9. pmc Enhanced genetic maps from family-based disease studies: population-specific comparisons
    Chunsheng He
    Department of Genetics, Rutgers University, Piscataway, NJ, USA
    BMC Med Genet 12:15. 2011
    ..A large set of genetic studies genotyped by the NHLBI Mammalian Genotyping Service (MGS) provide appropriate data for generating more accurate maps...
  10. pmc Handling marker-marker linkage disequilibrium: pedigree analysis with clustered markers
    Goncalo R Abecasis
    Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
    Am J Hum Genet 77:754-67. 2005
    ..To illustrate the possibilities, we examine a data set that provides evidence of linkage of psoriasis to chromosome 17...
  11. ncbi request reprint Linkage disequilibrium: ancient history drives the new genetics
    Goncalo R Abecasis
    Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
    Hum Hered 59:118-24. 2005
    ..Finally, we highlight the importance of using appropriate statistical procedures, such as the false discovery rate, to maximize the chances of success in large scale association studies...
  12. pmc New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk
    Josee Dupuis
    Department of Biostatistics, Boston University School of Public Health, Massachusetts, USA
    Nat Genet 42:105-16. 2010
    ....
  13. 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...
  14. pmc Global gene expression analysis reveals evidence for decreased lipid biosynthesis and increased innate immunity in uninvolved psoriatic skin
    Johann E Gudjonsson
    Department of Dermatology, University of Michigan, 1910 Taubman Center, Ann Arbor, Michigan 48109, USA
    J Invest Dermatol 129:2795-804. 2009
    ..Taken together, our results identify a "pre-psoriatic" gene expression signature, suggesting decreased lipid biosynthesis and increased innate immunity in uninvolved psoriatic skin...
  15. pmc Genetic variants near TIMP3 and high-density lipoprotein-associated loci influence susceptibility to age-related macular degeneration
    Wei Chen
    Center for Statistical Genetics, Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
    Proc Natl Acad Sci U S A 107:7401-6. 2010
    ..Our studies extend the catalog of AMD associated loci, help identify individuals at high risk of disease, and provide clues about underlying cellular pathways that should eventually lead to new therapies...
  16. pmc Discovery and refinement of loci associated with lipid levels
    Cristen J Willer
    1 Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, Michigan, USA 2 Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA 3 Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA 4 Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA 5 6
    Nat Genet 45:1274-83. 2013
    ..Our results demonstrate the value of using genetic data from individuals of diverse ancestry and provide insights into the biological mechanisms regulating blood lipids to guide future genetic, biological and therapeutic research...
  17. pmc Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes
    Eleftheria Zeggini
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
    Nat Genet 40:638-45. 2008
    ..1 x 10(-9)), ADAMTS9 (P = 1.2 x 10(-8)) and NOTCH2 (P = 4.1 x 10(-8)) gene regions. Our results illustrate the value of large discovery and follow-up samples for gaining further insights into the inherited basis of T2D...
  18. ncbi request reprint Newly identified loci that influence lipid concentrations and risk of coronary artery disease
    Cristen J Willer
    Center for Statistical Genetics, Department of Biostatistics, University of Michigan, 1420 Washington Heights, Ann Arbor, Michigan 48109, USA
    Nat Genet 40:161-9. 2008
    ..Notably, the 11 independent variants associated with increased LDL cholesterol concentrations in our study also showed increased frequency in a sample of coronary artery disease cases versus controls...
  19. pmc Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis
    Benjamin F Voight
    Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
    Nat Genet 42:579-89. 2010
    ..We also show that a high proportion of T2D susceptibility loci harbor independent association signals influencing apparently unrelated complex traits...
  20. ncbi request reprint Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies
    Andrew D Skol
    Department of Biostatistics and Center for Statistical Genetics, University of Michigan, 1420 Washington Heights, Ann Arbor, Michigan 48109 2029, USA
    Nat Genet 38:209-13. 2006
    ..30), and a relatively large proportion of markers are selected for follow-up in stage 2 (pi(markers) >or= 0.01)...
  21. pmc Accurate local-ancestry inference in exome-sequenced admixed individuals via off-target sequence reads
    Youna Hu
    Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA Center for Statistical Genetics, Department of Biostatistics, University of Michigan, School of Public Health, Ann Arbor, MI 48109, USA Electronic address
    Am J Hum Genet 93:891-9. 2013
    ..Software implementing this method, SEQMIX, can be applied to analysis of human population history or used for genetic association studies in admixed individuals. ..
  22. pmc Common variants in the GDF5-UQCC region are associated with variation in human height
    Serena Sanna
    Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA
    Nat Genet 40:198-203. 2008
    ..44 cm (overall P < 10(-15)). Our results indicate that there may be a link between the genetic basis of height and osteoarthritis, potentially mediated through alterations in bone growth and development...
  23. pmc Genome-wide association analysis identifies three psoriasis susceptibility loci
    Philip E Stuart
    Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, USA
    Nat Genet 42:1000-4. 2010
    ..We also replicated a recently identified association signal near RNF114 (rs495337, combined P = 2 × 10⁻⁷)...
  24. pmc A cross-platform analysis of 14,177 expression quantitative trait loci derived from lymphoblastoid cell lines
    Liming Liang
    Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts 02115, USA
    Genome Res 23:716-26. 2013
    ..The combined results identify strong local and distant effects for transcripts from 14,177 genes. Our eQTL database based on these results is freely available to help define the function of disease-associated variants...
  25. 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...
  26. ncbi request reprint GENOME: a rapid coalescent-based whole genome simulator
    Liming Liang
    Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
    Bioinformatics 23:1565-7. 2007
    ..The program can be used to study the sampling properties of any statistic for a whole genome study...
  27. pmc Transcriptome analysis of psoriasis in a large case-control sample: RNA-seq provides insights into disease mechanisms
    Bingshan Li
    1 Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, USA 2 Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
    J Invest Dermatol 134:1828-38. 2014
    ..These results show the power of WGCNA to elucidate gene regulatory circuits in psoriasis, and emphasize the influence of tissue architecture in both differential expression and coexpression analysis. ..
  28. pmc Biological, clinical and population relevance of 95 loci for blood lipids
    Tanya M Teslovich
    Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA
    Nature 466:707-13. 2010
    ..Taken together, our findings provide the foundation to develop a broader biological understanding of lipoprotein metabolism and to identify new therapeutic opportunities for the prevention of CAD...
  29. 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...
  30. pmc Identification of 15 new psoriasis susceptibility loci highlights the role of innate immunity
    Lam C Tsoi
    Department of Biostatistics, Center for Statistical Genetics, University of Michigan Ann Arbor, MI, USA
    Nat Genet 44:1341-8. 2012
    ..These results portend a better understanding of shared and distinctive genetic determinants of immune-mediated inflammatory disorders and emphasize the importance of the skin in innate and acquired host defense...
  31. pmc Variance components linkage analysis with repeated measurements
    Liming Liang
    Department of Biostatistics, University of Michigan, Ann Arbor, Mich, USA
    Hum Hered 67:237-47. 2009
    ..A number of methods have been proposed to model repeated measures in linkage analysis. Here, we focus on assessing the impact of repeated measures on the power and cost of a linkage study...
  32. pmc Genome-wide scan reveals association of psoriasis with IL-23 and NF-kappaB pathways
    Rajan P Nair
    Department of Dermatology, University of Michigan, Ann Arbor, Michigan 48109, USA
    Nat Genet 41:199-204. 2009
    ..Our results expand the catalog of genetic loci implicated in psoriasis susceptibility and suggest priority targets for study in other auto-immune disorders...
  33. pmc MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes
    Yun Li
    Department of Genetics, Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina, USA
    Genet Epidemiol 34:816-34. 2010
    ..Finally, we illustrate how association analyses of unobserved variants will benefit from ongoing advances such as larger HapMap reference panels and whole genome shotgun sequencing technologies...
  34. pmc Assessment of the psoriatic transcriptome in a large sample: additional regulated genes and comparisons with in vitro models
    Johann E Gudjonsson
    Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
    J Invest Dermatol 130:1829-40. 2010
    ..This comprehensive analysis of differentially regulated transcripts in psoriasis provides additional insight into the pathogenic mechanisms involved and emphasizes the need for more complex yet tractable experimental models of psoriasis...
  35. pmc Sequence and haplotype analysis supports HLA-C as the psoriasis susceptibility 1 gene
    Rajan P Nair
    Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI 48109 0932, USA
    Am J Hum Genet 78:827-51. 2006
    ..These results strongly suggest that HLA-Cw6 is the PSORS1 risk allele that confers susceptibility to early-onset psoriasis...
  36. pmc Age-related macular degeneration: a high-resolution genome scan for susceptibility loci in a population enriched for late-stage disease
    Goncalo R Abecasis
    Department of Biostatistics, University of Michigan, Ann Arbor, MI 48105, USA
    Am J Hum Genet 74:482-94. 2004
    ..Our results consolidate the chromosomal locations of several AMD susceptibility loci and, together with previous reports, should facilitate the search for disease-associated sequence variants...
  37. pmc Family-based association tests for genomewide association scans
    Wei Min Chen
    Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
    Am J Hum Genet 81:913-26. 2007
    ..Our genotype-inference algorithm and the proposed association tests are implemented in software that is available for free...
  38. pmc Gene expression in skin and lymphoblastoid cells: Refined statistical method reveals extensive overlap in cis-eQTL signals
    Jun Ding
    Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, 48109, USA
    Am J Hum Genet 87:779-89. 2010
    ....
  39. pmc A comparison of approaches to account for uncertainty in analysis of imputed genotypes
    Jin Zheng
    Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
    Genet Epidemiol 35:102-10. 2011
    ..However, for most realistic settings, we find that regressing the phenotype on the estimated allelic or genotypic dosage provides an attractive compromise between accuracy and computational tractability...
  40. ncbi request reprint Using haplotype blocks to map human complex trait loci
    Lon R Cardon
    Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
    Trends Genet 19:135-40. 2003
    ..Knowledge of local disequilibrium patterns may help identify common polymorphisms involved in complex disease, but completely new analytical methods and experimental designs will be required to identify important rare variants...
  41. pmc GWAS GUI: graphical browser for the results of whole-genome association studies with high-dimensional phenotypes
    Wei Chen
    Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
    Bioinformatics 25:284-5. 2009
    ..Windows, Linux and Mac binaries are available from our website...
  42. pmc A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants
    Laura J Scott
    Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
    Science 316:1341-5. 2007
    ..This brings the number of T2D loci now confidently identified to at least 10...
  43. pmc The influence of genomic context on mutation patterns in the human genome inferred from rare variants
    Valerie M Schaibley
    Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
    Genome Res 23:1974-84. 2013
    ..Our results highlight the distinct biases inherent in the initial mutation patterns and subsequent evolutionary processes that affect segregating variants...
  44. pmc Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution
    Iris M Heid
    Regensburg University Medical Center, Department of Epidemiology and Preventive Medicine, Regensburg, Germany
    Nat Genet 42:949-60. 2010
    ..9 × 10⁻³ to P = 1.2 × 10⁻¹³). These findings provide evidence for multiple loci that modulate body fat distribution independent of overall adiposity and reveal strong gene-by-sex interactions...
  45. pmc Ancestry estimation and control of population stratification for sequence-based association studies
    Chaolong Wang
    1 Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, USA 2 Department of Biostatistics, Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, Michigan, USA 3
    Nat Genet 46:409-15. 2014
    ..Finally, we show that our method can be used to improve case-control matching in genetic association studies and to reduce the risk of spurious findings due to population structure. ..
  46. pmc Exome array analysis identifies new loci and low-frequency variants influencing insulin processing and secretion
    Jeroen R Huyghe
    Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
    Nat Genet 45:197-201. 2013
    ..This study demonstrates that exome array genotyping is a valuable approach to identify low-frequency variants that contribute to complex traits...
  47. pmc Meta-analysis of gene-level tests for rare variant association
    Dajiang J Liu
    1 Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan, USA 2
    Nat Genet 46:200-4. 2014
    ..We show that our approach retains useful features from single-variant meta-analysis approaches and demonstrate its use in a study of blood lipid levels in ∼18,500 individuals genotyped with exome arrays. ..
  48. pmc Common variants at 30 loci contribute to polygenic dyslipidemia
    Sekar Kathiresan
    Cardiovascular Research Center and Cardiology Division, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
    Nat Genet 41:56-65. 2009
    ..These results suggest that the cumulative effect of multiple common variants contributes to polygenic dyslipidemia...
  49. pmc Variants in MTNR1B influence fasting glucose levels
    Inga Prokopenko
    1 Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford OX3 7LJ, UK 2 Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK 3 These authors contributed equally to this work
    Nat Genet 41:77-81. 2009
    ..Our analyses also confirm previous associations of fasting glucose with variants at the G6PC2 (rs560887, P = 1.1 x 10(-57)) and GCK (rs4607517, P = 1.0 x 10(-25)) loci...
  50. pmc Genome-wide association study identifies eight loci associated with blood pressure
    Christopher Newton-Cheh
    Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA
    Nat Genet 41:666-76. 2009
    ..These associations between common variants and blood pressure and hypertension offer mechanistic insights into the regulation of blood pressure and may point to novel targets for interventions to prevent cardiovascular disease...
  51. ncbi request reprint An efficient comprehensive search algorithm for tagSNP selection using linkage disequilibrium criteria
    Zhaohui S Qin
    Center for Statistical Genetics, Department of Biostatistics, School of Public Health, University of Michigan 1420 Washington Heights, Ann Arbor, MI 48109 2029, USA
    Bioinformatics 22:220-5. 2006
    ..The goal is to minimize the number of markers selected for genotyping in a particular platform and therefore reduce genotyping cost while simultaneously maximizing the information content provided by selected markers...
  52. ncbi request reprint Optimal designs for two-stage genome-wide association studies
    Andrew D Skol
    Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
    Genet Epidemiol 31:776-88. 2007
    ..Alternatively, the same cost savings can be had by relaxing the false positive rate by 2.5-fold, for example from 1/300,000 to 2.5/300,000, while retaining the same power...
  53. ncbi request reprint PEDSTATS: descriptive statistics, graphics and quality assessment for gene mapping data
    Janis E Wigginton
    Center for Statistical Genetics, Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI 48103, USA
    Bioinformatics 21:3445-7. 2005
    ..We describe a tool that produces summary statistics and basic quality assessments for gene-mapping data, accommodating either pedigree or case-control datasets. Our tool can also produce graphic output in the PDF format...
  54. doi request reprint Molecular dissection of psoriasis: integrating genetics and biology
    James T Elder
    Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, USA
    J Invest Dermatol 130:1213-26. 2010
    ..Here, we review the epidemiology, immunopathology, and genetics of psoriasis, and present a disease model integrating its genetics and immunology...
  55. doi request reprint Genome-wide association studies for complex traits: consensus, uncertainty and challenges
    Mark I McCarthy
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
    Nat Rev Genet 9:356-69. 2008
    ....
  56. pmc Genome-wide association study of PR interval
    Arne Pfeufer
    Institute of Human Genetics, Klinikum rechts der Isar der Technischen Universitat Munchen, Munich, Germany
    Nat Genet 42:153-9. 2010
    ..0056). This suggests a role for common variation in ion channel and developmental genes in atrial and atrioventricular conduction as well as in susceptibility to atrial fibrillation...
  57. pmc Meta-analysis and imputation refines the association of 15q25 with smoking quantity
    Jason Z Liu
    Department of Statistics, University of Oxford, Oxford, UK
    Nat Genet 42:436-40. 2010
    ..Our fine-mapping approach identified a SNP showing the highest significance, rs55853698, located within the promoter region of CHRNA5. Conditional analysis also identified a secondary locus (rs6495308) in CHRNA3...
  58. ncbi request reprint Estimating the power of variance component linkage analysis in large pedigrees
    Wei Min Chen
    Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
    Genet Epidemiol 30:471-84. 2006
    ..Our algorithms for power analysis together with polygenic analysis are implemented in a freely available computer program, POLY...
  59. pmc Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes
    Andrew P Morris
    Wellcome Trust Centre for Human Genetics, University of Oxford, UK
    Nat Genet 44:981-90. 2012
    ..Exploration of the enlarged set of susceptibility loci implicates several processes, including CREBBP-related transcription, adipocytokine signaling and cell cycle regulation, in diabetes pathogenesis...
  60. pmc Identification of a rare coding variant in complement 3 associated with age-related macular degeneration
    Xiaowei Zhan
    1 Department of Biostatistics, Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, Michigan, USA 2
    Nat Genet 45:1375-9. 2013
    ..06%; fcontrol = 0.39%; OR = 2.68). The variants suggest decreased inhibition of C3 by complement factor H, resulting in increased activation of the alternative complement pathway, as a key component of disease biology...
  61. pmc Imputation of coding variants in African Americans: better performance using data from the exome sequencing project
    Qing Duan
    Department of Genetics and Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599, USA, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27599, USA, Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA, Renaissance Computing Institute, University of North Carolina, Chapel Hill, NC 27599, USA, Department of Statistics and Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA, Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA, Department of Epidemiology, University of Washington, Seattle, WA 98195, USA, Division of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA, Department of Epidemiology and Medicine, University of Iowa, Iowa City, IA 52242, Division of Cardiology, George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA, Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, France
    Bioinformatics 29:2744-9. 2013
    ..We recommend using haplotypes from Exome Sequencing Project alone or concatenation of the two panels over quality score-based post-imputation selection or IMPUTE2's two-panel combination...
  62. pmc Common variants associated with plasma triglycerides and risk for coronary artery disease
    Ron Do
    1 Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, USA 2 Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA 3 Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA 4 Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
    Nat Genet 45:1345-52. 2013
    ..These results suggest that triglyceride-rich lipoproteins causally influence risk for CAD. ..
  63. pmc A note on exact tests of Hardy-Weinberg equilibrium
    Janis E Wigginton
    Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
    Am J Hum Genet 76:887-93. 2005
    ..They have been implemented in freely available code that will be useful for quality assessment of genotype data and for the detection of genetic association or population stratification in very large data sets...
  64. pmc Genetic loci influencing kidney function and chronic kidney disease
    John C Chambers
    Department of Epidemiology and Biostatistics, School of Public Health, Imperial College of London, London, UK
    Nat Genet 42:373-5. 2010
    ..0 x 10(-5) and P = 3.6 x 10(-4), respectively). Our findings provide insight into metabolic, solute and drug-transport pathways underlying susceptibility to chronic kidney disease...
  65. pmc The benefits of using genetic information to design prevention trials
    Youna Hu
    Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
    Am J Hum Genet 92:547-57. 2013
    ....
  66. pmc Detecting and estimating contamination of human DNA samples in sequencing and array-based genotype data
    Goo Jun
    Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
    Am J Hum Genet 91:839-48. 2012
    ..We evaluate the impact of DNA contamination on genotype accuracy and propose effective strategies to screen for and prevent DNA contamination in sequencing studies...
  67. ncbi request reprint An evaluation of the replicate pool method: quick estimation of genome-wide linkage peak p-values
    Janis E Wigginton
    Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
    Genet Epidemiol 30:320-32. 2006
    ..We have implemented the replicate pool method along with our variance estimator in a new program called Pseudo, which is the first widely available automated implementation of the replicate pool method...
  68. pmc Genome-wide association analysis identifies variants associated with nonalcoholic fatty liver disease that have distinct effects on metabolic traits
    Elizabeth K Speliotes
    Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, Michigan, United States of America
    PLoS Genet 7:e1001324. 2011
    ....
  69. pmc Genomewide scan in families with schizophrenia from the founder population of Afrikaners reveals evidence for linkage and uniparental disomy on chromosome 1
    Goncalo R Abecasis
    Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
    Am J Hum Genet 74:403-17. 2004
    ..This is the first time a UPD has been described in a patient with schizophrenia, lending further support to involvement of chromosome 1 in schizophrenia susceptibility in the Afrikaners...
  70. pmc AbCD: arbitrary coverage design for sequencing-based genetic studies
    Jian Kang
    Faculty of Kinesiology, University of Calgary, Calgary, AB T2N1N4, Canada
    Bioinformatics 29:799-801. 2013
    ....
  71. pmc Increasing the power and efficiency of disease-marker case-control association studies through use of allele-sharing information
    Tasha E Fingerlin
    Department of Epidemiology, School of Public Health, and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
    Am J Hum Genet 74:432-43. 2004
    ..We show that these properties hold even when the power to detect linkage to a region in the entire sample is negligible. This approach can be extended to more-general pedigree structures and quantitative traits...
  72. pmc A comparison of phasing algorithms for trios and unrelated individuals
    Jonathan Marchini
    Department of Statistics, University of Oxford, Oxford OX1 3TG, United Kingdom
    Am J Hum Genet 78:437-50. 2006
    ..Finally, we evaluated methods of estimating the value of r(2) between a pair of SNPs and concluded that all methods estimated r(2) well when the estimated value was >or=0.8...
  73. pmc Genetic variation in the 22q11 locus and susceptibility to schizophrenia
    Hui Liu
    The Rockefeller University, Human Neurogenetics Laboratory, New York, NY 10021 USA
    Proc Natl Acad Sci U S A 99:16859-64. 2002
    ..Finer-scale haplotype mapping has identified two subregions within the 1.5-Mb locus that are likely to harbor candidate schizophrenia susceptibility genes...
  74. pmc Common variants near MC4R are associated with fat mass, weight and risk of obesity
    Ruth J F Loos
    MRC Epidemiology Unit, Addenbrooke s Hospital, Cambridge CB2 0QQ, UK
    Nat Genet 40:768-75. 2008
    ....
  75. ncbi request reprint Regression-based sib pair linkage analysis for binary traits
    Maurice P A Zeegers
    Department of Epidemiology, Faculty of Health Science, Maastricht University, Maastricht, The Netherlands
    Hum Hered 55:125-31. 2003
    ....
  76. ncbi request reprint Meta-analysis of genome scans of age-related macular degeneration
    Sheila A Fisher
    Department of Medical and Molecular Genetics, Guy s, King s and St Thomas School of Medicine, King s College London, London SE1 9RT, UK
    Hum Mol Genet 14:2257-64. 2005
    ..Several of the regions identified here showed only weak evidence for linkage in the individual studies. These results will help prioritize regions for future positional and functional candidate gene studies in AMD...

Research Grants14

  1. Gene Mapping of Complex Traits Using Resequencing Data
    GONCALO ROCHA ABECASIS; Fiscal Year: 2010
    ..Here, we propose to develop efficient methods for analyzing high-throughput sequence data and to distribute software tools that allow others to extract maximum benefit from our methods. ..
  2. Computational and Statistical Models for Human Pedigrees
    Goncalo Abecasis; Fiscal Year: 2007
    ..abstract_text> ..
  3. Computational and Statistical Models for Human Pedigrees
    Goncalo Abecasis; Fiscal Year: 2003
    ..abstract_text> ..
  4. Gene Mapping of Complex Traits Using Resequencing Data
    GONCALO ROCHA ABECASIS; Fiscal Year: 2009
    ..Here, we propose to develop efficient methods for analyzing high-throughput sequence data and to distribute software tools that allow others to extract maximum benefit from our methods. ..
  5. Computational and Statistical Models for Human Pedigrees
    GONCALO ROCHA ABECASIS; Fiscal Year: 2008
    ..abstract_text> ..
  6. Computational and Statistical Models for Human Pedigrees
    GONCALO ROCHA ABECASIS; Fiscal Year: 2008
    ..abstract_text> ..
  7. Gene Mapping of Complex Traits Using Resequencing Data
    Goncalo Abecasis; Fiscal Year: 2008
    ..Here, we propose to develop efficient methods for analyzing high-throughput sequence data and to distribute software tools that allow others to extract maximum benefit from our methods. ..
  8. Integrated Parametric and Non-parametric Mapping for Genome-Wife Association Data
    GONCALO ROCHA ABECASIS; Fiscal Year: 2008
    ..The resulting data, together with genotype data from at least two other genome-wide association scans, will allow us to evaluate and calibrate our methods for association mapping. [unreadable] [unreadable] [unreadable] [unreadable]..
  9. Integrated Parametric and Non-parametric Mapping for Genome-Wide Association Data
    Goncalo Abecasis; Fiscal Year: 2007
    ..The resulting data, together with genotype data from at least two other genome-wide association scans, will allow us to evaluate and calibrate our methods for association mapping. [unreadable] [unreadable] [unreadable] [unreadable]..
  10. Computational and Statistical Models for Human Pedigrees
    Goncalo Abecasis; Fiscal Year: 2006
    ..abstract_text> ..
  11. Computational and Statistical Models for Human Pedigrees
    Goncalo Abecasis; Fiscal Year: 2004
    ..abstract_text> ..
  12. Computational and Statistical Models for Human Pedigrees
    Goncalo Abecasis; Fiscal Year: 2005
    ..abstract_text> ..
  13. Computational and Statistical Models for Human Pedigrees
    Goncalo Abecasis; Fiscal Year: 2004
    ..abstract_text> ..
  14. Gene Mapping of Complex Traits Using Resequencing Data
    GONCALO ROCHA ABECASIS; Fiscal Year: 2010
    ..Here, we propose to develop efficient methods for analyzing high-throughput sequence data and to distribute software tools that allow others to extract maximum benefit from our methods. ..