Copy number variation prevalence in known asthma genes and their impact on asthma susceptibility

Genetic studies have identified numerous genes reproducibly associated with asthma, yet these studies have focussed almost entirely on single nucleotide polymorphisms (SNPs), and virtually ignored another highly prevalent form of genetic variation: Copy Number Variants (CNVs).

[1]  J. Stockman,et al.  A Large-Scale, Consortium-Based Genomewide Association Study of Asthma , 2012 .

[2]  Y. Guo,et al.  The Association Between Glutathione S-Transferase P1, M1 Polymorphisms and Asthma in Taiwanese Schoolchildren , 2005 .

[3]  E. Silverman,et al.  Exhaled nitric oxide in patients with asthma: association with NOS1 genotype. , 2000, American journal of respiratory and critical care medicine.

[4]  D. Meyers Genetics of asthma and allergy: what have we learned? , 2010, The Journal of allergy and clinical immunology.

[5]  Joshua M. Korn,et al.  Integrated detection and population-genetic analysis of SNPs and copy number variation , 2008, Nature Genetics.

[6]  K. Frazer,et al.  Common deletions and SNPs are in linkage disequilibrium in the human genome , 2006, Nature Genetics.

[7]  I. Ionita-Laza,et al.  The interaction of glutathione S‐transferase M1‐null variants with tobacco smoke exposure and the development of childhood asthma , 2009, Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology.

[8]  D. Curran‐Everett,et al.  Identification of asthma phenotypes using cluster analysis in the Severe Asthma Research Program. , 2010, American journal of respiratory and critical care medicine.

[9]  C. Ober,et al.  Asthma genetics 2006: the long and winding road to gene discovery , 2006, Genes and Immunity.

[10]  R. Redon,et al.  Relative Impact of Nucleotide and Copy Number Variation on Gene Expression Phenotypes , 2007, Science.

[11]  H. Kim,et al.  The genetics of asthma. , 1998, Current opinion in pulmonary medicine.

[12]  S. Steer,et al.  Evidence for an influence of chemokine ligand 3-like 1 (CCL3L1) gene copy number on susceptibility to rheumatoid arthritis , 2007, Annals of the rheumatic diseases.

[13]  Judy H Cho,et al.  Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease , 2008, Nature Genetics.

[14]  Manuel A. R. Ferreira,et al.  PLINK: a tool set for whole-genome association and population-based linkage analyses. , 2007, American journal of human genetics.

[15]  B. Maher Personal genomes: The case of the missing heritability , 2008, Nature.

[16]  J. Drazen,et al.  Neuronal NO synthase (NOS1) is a major candidate gene for asthma. , 1999, Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology.

[17]  N Franklin Adkinson,et al.  Long-term effects of budesonide or nedocromil in children with asthma. , 2000, The New England journal of medicine.

[18]  A. Nekrutenko,et al.  Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences , 2010, Genome Biology.

[19]  V. Baranov,et al.  Glutathione-S-transferase µ and theta gene polymorphisms as new risk factors of atopic bronchial asthma , 2002, Journal of Molecular Medicine.

[20]  Daniel J. Blankenberg,et al.  Galaxy: A Web‐Based Genome Analysis Tool for Experimentalists , 2010, Current protocols in molecular biology.

[21]  L. Christiansen,et al.  Possible gene dosage effect of glutathione‐S‐transferases on atopic asthma: Using real‐time PCR for quantification of GSTM1 and GSTT1 gene copy numbers , 2004, Human mutation.

[22]  Wolfgang Huber,et al.  Relating CNVs to transcriptome data at fine resolution: assessment of the effect of variant size, type, and overlap with functional regions. , 2011, Genome research.

[23]  Bi Zhou,et al.  Gene copy-number variation and associated polymorphisms of complement component C4 in human systemic lupus erythematosus (SLE): low copy number is a risk factor for and high copy number is a protective factor against SLE susceptibility in European Americans. , 2007, American journal of human genetics.

[24]  Thomas D. Wu,et al.  A highly annotated whole-genome sequence of a Korean individual , 2009, Nature.

[25]  Ryan D. Hernandez,et al.  Meta-analysis of Genome-wide Association Studies of Asthma In Ethnically Diverse North American Populations , 2011, Nature Genetics.

[26]  V. Paschall Long-Term Effects of Budesonide or Nedocromil in Children with Asthma , 2001 .

[27]  W James Gauderman,et al.  Effects of glutathione-S-transferase M1, T1, and P1 on childhood lung function growth. , 2002, American journal of respiratory and critical care medicine.

[28]  Tomas W. Fitzgerald,et al.  A robust statistical method for case-control association testing with copy number variation , 2008, Nature Genetics.

[29]  D. Altshuler,et al.  A map of human genome variation from population-scale sequencing , 2010, Nature.

[30]  Christoph Lange,et al.  Assessing the reproducibility of asthma candidate gene associations, using genome-wide data. , 2009, American journal of respiratory and critical care medicine.

[31]  M. Church,et al.  Non‐H1‐receptor effects of antihistamines , 1999, Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology.

[32]  Kenny Q. Ye,et al.  Mapping copy number variation by population scale genome sequencing , 2010, Nature.

[33]  E. Eichler,et al.  Mutational and selective effects on copy-number variants in the human genome , 2007, Nature Genetics.

[34]  Judy H. Cho,et al.  Finding the missing heritability of complex diseases , 2009, Nature.

[35]  M. Adams,et al.  Recent Segmental Duplications in the Human Genome , 2002, Science.

[36]  S. London,et al.  Evaluation of candidate genes in a genome-wide association study of childhood asthma in Mexicans. , 2010, The Journal of allergy and clinical immunology.

[37]  Timothy B. Stockwell,et al.  The Diploid Genome Sequence of an Individual Human , 2007, PLoS biology.

[38]  Tomas W. Fitzgerald,et al.  Origins and functional impact of copy number variation in the human genome , 2010, Nature.

[39]  P. Yang,et al.  Genetic polymorphism of epoxide hydrolase and glutathione S-transferase in COPD , 2004, European Respiratory Journal.

[40]  Wj Gauderman,et al.  QUANTO 1.1: A computer program for power and sample size calculations for genetic-epidemiology studies , 2006 .

[41]  Florence Demenais,et al.  A large-scale, consortium-based genomewide association study of asthma. , 2010, The New England journal of medicine.

[42]  Heather Eliassen,et al.  The Childhood Asthma Management Program (CAMP): design, rationale, and methods. Childhood Asthma Management Program Research Group. , 1999, Controlled clinical trials.

[43]  E. Eichler,et al.  Segmental duplications and copy-number variation in the human genome. , 2005, American journal of human genetics.

[44]  Kenny Q. Ye,et al.  Large-Scale Copy Number Polymorphism in the Human Genome , 2004, Science.

[45]  Iuliana Ionita-Laza,et al.  On the analysis of copy‐number variations in genome‐wide association studies: a translation of the family‐based association test , 2008, Genetic epidemiology.

[46]  L. Feuk,et al.  Detection of large-scale variation in the human genome , 2004, Nature Genetics.

[47]  Iuliana Ionita-Laza,et al.  Genetic association analysis of copy-number variation (CNV) in human disease pathogenesis. , 2009, Genomics.

[48]  Yusuke Nakamura,et al.  Independent and population-specific association of risk variants at the IRGM locus with Crohn's disease , 2010, Human molecular genetics.

[49]  Life Technologies,et al.  A map of human genome variation from population-scale sequencing , 2011 .

[50]  A. Doney,et al.  Glutathione S-Transferase M1 and P1 Genotype, Passive Smoking, and Peak Expiratory Flow in Asthma , 2006, Pediatrics.