TITLE

Phenotype-genotype association grid: a convenient method for summarizing multiple association analyses

AUTHOR(S)
Levy, Daniel; DePalma, Steven R; Benjamin, Emelia J; O'Donnell, Christopher J; Parise, Helen; Hirschhorn, Joel N; Vasan, Ramachandran S; Izumo, Seigo; Larson, Martin G
PUB. DATE
January 2006
SOURCE
BMC Genetics;2006, Vol. 7, p30
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Background: High-throughput genotyping generates vast amounts of data for analysis; results can be difficult to summarize succinctly. A single project may involve genotyping many genes with multiple variants per gene and analyzing each variant in relation to numerous phenotypes, using several genetic models and population subgroups. Hundreds of statistical tests may be performed for a single SNP, thereby complicating interpretation of results and inhibiting identification of patterns of association. Results: To facilitate visual display and summary of large numbers of association tests of genetic loci with multiple phenotypes, we developed a Phenotype-Genotype Association (PGA) grid display. A database-backed web server was used to create PGA grids from phenotypic and genotypic data (sample sizes, means and standard errors, P-value for association). HTML pages were generated using Tcl scripts on an AOLserver platform, using an Oracle database, and the ArsDigita Community System web toolkit. The grids are interactive and permit display of summary data for individual cells by a mouse click (i.e. least squares means for a given SNP and phenotype, specified genetic model and study sample). PGA grids can be used to visually summarize results of individual SNP associations, gene-environment associations, or haplotype associations. Conclusion: The PGA grid, which permits interactive exploration of large numbers of association test results, can serve as an easily adapted common and useful display format for large-scale genetic studies. Doing so would reduce the problem of publication bias, and would simplify the task of summarizing large-scale association studies.
ACCESSION #
29324052

 

Related Articles

  • A brief note on the resemblance between relatives in the presence of population stratification. Sebro, R; Risch, N J // Heredity;May2012, Vol. 108 Issue 5, p563 

    Population stratification occurs when a study population is comprised of several sub-populations, and can result in increased false positive findings in genomewide-association studies. Recently published work shows that sub-population-specific positive assortative mating at the genotypic level...

  • Power of selective genotyping in genome-wide association studies of quantitative traits. Chao Xing; Guan Xing // BMC Proceedings;2009 Supplement 7, Vol. 3, Special section p1 

    The selective genotyping approach in quantitative genetics means genotyping only individuals with extreme phenotypes. This approach is considered an efficient way to perform gene mapping, and can be applied in both linkage and association studies. Selective genotyping in association mapping of...

  • Genotype-phenotype correlation in 22q11.2 deletion syndrome. Michaelovsky, Elena; Frisch, Amos; Carmel, Miri; Patya, Miriam; Zarchi, Omer; Green, Tamar; Basel-Vanagaite, Lina; Weizman, Abraham; Gothelf, Doron // BMC Medical Genetics;2012, Vol. 13 Issue 1, p122 

    Background: The 22q11.2 deletion syndrome (22q11.2DS) is caused by hemizygous microdeletions on chromosome 22q11.2 with highly variable physical and neuropsychiatric manifestations. We explored the genotype-phenotype relationship in a relatively large 22q11.2DS cohort treated and monitored in...

  • Association of genetic variations of PRDM16 with metabolic syndrome in a general Xinjiang Uygur population. Zhang, Ju; Li, Nan; Yan, Zhi; Zhang, De; Wang, Hong; Guo, Yan; Ling, Zhou // Endocrine (1355008X);Jun2012, Vol. 41 Issue 3, p539 

    The article discusses a study which examined variations in positive regulatory domain containing 16 (PRDM 16) sequence which may affect susceptibility to metabolic syndrome (MetS). A comparison of genotype frequencies in distributions for genetic polymorphisms of PRDM 16 in Uygur subjects with...

  • Associating multiple longitudinal traits with high-dimensional single-nucleotide polymorphism data: application to the Framingham Heart Study. Waaijenborg, Sandra; Zwinderman, Aeilko H. // BMC Proceedings;2009 Supplement 7, Vol. 3, Special section p1 

    Cardiovascular diseases are associated with combinations of phenotypic traits, which are in turn caused by a combination of environmental and genetic factors. Because of the diversity of pathways that may lead to cardiovascular diseases, we examined the so-called intermediate phenotypes, which...

  • The Impact of Phenocopy on the Genetic Analysis of Complex Traits. Lescai, Francesco; Franceschi, Claudio // PLoS ONE;2010, Vol. 5 Issue 7, p1 

    A consistent debate is ongoing on genome-wide association studies (GWAs). A key point is the capability to identify low-penetrance variations across the human genome. Among the phenomena reducing the power of these analyses, phenocopy level (PE) hampers very seriously the investigation of...

  • Critical region in 2q31.2q32.3 deletion syndrome: Report of two phenotypically distinct patients, one with an additional deletion in Alagille syndrome region. Ferreira, Susana Isabel; Matoso, Eunice; Venncio, Margarida; Saraiva, Jorge; Melo, Joana B.; Marques Carreira, Isabel // Molecular Cytogenetics (17558166);2012, Vol. 5 Issue 1, p25 

    Background: Standard cytogenetic analysis has revealed to date more than 30 reported cases presenting interstitial deletions involving region 2q31-q32, but with poorly defined breakpoints. After the postulation of 2q31.2q32.3 deletion as a clinically recognizable disorder, more patients were...

  • Clinical hallmarks and genetic polymorphisms in the CFTR gene contribute to the disclosure of the A1006E mutation. Tomaiuolo, Anna Cristina; Alghisi, Federico; Petrocchi, Stefano; Surace, Cecilia; Roberti, Maria Cristina; Bella, Sergio; Lucidi, Vincenzina; Angioni, Adriano // Clinical & Investigative Medicine;Aug2010, Vol. 33 Issue 4, pE234 

    Since the identification of the Cystic Fibrosis transmembrane conductance regulator (CFTR) gene in 1989, many genetic mutations have been found in cystic fibrosis (CF) patients. Dysfunctions of the CFTR gene are responsible for the highly variable clinical presentation ranging from severe CF,...

  • Relating fitness phenotypes to genotypes in Lithuanian elite athletes. Ginevičienė, Valentina; Pranckevičienė, Erinija; Milašius, Kazys; Kučinskas, Vaidutis // Acta Medica Lituanica;2010, Vol. 17 Issue 1/2, p1 

    Background. We aim to link fitness-related genotypes to the development of specific physical fitness phenotypes and a predisposition towards a specific sport category in Lithuanian elite athletes. Materials and methods. The study involved 193 athletes (152 male and 41 female) and 250 controls....

Share

Read the Article

Courtesy of THE LIBRARY OF VIRGINIA

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics