title: Quantitative Assessment of Eye Phenotypes for Functional Genetic Studies Using Drosophila melanogaster.
abstract: About two-thirds of the vital genes in the Drosophila genome are involved in eye development, making the fly eye an excellent genetic system to study cellular function and development, neurodevelopment/degeneration, and complex diseases such as cancer and diabetes. We developed a novel computational method, implemented as Flynotyper software (http://flynotyper.sourceforge.net), to quantitatively assess the morphological defects in the Drosophila eye resulting from genetic alterations affecting basic cellular and developmental processes. Flynotyper utilizes a series of image processing operations to automatically detect the fly eye and the individual ommatidium, and calculates a phenotypic score as a measure of the disorderliness of ommatidial arrangement in the fly eye. As a proof of principle, we tested our method by analyzing the defects due to eye-specific knockdown of Drosophila orthologs of 12 neurodevelopmental genes to accurately document differential sensitivities of these genes to dosage alteration. We also evaluated eye images from six independent studies assessing the effect of overexpression of repeats, candidates from peptide library screens, and modifiers of neurotoxicity and developmental processes on eye morphology, and show strong concordance with the original assessment. We further demonstrate the utility of this method by analyzing 16 modifiers of sine oculis obtained from two genome-wide deficiency screens of Drosophila and accurately quantifying the effect of its enhancers and suppressors during eye development. Our method will complement existing assays for eye phenotypes, and increase the accuracy of studies that use fly eyes for functional evaluation of genes and genetic interactions.
authors.affiliation: Department of Biochemistry and Molecular Biology, The Pennsylvania State University, Pennsylvania 16802.
authors.forename: Janani
authors.initials: J
authors.lastname: Iyer
authors.affiliation: Bioinformatics and Genomics Program, The Huck Institutes of of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802.
authors.forename: Qingyu
authors.initials: Q
authors.lastname: Wang
authors.affiliation: Bioinformatics and Genomics Program, The Huck Institutes of of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802.
authors.forename: Thanh
authors.initials: T
authors.lastname: Le
authors.affiliation: Department of Biochemistry and Molecular Biology, The Pennsylvania State University, Pennsylvania 16802.
authors.forename: Lucilla
authors.initials: L
authors.lastname: Pizzo
authors.affiliation: Biological Mechanisms of Ageing, Max-Planck Institute for Biology of Aging, 50931 Cologne, Germany.
authors.forename: Sebastian
authors.identifier: 0000-0003-0598-4945
authors.initials: S
authors.lastname: Grönke
authors.affiliation: Department of Botany and Microbiology, Ohio Wesleyan University, Delaware, Ohio 43015.
authors.forename: Surendra S
authors.initials: SS
authors.lastname: Ambegaokar
authors.affiliation: Department of Research for Parkinson's Disease, Juntendo University Graduate School of Medicine, 113-8421 Tokyo, Japan.
authors.forename: Yuzuru
authors.initials: Y
authors.lastname: Imai
authors.affiliation: Department of Biochemistry and Molecular Biology, The Pennsylvania State University, Pennsylvania 16802.
authors.forename: Ashutosh
authors.initials: A
authors.lastname: Srivastava
authors.affiliation: Translational Genetics Group, Department of Genetics, University of Valencia, 46100 Burjassot, Spain Program of Rare Diseases, Incliva Health Research Institute, 46010 Valencia, Spain.
authors.forename: Beatriz Llamusí
authors.initials: BL
authors.lastname: Troisí
authors.affiliation: Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas 77030 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030.
authors.forename: Graeme
authors.initials: G
authors.lastname: Mardon
authors.affiliation: Translational Genetics Group, Department of Genetics, University of Valencia, 46100 Burjassot, Spain Program of Rare Diseases, Incliva Health Research Institute, 46010 Valencia, Spain.
authors.forename: Ruben
authors.initials: R
authors.lastname: Artero
authors.affiliation: Department of Neurology, Baylor College of Medicine, Houston, Texas 77030.
authors.forename: George R
authors.initials: GR
authors.lastname: Jackson
authors.affiliation: Department of Neurodegenerative Disease, UCL Institute of Neurology, London, WC1N 3BG, United Kingdom.
authors.forename: Adrian M
authors.initials: AM
authors.lastname: Isaacs
authors.affiliation: Biological Mechanisms of Ageing, Max-Planck Institute for Biology of Aging, 50931 Cologne, Germany.
authors.forename: Linda
authors.initials: L
authors.lastname: Partridge
authors.affiliation: Department of Pathology, Stanford University, Palo Alto, California 94305.
authors.forename: Bingwei
authors.initials: B
authors.lastname: Lu
authors.affiliation: Department of Biology, Indiana University, Bloomington, Indiana 47405.
authors.forename: Justin P
authors.initials: JP
authors.lastname: Kumar
authors.affiliation: Department of Biochemistry and Molecular Biology, The Pennsylvania State University, Pennsylvania 16802 Bioinformatics and Genomics Program, The Huck Institutes of of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802 Department of Anthropology, The Pennsylvania State University, University Park, Pennsylvania 16802 sxg47@psu.edu.
authors.forename: Santhosh
authors.initials: S
authors.lastname: Girirajan
mesh_terms: D000465:Algorithms; D000818:Animals; D030801:Animals, Genetically Modified; D029721:Drosophila Proteins / Q000235:genetics / Q000378:metabolism; D004331:Drosophila melanogaster / Q000235:genetics*; D005123:Eye / Q000033:anatomy & histology / Q000648:ultrastructure; D055785:Gene Knockdown Techniques; D056726:Genetic Association Studies; D008957:Models, Genetic; D055495:Neurogenesis / Q000235:genetics; D010641:Phenotype; D015203:Reproducibility of Results
chemical_list: D029721:Drosophila Proteins
keywords: Drosophila melanogaster; human disease models; modifier screens; neurodevelopmental disorders; ommatidia; rough eye