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Citation
Iyer, J., Wang, Q., Le, T., Pizzo, L., Grönke, S., Ambegaokar, S.S., Imai, Y., Srivastava, A., Troisí, B.L., Mardon, G., Artero, R., Jackson, G.R., Isaacs, A.M., Partridge, L., Lu, B., Kumar, J.P., Girirajan, S. (2016). Quantitative Assessment of Eye Phenotypes for Functional Genetic Studies Using Drosophila melanogaster.  G3 (Bethesda) 6(5): 1427--1437.
FlyBase ID
FBrf0232309
Publication Type
Research paper
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.
PubMed ID
PubMed Central ID
PMC4856093 (PMC) (EuropePMC)
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Secondary IDs
    Language of Publication
    English
    Additional Languages of Abstract
    Parent Publication
    Publication Type
    Journal
    Abbreviation
    G3 (Bethesda)
    Title
    G3 : genes - genomes - genetics
    ISBN/ISSN
    2160-1836
    Data From Reference
    Aberrations (14)
    Alleles (51)
    Genes (35)
    Natural transposons (1)
    Insertions (1)
    Experimental Tools (1)
    Transgenic Constructs (38)