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Quantitative assessment of eye phenotypes for functional genetic studies using Drosophila melanogaster

Janani Iyer, Qingyu Wang, Thanh Le, Lucilla Pizzo, Sebastian Grönke, Surendra S. Ambegaokar, Yuzuru Imai, Ashutosh Srivastava, Beatriz Llamusí Troisí, Graeme Mardon, Ruben Artero, George R. Jackson, Adrian M. Isaacs, Linda Partridge, Bingwei Lu, Justin P. Kumar, Santhosh Girirajan
doi: https://doi.org/10.1101/036368
Janani Iyer
1Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
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Qingyu Wang
2Bioinformatics and Genomics Program, Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA 16802
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Thanh Le
2Bioinformatics and Genomics Program, Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA 16802
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Lucilla Pizzo
1Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
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Sebastian Grönke
3Max-Planck Institute for Biology of Aging, Cologne, Germany
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Surendra S. Ambegaokar
4Department of Botany and Microbiology, Ohio Wesleyan University, Delaware, OH 43015
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Yuzuru Imai
5Department of Research for Parkinson's Disease, Juntendo University Graduate School of Medicine, Tokyo, Japan
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Ashutosh Srivastava
1Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
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Beatriz Llamusí Troisí
6Translational Genetics Group, Department of Genetics, University of Valencia, Burjassot, Spain
7Incliva Health Research Institute, Avda. Menéndez Pelayo, 4 accesorio, 46010 Valencia. Spain.
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Graeme Mardon
8Departments of Pathology and Immunology and Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030
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Ruben Artero
6Translational Genetics Group, Department of Genetics, University of Valencia, Burjassot, Spain
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George R. Jackson
9Department of Neurology, Baylor College of Medicine, Houston, TX 77030
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Adrian M. Isaacs
10Department of Neurodegenerative Disease, UCL Institute of Neurology, London, WC1N 3BG, UK
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Linda Partridge
3Max-Planck Institute for Biology of Aging, Cologne, Germany
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Bingwei Lu
11Department of Pathology, Stanford University, Palo Alto, CA
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Justin P. Kumar
12Department of Biology, Indiana University, Bloomington, IA 47405
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Santhosh Girirajan
1Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
2Bioinformatics and Genomics Program, Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA 16802
13Department of Anthropology, The Pennsylvania State University, University Park, PA 16802
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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.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted January 15, 2016.
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Quantitative assessment of eye phenotypes for functional genetic studies using Drosophila melanogaster
Janani Iyer, Qingyu Wang, Thanh Le, Lucilla Pizzo, Sebastian Grönke, Surendra S. Ambegaokar, Yuzuru Imai, Ashutosh Srivastava, Beatriz Llamusí Troisí, Graeme Mardon, Ruben Artero, George R. Jackson, Adrian M. Isaacs, Linda Partridge, Bingwei Lu, Justin P. Kumar, Santhosh Girirajan
bioRxiv 036368; doi: https://doi.org/10.1101/036368
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Quantitative assessment of eye phenotypes for functional genetic studies using Drosophila melanogaster
Janani Iyer, Qingyu Wang, Thanh Le, Lucilla Pizzo, Sebastian Grönke, Surendra S. Ambegaokar, Yuzuru Imai, Ashutosh Srivastava, Beatriz Llamusí Troisí, Graeme Mardon, Ruben Artero, George R. Jackson, Adrian M. Isaacs, Linda Partridge, Bingwei Lu, Justin P. Kumar, Santhosh Girirajan
bioRxiv 036368; doi: https://doi.org/10.1101/036368

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