Quantitative Assessment of Eye Phenotypes for Functional Genetic Studies Using Drosophila melanogaster.
Quantitative Assessment of Eye Phenotypes for Functional Genetic Studies Using Drosophila melanogaster.
复制标题
DOI：
10.1534/g3.116.027060
复制
发表时间：
2016-05-03
期刊：
影响因子：
--
通讯作者：
Girirajan S
中科院分区：
文献类型：
--
作者：
Iyer J;Wang Q;Le T;Pizzo L;Grönke S;Ambegaokar SS;Imai Y;Srivastava A;Troisí BL;Mardon G;Artero R;Jackson GR;Isaacs AM;Partridge L;Lu B;Kumar JP;Girirajan S
果蝇基因组中大约三分之二的重要基因与眼睛发育有关，这使得果蝇眼睛成为研究细胞功能和发育、神经发育/退化以及癌症和糖尿病等复杂疾病的绝佳遗传系统。我们开发了一种新型计算方法，作为Flynotyper软件（http：//www.example.com）实施，以定量评估果蝇眼睛中因影响基本细胞和发育过程的遗传变异而导致的形态缺陷。flynotyper.sourceforge.net Flynotyper利用一系列的图像处理操作来自动检测蝇眼和单个小眼，并计算表型得分作为蝇眼中小眼排列的无序性的度量。作为原理的证明，我们通过分析由于眼睛特异性敲除果蝇直系同源物的12个神经发育基因的缺陷来测试我们的方法，以准确地记录这些基因对剂量改变的差异敏感性。我们还评估了来自六项独立研究的眼睛图像，这些研究评估了重复序列过表达、肽库筛选的候选物以及神经毒性和发育过程修饰剂对眼睛形态的影响，并显示出与原始评估的强烈一致性。我们进一步证明了这种方法的实用性，通过分析从果蝇的两个全基因组缺陷筛选获得的16个sine oculis修饰符，并准确定量其增强子和抑制子在眼睛发育过程中的作用。我们的方法将补充现有的眼睛表型测定，并提高使用蝇眼进行基因和遗传相互作用功能评估的研究的准确性。
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.