Automated Detection of Gene Duplications or Deletions

自动检测基因重复或缺失

• 批准号: 6874478
• 负责人: Fatima Aziz Merchant
• 金额: $ 35.99万
• 依托单位: ADVANCED DIGITAL IMAGING RESEARCH, LLC
• 依托单位国家: 美国
• 财政年份: 2000
• 资助国家: 美国
• 起止时间: 2000-04-01 至 2007-03-19
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6874478
• 关键词: Smith Magenis syndrome; bioimaging /biomedical imaging; biomedical automation; biomedical equipment development; clinical research; computer program /software; digital imaging; fluorescence microscopy; fluorescent in situ hybridization; gene deletion mutation; gene duplication; genetic screening; hereditary motor and sensory neuropathy; human subject; imaging /visualization /scanning; leukodystrophy; molecular probes; myotonic dystrophy; nucleic acid probes; three dimensional imaging /topography

DESCRIPTION (provided by applicant): This project will further develop automated instrumentation and image analysis techniques to detect gene duplications or deletions in interphase FISH, which are difficult to detect by routine cytogenetics. There is a growing list of genetic disorders that result from chromosomal anomalies, related to either duplications or deletions. These include: (1) neuropathies; Charcot-Marie-Tooth Disease (CMT1A) and Hereditary Neuropathy with Pressure Palsies (HNPP), (2) neurological disorders; Pelizaeus-Merzbacher Disease (PMD) and X-Linked Spastic Paraplegia (SPG2), (3) muscular wasting disorders; Duchene (DMD) and Becker Muscular Dystrophy (BMD), (4) contiguous-gene syndromes; Smith-Magenis Syndrome (SMS). Our approach is to use readily available DNA probes, followed by automated genetic screening to detect duplications/deletions. We will develop an imaging system for the automated identification of interphase cells, and use sophisticated image analysis for high-resolution detection and separation of microscopic rearrangements. In the Phase I project we evaluated the feasibility of newly developed imaging algorithms, for effectively and precisely identifying the separation of FISH dot duplicates. Algorithms were developed for automatically (1) segmenting dots, (2) computing the integrated fluorescence intensity of dots, (3) determining the separation distance, and (4) classifying duplicates and single dots. In Phase II we will incorporate the newly developed imaging algorithms into our automated imaging system, and test the prototype clinically. We will also develop and implement three-dimensional modeling techniques to obtain an unbiased estimate of the spatial distance between duplicated genes. Phase III will commercialize the instrument. Computer automation will make genetic screening practical on a large scale by reducing costs and relieving humans of tedious duties. This approach will be most valuable to medical genetics, particularly for screening CMT1A/HNPP, PMD/SPG2, DMD/BMD, and SMS. Duplications have also been identified for the Prader-Willi /Angelman syndrome region that result in autism. Duplications, such as for 22ql 1.2 and 17pl 1.2 have been described and result in a rather mild phenotype. But duplications of the Williams syndrome region have not been described and thus, the phenotype is unknown. The ability to screen patients for duplications by interphase FISH analysis will likely identify a large number of individuals that would benefit from medical intervention. It may uncover syndromes that previously had no identifiable etiology. This will provide a screening test and eventually a diagnostic test for those individuals with perhaps mild phenotypes, such as learning disabilities.

描述（由申请人提供）： 该项目将进一步开发自动化仪器和图像分析技术，以检测间期 FISH 中的基因重复或缺失，这是常规细胞遗传学难以检测的。由染色体异常引起的遗传性疾病越来越多，这些异常与重复或缺失有关。这些包括：（1）神经病；腓骨肌萎缩症 (CMT1A) 和遗传性神经病伴压力性麻痹 (HNPP)，(2) 神经系统疾病； Pelizaeus-Merzbacher 病 (PMD) 和 X 连锁痉挛性截瘫 (SPG2)，(3) 肌肉萎缩症； Duchene (DMD) 和 Becker 肌营养不良症 (BMD)，(4) 邻近基因综合征；史密斯-马吉尼斯综合症（SMS）。 我们的方法是使用现成的 DNA 探针，然后进行自动基因筛查来检测重复/缺失。我们将开发一种用于自动识别间期细胞的成像系统，并使用复杂的图像分析来进行高分辨率检测和微观重排的分离。 在第一阶段项目中，我们评估了新开发的成像算法的可行性，以有效、精确地识别 FISH 点重复的分离。开发了自动（1）分割点，（2）计算点的综合荧光强度，（3）确定分离距离，以及（4）对重复点和单个点进行分类的算法。 在第二阶段，我们将把新开发的成像算法整合到我们的自动成像系统中，并对原型进行临床测试。我们还将开发和实施三维建模技术，以获得重复基因之间空间距离的无偏估计。第三阶段将使该仪器商业化。 计算机自动化将降低成本并减轻人类繁琐的工作，从而使基因筛查大规模实用。这种方法对于医学遗传学最有价值，特别是对于筛查 CMT1A/HNPP、PMD/SPG2、DMD/BMD 和 SMS。普瑞德-威利/安格曼综合征区域的重复也已被发现，导致自闭症。已经描述了重复，例如 22ql 1.2 和 17pl 1.2，并导致相当温和的表型。但威廉姆斯综合征区域的重复尚未被描述，因此，表型未知。通过间期 FISH 分析筛选患者重复的能力可能会识别出大量可以从医疗干预中受益的个体。它可能会发现以前没有明确病因的综合症。这将为那些可能具有轻微表型（例如学习障碍）的个体提供筛查测试，并最终提供诊断测试。