Genotyping microarray (disease chip) for Leber congenital amaurosis:: Detection of modifier alleles
Genotyping microarray (disease chip) for Leber congenital amaurosis:: Detection of modifier alleles
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DOI：
10.1167/iovs.05-0111
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发表时间：
2005-09-01
影响因子：
4.4
通讯作者：
Allikmets, R
中科院分区：
文献类型：
--
作者：
Zernant, J;Külm, M;Allikmets, R
目的。莱伯先天性黑蒙 (LCA) 是一种早发性儿童失明遗传性疾病，其特征是出生后不久即出现视力障碍。至少 6 个基因（AIPL1、CRB1、CRX、GUCY2D、RPE65 和 RPGRIP1）的变异与 LCA 或早发性视网膜色素变性 (RP) 的诊断相关。遗传异质性遗传使 LCA 病例的分析变得复杂，特别是对于没有该疾病家族史的患者，并且传统方法的价值有限。为了克服这些限制，使用阵列引物延伸（APEX）技术设计了一种针对早发性严重视网膜变性的基因分型微阵列，其中包括目前在八个基因中描述的所有> 300个疾病相关变异（除了刚刚列出的六个之外，还添加了早发性RP基因LRAT和MERTK）。由此产生的 LCA 阵列可以同时检测任何早发 RP 患者的所有已知疾病相关等位基因。该阵列通过筛查 93 名已知突变的 LCA 确诊患者得到验证。随后，在芯片上筛选了 205 个新的 LCA 病例，然后在适用的情况下进行家庭隔离分析。结果。该微阵列在确定现有遗传变异方面的效率> 99%，并且在大约三分之一的新患者中产生了至少一种与疾病相关的等位基因。在相当一部分（22/300）的患者中发现了超过两种（预期的）变异，这表明来自多个基因的修饰效应。为了支持后一个假设，第三个等位基因在至少五个家族中与更严重的疾病表型分离。结论。 LCA 基因分型微阵列是一种强大且经济高效的筛查工具，代表了用于对患有遗传异质性疾病的患者进行基因分型的疾病芯片的原型。在大型 LCA 队列中同时筛查所有已知的 LCA 相关变异可以系统地检测和分析遗传变异，从而促进前瞻性诊断并最终预测疾病进展。
PURPOSE. Leber congenital amaurosis (LCA) is an early-onset inherited disorder of childhood blindness characterized by visual impairment noted soon after birth. Variants in at least six genes (AIPL1, CRB1, CRX, GUCY2D, RPE65, and RPGRIP1) have been associated with a diagnosis consistent with LCA or early-onset retinitis pigmentosa ( RP). Genetically heterogeneous inheritance complicates the analyses of LCA cases, especially in patients without a family history of the disorder, and conventional methods are of limited value.METHODS. To overcome these limitations, arrayed primer extension ( APEX) technology was used to design a genotyping microarray for early-onset, severe retinal degenerations that includes all of the > 300 disease-associated variants currently described in eight genes ( in addition to the six just listed, the early-onset RP genes LRAT and MERTK were added). The resultant LCA array allows simultaneous detection of all known disease-associated alleles in any patient with early-onset RP. The array was validated by screening 93 confirmed patients with LCA who had known mutations. Subsequently, 205 novel LCA cases were screened on the array, followed by segregation analyses in families, if applicable.RESULTS. The microarray was > 99% effective in determining the existing genetic variation and yielded at least one disease-associated allele in approximately one third of the novel patients.More than two ( expected) variants were discovered in a substantial fraction (22/300) of the patients, suggesting a modifier effect from more than one gene. In support of the latter hypothesis, the third allele segregated with a more severe disease phenotype in at least five families.CONCLUSIONS. The LCA genotyping microarray is a robust and cost-effective screening tool, representing the prototype of a disease chip for genotyping patients with a genetically heterogeneous condition. Simultaneous screening for all known LCA-associated variants in large LCA cohorts allows systematic detection and analysis of genetic variation, facilitating prospective diagnosis and ultimately predicting disease progression.