Identification of Potentially Pathogenic Variants in the Posterior Polymorphous Corneal Dystrophy 1 Locus.
Identification of Potentially Pathogenic Variants in the Posterior Polymorphous Corneal Dystrophy 1 Locus.
复制标题
鉴定后多态角膜营养不良1个基因座中潜在的致病变异。
DOI：
10.1371/journal.pone.0158467
复制
发表时间：
2016
期刊：
影响因子：
3.7
通讯作者：
Aldave AJ
中科院分区：
文献类型：
--
作者：
Le DJ;Chung DW;Frausto RF;Kim MJ;Aldave AJ
后多形性角膜营养不良1 （PPCD1）是一种影响角膜内皮细胞功能并导致视力丧失的遗传性疾病。PPCD1与多个家族中20号染色体上的一个位点有关；然而，在共识区蛋白质编码基因的Sanger测序未能识别任何致病的错义突变。在这项研究中，定制捕获探针被用于对先前报道的PPCD1家族的连接区域进行靶向下一代测序。变异通过两个生物信息学管道检测，并根据多个标准进行过滤。此外，高分辨率微阵列用于检测拷贝数变化。在注释基因的蛋白质编码区未发现非同义变异。然而，10个基因中的12个单核苷酸变异和7个基因中的9个indel符合筛选标准，被认为是PPCD1的候选变异。Sanger测序证实了9个基因的11个单核苷酸变异，包括2个同义变异和9个非编码变异。微阵列在OVOL2的内含子中检测到一个微缺失，但随后未通过PCR鉴定。使用全面的下一代测序方法，共鉴定了16个基因，这些基因含有单核苷酸变异或索引，这些基因在先前定位到PPCD1位点的受影响家族中与受影响表型分离。筛选先前定位到PPCD1位点的其他家族中的这些候选基因可能会导致PPCD1的遗传基础鉴定。
Posterior polymorphous corneal dystrophy 1 (PPCD1) is a genetic disorder that affects corneal endothelial cell function and leads to loss of visual acuity. PPCD1 has been linked to a locus on chromosome 20 in multiple families; however, Sanger sequencing of protein-coding genes in the consensus region failed to identify any causative missense mutations. In this study, custom capture probes were utilized for targeted next-generation sequencing of the linked region in a previously reported family with PPCD1. Variants were detected through two bioinformatics pipelines and filtered according to multiple criteria. Additionally, a high-resolution microarray was used to detect copy number variations. No non-synonymous variants in the protein-coding region of annotated genes were identified. However, 12 single nucleotide variants in 10 genes, and 9 indels in 7 genes met the filtering criteria and were considered candidate variants for PPCD1. Eleven single nucleotide variants were confirmed by Sanger sequencing, including 2 synonymous variants and 9 non-coding variants, in 9 genes. One microdeletion was detected in an intron of OVOL2 by microarray but was subsequently not identified by PCR. Using a comprehensive next-generation sequencing approach, a total of 16 genes containing single nucleotide variants or indels that segregated with the affected phenotype in an affected family previously mapped to the PPCD1 locus were identified. Screening of these candidate genes in other families previously mapped to the PPCD1 locus will likely result in the identification of the genetic basis of PPCD1.