Zheng Yu, Wang Hai-Lin, Li Jian-Kang, Xu Li, Tellier Laurent, Li Xiao-Lin, Huang Xiao-Yan, Li Wei, Niu Tong-Tong, Yang Huan-Ming, Zhang Jian-Guo, Liu Dong-Ning
BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
BGI-Shenzhen, Shenzhen 518083, China.
Int J Ophthalmol. 2018 Jan 18;11(1):31-35. doi: 10.18240/ijo.2018.01.06. eCollection 2018.
To study the genes responsible for retinitis pigmentosa.
A total of 15 Chinese families with retinitis pigmentosa, containing 94 sporadically afflicted cases, were recruited. The targeted sequences were captured using the Target_Eye_365_V3 chip and sequenced using the BGISEQ-500 sequencer, according to the manufacturer's instructions. Data were aligned to UCSC Genome Browser build hg19, using the Burroughs Wheeler Aligner MEM algorithm. Local realignment was performed with the Genome Analysis Toolkit (GATK v.3.3.0) IndelRealigner, and variants were called with the Genome Analysis Toolkit Haplotypecaller, without any use of imputation. Variants were filtered against a panel derived from 1000 Genomes Project, 1000G_ASN, ESP6500, ExAC and dbSNP138. In all members of Family ONE and Family TWO with available DNA samples, the genetic variant was validated using Sanger sequencing.
A novel, pathogenic variant of retinitis pigmentosa, c.357_358delAA (p.Ser119SerfsX5) was identified in in 2 of 15 autosomal-dominant retinitis pigmentosa (ADRP) families, as well as in one, sporadic case. Sanger sequencing was performed upon probands, as well as upon other family members. This novel, pathogenic genotype co-segregated with retinitis pigmentosa phenotype in these two families.
ADRP is a subtype of retinitis pigmentosa, defined by its genotype, which accounts for 20%-40% of the retinitis pigmentosa patients. Our study thus expands the spectrum of mutations known to occur in ADRP, and provides further demonstration of the applicability of the BGISEQ500 sequencer for genomics research.
研究导致视网膜色素变性的基因。
招募了15个患有视网膜色素变性的中国家庭，其中包括94例散发病例。按照制造商的说明，使用Target_Eye_365_V3芯片捕获目标序列，并使用BGISEQ - 500测序仪进行测序。数据使用Burroughs Wheeler比对器MEM算法与UCSC基因组浏览器构建版本hg19进行比对。使用基因组分析工具包（GATK v.3.3.0）IndelRealigner进行局部重新比对，并使用基因组分析工具包单倍型分型器调用变异，不使用任何填充。变异与来自千人基因组计划、1000G_ASN、ESP6500、ExAC和dbSNP138的面板进行过滤。在有可用DNA样本的家族一和家族二的所有成员中，使用桑格测序法验证遗传变异。
在15个常染色体显性视网膜色素变性（ADRP）家族中的2个家族以及1例散发病例中，鉴定出一种新的视网膜色素变性致病变异，即c.357_358delAA（p.Ser119SerfsX5）。对先证者以及其他家庭成员进行了桑格测序。在这两个家族中，这种新的致病基因型与视网膜色素变性表型共分离。
ADRP是视网膜色素变性的一种亚型，由其基因型定义，占视网膜色素变性患者的20% - 40%。我们的研究因此扩展了已知发生在ADRP中的突变谱，并进一步证明了BGISEQ500测序仪在基因组学研究中的适用性。
