Massively Parallel Sequencing of Patients with Intellectual Disability, Congenital Anomalies and/or Autism Spectrum Disorders with a Targeted Gene Panel
Massively Parallel Sequencing of Patients with Intellectual Disability, Congenital Anomalies and/or Autism Spectrum Disorders with a Targeted Gene Panel
复制标题
DOI：
10.1371/journal.pone.0093409
复制
发表时间：
2014-04-01
期刊：
影响因子：
3.7
通讯作者：
Tan, Ene-Choo
中科院分区：
文献类型：
--
作者：
Brett, Maggie;McPherson, John;Tan, Ene-Choo
发育迟缓及/或智力残疾（DD/ID）影响着1 - 3%的儿童。据认为，其中至少一半有遗传病因。近期研究表明，使用靶向基因 panel的大规模平行测序（MPS）特别适用于遗传异质性疾病的诊断检测。我们报告了使用针对355个基因的靶向基因panel进行大规模平行测序以研究8名具有多种表型（包括DD/ID、先天性异常及/或自闭症谱系障碍）患者的遗传病因的经验。使用安捷伦SureSelect靶向富集试剂盒进行靶向序列富集，并在Illumina HiSeq2000上使用双端测序进行测序。对于所有8名患者，81 - 84%的靶向区域达到了至少20倍的测序深度，覆盖靶点的平均测序深度范围为322倍至798倍。在8名患者中的2名患者中成功鉴定出致病变异：ATRX基因的无义突变和L1CAM基因的经典剪接位点突变。在第3名患者中，USP9X基因的经典剪接位点变异可能解释其全部或部分临床表型。这些结果证实了靶向MPS用于儿童DD/ID诊断研究的价值。然而，对于表型包括自闭症的儿童，靶向基因MPS不太可能提供遗传诊断。
Developmental delay and/or intellectual disability (DD/ID) affects 1-3% of all children. At least half of these are thought to have a genetic etiology. Recent studies have shown that massively parallel sequencing (MPS) using a targeted gene panel is particularly suited for diagnostic testing for genetically heterogeneous conditions. We report on our experiences with using massively parallel sequencing of a targeted gene panel of 355 genes for investigating the genetic etiology of eight patients with a wide range of phenotypes including DD/ID, congenital anomalies and/or autism spectrum disorder. Targeted sequence enrichment was performed using the Agilent SureSelect Target Enrichment Kit and sequenced on the Illumina HiSeq2000 using paired-end reads. For all eight patients, 81-84% of the targeted regions achieved read depths of at least 20x, with average read depths overlapping targets ranging from 322x to 798x. Causative variants were successfully identified in two of the eight patients: a nonsense mutation in the ATRX gene and a canonical splice site mutation in the L1CAM gene. In a third patient, a canonical splice site variant in the USP9X gene could likely explain all or some of her clinical phenotypes. These results confirm the value of targeted MPS for investigating DD/ID in children for diagnostic purposes. However, targeted gene MPS was less likely to provide a genetic diagnosis for children whose phenotype includes autism.