Department of Laboratory Medicine, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea.
Division of Rare Diseases, Centers for Biomedical Sciences, Korea National Institute of Health, Korea Centers for Disease Control, Seoul, South Korea.
Sci Rep. 2021 Jun 28;11(1):13381. doi: 10.1038/s41598-021-92834-4.
Mobile element insertions (MEIs) typically exceed the read lengths of short-read sequencing technologies and are therefore frequently missed. Recently, a founder Alu insertion in exon 4 of RP1 has been detected in Japanese patients with macular dystrophy by PCR and gel electrophoresis. We aimed to develop a grep search program for the detection of the Alu insertion in exon 4 of RP1 using unprocessed short reads. Among 494 unrelated Korean patients with inherited eye diseases, 273 patients with specific retinal phenotypes who were previously genotyped by targeted panel or whole exome sequencing were selected. Five probands had a single heterozygous truncating RP1 variant, and one of their unaffected parents also carry this variant. To find a hidden genetic variant, whole genome sequencing was performed in two patients, and it revealed AluY c.4052_4053ins328/p.(Tyr1352Alafs*9) insertion in RP1 exon 4. This AluY insertion was additionally identified in other 3 families, which was confirmed by PCR and gel electrophoresis. We developed simplified grep search program to detect this AluY insertion in RP1 exon 4. The simple grep search revealed a median variant allele frequency of 0.282 (interquartile range, 0.232-0.383), with no false-positive results using 120 control samples. The MEI in RP1 exon 4 was a common founder mutation in Korean, occurring in 1.8% of our cohort. The RP1-Alu grep program efficiently detected the AluY insertion, without the preprocessing of raw data or complex installation processes.
移动元件插入（MEIs）通常超过短读测序技术的读长，因此经常被遗漏。最近，通过 PCR 和凝胶电泳在日本黄斑营养不良患者中检测到 RP1 外显子 4 的一个 Alu 插入突变。我们旨在开发一种 grep 搜索程序，用于检测 RP1 外显子 4 中的 Alu 插入，该程序使用未经处理的短读长。在 494 名无关的遗传性眼病韩国患者中，选择了 273 名具有特定视网膜表型的患者，这些患者之前通过靶向panel 或全外显子组测序进行了基因分型。有 5 名先证者携带单一杂合截断 RP1 变异，他们的 1 名未受影响的父母也携带这种变异。为了寻找隐藏的遗传变异，对 2 名患者进行了全基因组测序，结果显示 RP1 外显子 4 中的 AluY c.4052_4053ins328/p.(Tyr1352Alafs*9)插入。该 AluY 插入在另外 3 个家庭中也被发现，通过 PCR 和凝胶电泳得到证实。我们开发了简化的 grep 搜索程序来检测 RP1 外显子 4 中的这种 AluY 插入。简单的 grep 搜索显示，该变异等位基因频率的中位数为 0.282（四分位间距，0.232-0.383），使用 120 个对照样本没有假阳性结果。RP1 外显子 4 中的 MEI 是韩国常见的共同致病突变，在我们的队列中发生率为 1.8%。RP1-Alu grep 程序有效地检测到 AluY 插入，无需对原始数据进行预处理或复杂的安装过程。
