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In Silico identification of a common mobile element insertion in exon 4 of RP1

Authors
 Dongju Won  ;  Joo-Yeon Hwang  ;  Yeeun Shim  ;  Suk Ho Byeon  ;  Junwon Lee  ;  Christopher Seungkyu Lee  ;  Min Kim  ;  Hyun Taek Lim  ;  Jong Rak Choi  ;  Seung-Tae Lee  ;  Jinu Han 
Citation
 SCIENTIFIC REPORTS, Vol.11(1) : 13381, 2021-06 
Journal Title
SCIENTIFIC REPORTS
Issue Date
2021-06
Abstract
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.
Files in This Item:
T202102610.pdf Download
DOI
10.1038/s41598-021-92834-4
Appears in Collections:
1. College of Medicine (의과대학) > Dept. of Laboratory Medicine (진단검사의학교실) > 1. Journal Papers
1. College of Medicine (의과대학) > Dept. of Ophthalmology (안과학교실) > 1. Journal Papers
Yonsei Authors
Kim, Min(김민) ORCID logo https://orcid.org/0000-0003-1873-6959
Byeon, Suk Ho(변석호) ORCID logo https://orcid.org/0000-0001-8101-0830
Won, Dongju(원동주) ORCID logo https://orcid.org/0000-0002-0084-0216
Lee, Christopher Seungkyu(이승규) ORCID logo https://orcid.org/0000-0001-5054-9470
Lee, Seung-Tae(이승태) ORCID logo https://orcid.org/0000-0003-1047-1415
Lee, Jun Won(이준원) ORCID logo https://orcid.org/0000-0003-0543-7132
Choi, Jong Rak(최종락) ORCID logo https://orcid.org/0000-0002-0608-2989
Han, Jinu(한진우) ORCID logo https://orcid.org/0000-0002-8607-6625
URI
https://ir.ymlib.yonsei.ac.kr/handle/22282913/184205
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