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

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 a...

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Autores principales:	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
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/a0388748636643d7a5c4cff4f1d14478
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spelling	oai:doaj.org-article:a0388748636643d7a5c4cff4f1d144782021-12-02T16:10:35ZIn Silico identification of a common mobile element insertion in exon 4 of RP110.1038/s41598-021-92834-42045-2322https://doaj.org/article/a0388748636643d7a5c4cff4f1d144782021-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-92834-4https://doaj.org/toc/2045-2322Abstract 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.Dongju WonJoo-Yeon HwangYeeun ShimSuk Ho ByeonJunwon LeeChristopher Seungkyu LeeMin KimHyun Taek LimJong Rak ChoiSeung-Tae LeeJinu HanNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-8 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q 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 In Silico identification of a common mobile element insertion in exon 4 of RP1
description	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.
format	article
author	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
author_facet	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
author_sort	Dongju Won
title	In Silico identification of a common mobile element insertion in exon 4 of RP1
title_short	In Silico identification of a common mobile element insertion in exon 4 of RP1
title_full	In Silico identification of a common mobile element insertion in exon 4 of RP1
title_fullStr	In Silico identification of a common mobile element insertion in exon 4 of RP1
title_full_unstemmed	In Silico identification of a common mobile element insertion in exon 4 of RP1
title_sort	in silico identification of a common mobile element insertion in exon 4 of rp1
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/a0388748636643d7a5c4cff4f1d14478
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In Silico identification of a common mobile element insertion in exon 4 of RP1

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