Detection of subclonal L1 transductions in colorectal cancer by long-distance inverse-PCR and Nanopore sequencing

Abstract Long interspersed nuclear elements-1 (L1s) are a large family of retrotransposons. Retrotransposons are repetitive sequences that are capable of autonomous mobility via a copy-and-paste mechanism. In most copy events, only the L1 sequence is inserted, however, they can also mobilize the fla...

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Autores principales:	Barun Pradhan, Tatiana Cajuso, Riku Katainen, Päivi Sulo, Tomas Tanskanen, Outi Kilpivaara, Esa Pitkänen, Lauri A. Aaltonen, Liisa Kauppi, Kimmo Palin
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Nanopore Sequencing Oxford Nanopore Technologies Long Interspersed Nuclear Elements (LINE) Candidate Insertion Target-primed Reverse Transcription (TPRT) Medicine R Science Q
Acceso en línea:	https://doaj.org/article/5b65de7bdaab4ee0bba34409a6347665
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spelling	oai:doaj.org-article:5b65de7bdaab4ee0bba34409a63476652021-12-02T11:52:31ZDetection of subclonal L1 transductions in colorectal cancer by long-distance inverse-PCR and Nanopore sequencing10.1038/s41598-017-15076-32045-2322https://doaj.org/article/5b65de7bdaab4ee0bba34409a63476652017-11-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-15076-3https://doaj.org/toc/2045-2322Abstract Long interspersed nuclear elements-1 (L1s) are a large family of retrotransposons. Retrotransposons are repetitive sequences that are capable of autonomous mobility via a copy-and-paste mechanism. In most copy events, only the L1 sequence is inserted, however, they can also mobilize the flanking non-repetitive region by a process known as 3′ transduction. L1 insertions can contribute to genome plasticity and cause potentially tumorigenic genomic instability. However, detecting the activity of a particular source L1 and identifying new insertions stemming from it is a challenging task with current methodological approaches. We developed a long-distance inverse PCR (LDI-PCR) based approach to monitor the mobility of active L1 elements based on their 3′ transduction activity. LDI-PCR requires no prior knowledge of the insertion target region. By applying LDI-PCR in conjunction with Nanopore sequencing (Oxford Nanopore Technologies) on one L1 reported to be particularly active in human cancer genomes, we detected 14 out of 15 3′ transductions previously identified by whole genome sequencing in two different colorectal tumour samples. In addition we discovered 25 novel highly subclonal insertions. Furthermore, the long sequencing reads produced by LDI-PCR/Nanopore sequencing enabled the identification of both the 5′ and 3′ junctions and revealed detailed insertion sequence information.Barun PradhanTatiana CajusoRiku KatainenPäivi SuloTomas TanskanenOuti KilpivaaraEsa PitkänenLauri A. AaltonenLiisa KauppiKimmo PalinNature PortfolioarticleNanopore SequencingOxford Nanopore TechnologiesLong Interspersed Nuclear Elements (LINE)Candidate InsertionTarget-primed Reverse Transcription (TPRT)MedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-12 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Nanopore Sequencing Oxford Nanopore Technologies Long Interspersed Nuclear Elements (LINE) Candidate Insertion Target-primed Reverse Transcription (TPRT) Medicine R Science Q
spellingShingle	Nanopore Sequencing Oxford Nanopore Technologies Long Interspersed Nuclear Elements (LINE) Candidate Insertion Target-primed Reverse Transcription (TPRT) Medicine R Science Q Barun Pradhan Tatiana Cajuso Riku Katainen Päivi Sulo Tomas Tanskanen Outi Kilpivaara Esa Pitkänen Lauri A. Aaltonen Liisa Kauppi Kimmo Palin Detection of subclonal L1 transductions in colorectal cancer by long-distance inverse-PCR and Nanopore sequencing
description	Abstract Long interspersed nuclear elements-1 (L1s) are a large family of retrotransposons. Retrotransposons are repetitive sequences that are capable of autonomous mobility via a copy-and-paste mechanism. In most copy events, only the L1 sequence is inserted, however, they can also mobilize the flanking non-repetitive region by a process known as 3′ transduction. L1 insertions can contribute to genome plasticity and cause potentially tumorigenic genomic instability. However, detecting the activity of a particular source L1 and identifying new insertions stemming from it is a challenging task with current methodological approaches. We developed a long-distance inverse PCR (LDI-PCR) based approach to monitor the mobility of active L1 elements based on their 3′ transduction activity. LDI-PCR requires no prior knowledge of the insertion target region. By applying LDI-PCR in conjunction with Nanopore sequencing (Oxford Nanopore Technologies) on one L1 reported to be particularly active in human cancer genomes, we detected 14 out of 15 3′ transductions previously identified by whole genome sequencing in two different colorectal tumour samples. In addition we discovered 25 novel highly subclonal insertions. Furthermore, the long sequencing reads produced by LDI-PCR/Nanopore sequencing enabled the identification of both the 5′ and 3′ junctions and revealed detailed insertion sequence information.
format	article
author	Barun Pradhan Tatiana Cajuso Riku Katainen Päivi Sulo Tomas Tanskanen Outi Kilpivaara Esa Pitkänen Lauri A. Aaltonen Liisa Kauppi Kimmo Palin
author_facet	Barun Pradhan Tatiana Cajuso Riku Katainen Päivi Sulo Tomas Tanskanen Outi Kilpivaara Esa Pitkänen Lauri A. Aaltonen Liisa Kauppi Kimmo Palin
author_sort	Barun Pradhan
title	Detection of subclonal L1 transductions in colorectal cancer by long-distance inverse-PCR and Nanopore sequencing
title_short	Detection of subclonal L1 transductions in colorectal cancer by long-distance inverse-PCR and Nanopore sequencing
title_full	Detection of subclonal L1 transductions in colorectal cancer by long-distance inverse-PCR and Nanopore sequencing
title_fullStr	Detection of subclonal L1 transductions in colorectal cancer by long-distance inverse-PCR and Nanopore sequencing
title_full_unstemmed	Detection of subclonal L1 transductions in colorectal cancer by long-distance inverse-PCR and Nanopore sequencing
title_sort	detection of subclonal l1 transductions in colorectal cancer by long-distance inverse-pcr and nanopore sequencing
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/5b65de7bdaab4ee0bba34409a6347665
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Detection of subclonal L1 transductions in colorectal cancer by long-distance inverse-PCR and Nanopore sequencing

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