PCIP-seq: simultaneous sequencing of integrated viral genomes and their insertion sites with long reads

Abstract The integration of a viral genome into the host genome has a major impact on the trajectory of the infected cell. Integration location and variation within the associated viral genome can influence both clonal expansion and persistence of infected cells. Methods based on short-read sequenci...
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Autor*in:	Maria Artesi [verfasserIn] Vincent Hahaut [verfasserIn] Basiel Cole [verfasserIn] Laurens Lambrechts [verfasserIn] Fereshteh Ashrafi [verfasserIn] Ambroise Marçais [verfasserIn] Olivier Hermine [verfasserIn] Philip Griebel [verfasserIn] Natasa Arsic [verfasserIn] Frank van der Meer [verfasserIn] Arsène Burny [verfasserIn] Dominique Bron [verfasserIn] Elettra Bianchi [verfasserIn] Philippe Delvenne [verfasserIn] Vincent Bours [verfasserIn] Carole Charlier [verfasserIn] Michel Georges [verfasserIn] Linos Vandekerckhove [verfasserIn] Anne Van den Broeke [verfasserIn] Keith Durkin [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2021

Schlagwörter:	Viral genome Integration site analysis Clonal expansion NGS Long-read sequencing Retrovirus

Übergeordnetes Werk:	In: Genome Biology - BMC, 2014, 22(2021), 1, Seite 24
Übergeordnetes Werk:	volume:22 ; year:2021 ; number:1 ; pages:24

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.1186/s13059-021-02307-0

Katalog-ID:	DOAJ004343514

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520			\|a Abstract The integration of a viral genome into the host genome has a major impact on the trajectory of the infected cell. Integration location and variation within the associated viral genome can influence both clonal expansion and persistence of infected cells. Methods based on short-read sequencing can identify viral insertion sites, but the sequence of the viral genomes within remains unobserved. We develop PCIP-seq, a method that leverages long reads to identify insertion sites and sequence their associated viral genome. We apply the technique to exogenous retroviruses HTLV-1, BLV, and HIV-1, endogenous retroviruses, and human papillomavirus.
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650		4	\|a Clonal expansion
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650		4	\|a Long-read sequencing
650		4	\|a Retrovirus
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700	0		\|a Anne Van den Broeke \|e verfasserin \|4 aut
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allfieldsSound	10.1186/s13059-021-02307-0 doi (DE-627)DOAJ004343514 (DE-599)DOAJ87d64560673f4a9ca90efdd587b91997 DE-627 ger DE-627 rakwb eng QH301-705.5 QH426-470 Maria Artesi verfasserin aut PCIP-seq: simultaneous sequencing of integrated viral genomes and their insertion sites with long reads 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract The integration of a viral genome into the host genome has a major impact on the trajectory of the infected cell. Integration location and variation within the associated viral genome can influence both clonal expansion and persistence of infected cells. Methods based on short-read sequencing can identify viral insertion sites, but the sequence of the viral genomes within remains unobserved. We develop PCIP-seq, a method that leverages long reads to identify insertion sites and sequence their associated viral genome. We apply the technique to exogenous retroviruses HTLV-1, BLV, and HIV-1, endogenous retroviruses, and human papillomavirus. Viral genome Integration site analysis Clonal expansion NGS Long-read sequencing Retrovirus Biology (General) Genetics Vincent Hahaut verfasserin aut Basiel Cole verfasserin aut Laurens Lambrechts verfasserin aut Fereshteh Ashrafi verfasserin aut Ambroise Marçais verfasserin aut Olivier Hermine verfasserin aut Philip Griebel verfasserin aut Natasa Arsic verfasserin aut Frank van der Meer verfasserin aut Arsène Burny verfasserin aut Dominique Bron verfasserin aut Elettra Bianchi verfasserin aut Philippe Delvenne verfasserin aut Vincent Bours verfasserin aut Carole Charlier verfasserin aut Michel Georges verfasserin aut Linos Vandekerckhove verfasserin aut Anne Van den Broeke verfasserin aut Keith Durkin verfasserin aut In Genome Biology BMC, 2014 22(2021), 1, Seite 24 (DE-627)326173617 (DE-600)2040529-7 1474760X nnns volume:22 year:2021 number:1 pages:24 https://doi.org/10.1186/s13059-021-02307-0 kostenfrei https://doaj.org/article/87d64560673f4a9ca90efdd587b91997 kostenfrei https://doi.org/10.1186/s13059-021-02307-0 kostenfrei https://doaj.org/toc/1474-760X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 22 2021 1 24
language	English
source	In Genome Biology 22(2021), 1, Seite 24 volume:22 year:2021 number:1 pages:24
sourceStr	In Genome Biology 22(2021), 1, Seite 24 volume:22 year:2021 number:1 pages:24
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topic_facet	Viral genome Integration site analysis Clonal expansion NGS Long-read sequencing Retrovirus Biology (General) Genetics
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authorswithroles_txt_mv	Maria Artesi @@aut@@ Vincent Hahaut @@aut@@ Basiel Cole @@aut@@ Laurens Lambrechts @@aut@@ Fereshteh Ashrafi @@aut@@ Ambroise Marçais @@aut@@ Olivier Hermine @@aut@@ Philip Griebel @@aut@@ Natasa Arsic @@aut@@ Frank van der Meer @@aut@@ Arsène Burny @@aut@@ Dominique Bron @@aut@@ Elettra Bianchi @@aut@@ Philippe Delvenne @@aut@@ Vincent Bours @@aut@@ Carole Charlier @@aut@@ Michel Georges @@aut@@ Linos Vandekerckhove @@aut@@ Anne Van den Broeke @@aut@@ Keith Durkin @@aut@@
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author	Maria Artesi
spellingShingle	Maria Artesi misc QH301-705.5 misc QH426-470 misc Viral genome misc Integration site analysis misc Clonal expansion misc NGS misc Long-read sequencing misc Retrovirus misc Biology (General) misc Genetics PCIP-seq: simultaneous sequencing of integrated viral genomes and their insertion sites with long reads
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topic_title	QH301-705.5 QH426-470 PCIP-seq: simultaneous sequencing of integrated viral genomes and their insertion sites with long reads Viral genome Integration site analysis Clonal expansion NGS Long-read sequencing Retrovirus
topic	misc QH301-705.5 misc QH426-470 misc Viral genome misc Integration site analysis misc Clonal expansion misc NGS misc Long-read sequencing misc Retrovirus misc Biology (General) misc Genetics
topic_unstemmed	misc QH301-705.5 misc QH426-470 misc Viral genome misc Integration site analysis misc Clonal expansion misc NGS misc Long-read sequencing misc Retrovirus misc Biology (General) misc Genetics
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title	PCIP-seq: simultaneous sequencing of integrated viral genomes and their insertion sites with long reads
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title_full	PCIP-seq: simultaneous sequencing of integrated viral genomes and their insertion sites with long reads
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title_sort	pcip-seq: simultaneous sequencing of integrated viral genomes and their insertion sites with long reads
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title_auth	PCIP-seq: simultaneous sequencing of integrated viral genomes and their insertion sites with long reads
abstract	Abstract The integration of a viral genome into the host genome has a major impact on the trajectory of the infected cell. Integration location and variation within the associated viral genome can influence both clonal expansion and persistence of infected cells. Methods based on short-read sequencing can identify viral insertion sites, but the sequence of the viral genomes within remains unobserved. We develop PCIP-seq, a method that leverages long reads to identify insertion sites and sequence their associated viral genome. We apply the technique to exogenous retroviruses HTLV-1, BLV, and HIV-1, endogenous retroviruses, and human papillomavirus.
abstractGer	Abstract The integration of a viral genome into the host genome has a major impact on the trajectory of the infected cell. Integration location and variation within the associated viral genome can influence both clonal expansion and persistence of infected cells. Methods based on short-read sequencing can identify viral insertion sites, but the sequence of the viral genomes within remains unobserved. We develop PCIP-seq, a method that leverages long reads to identify insertion sites and sequence their associated viral genome. We apply the technique to exogenous retroviruses HTLV-1, BLV, and HIV-1, endogenous retroviruses, and human papillomavirus.
abstract_unstemmed	Abstract The integration of a viral genome into the host genome has a major impact on the trajectory of the infected cell. Integration location and variation within the associated viral genome can influence both clonal expansion and persistence of infected cells. Methods based on short-read sequencing can identify viral insertion sites, but the sequence of the viral genomes within remains unobserved. We develop PCIP-seq, a method that leverages long reads to identify insertion sites and sequence their associated viral genome. We apply the technique to exogenous retroviruses HTLV-1, BLV, and HIV-1, endogenous retroviruses, and human papillomavirus.
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title_short	PCIP-seq: simultaneous sequencing of integrated viral genomes and their insertion sites with long reads
url	https://doi.org/10.1186/s13059-021-02307-0 https://doaj.org/article/87d64560673f4a9ca90efdd587b91997 https://doaj.org/toc/1474-760X
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author2Str	Vincent Hahaut Basiel Cole Laurens Lambrechts Fereshteh Ashrafi Ambroise Marçais Olivier Hermine Philip Griebel Natasa Arsic Frank van der Meer Arsène Burny Dominique Bron Elettra Bianchi Philippe Delvenne Vincent Bours Carole Charlier Michel Georges Linos Vandekerckhove Anne Van den Broeke Keith Durkin
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up_date	2024-07-03T23:16:35.635Z
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Integration location and variation within the associated viral genome can influence both clonal expansion and persistence of infected cells. Methods based on short-read sequencing can identify viral insertion sites, but the sequence of the viral genomes within remains unobserved. We develop PCIP-seq, a method that leverages long reads to identify insertion sites and sequence their associated viral genome. 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PCIP-seq: simultaneous sequencing of integrated viral genomes and their insertion sites with long reads

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