An advanced enrichment method for rare somatic retroelement insertions sequencing

Abstract Background There is increasing evidence that the transpositional activity of retroelements (REs) is not limited to germ line cells, but often occurs in tumor and normal somatic cells. Somatic transpositions were found in several human tissues and are especially typical for the brain. Severa...
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Autor*in:	Alexander Y. Komkov [verfasserIn] Anastasia A. Minervina [verfasserIn] Gaiaz A. Nugmanov [verfasserIn] Mariia V. Saliutina [verfasserIn] Konstantin V. Khodosevich [verfasserIn] Yuri B. Lebedev [verfasserIn] Ilgar Z. Mamedov [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2018

Schlagwörter:	Somatic retroelement insertions Genomic normalization Kamchatka Crab duplex-specific nuclease

Übergeordnetes Werk:	In: Mobile DNA - BMC, 2010, 9(2018), 1, Seite 11
Übergeordnetes Werk:	volume:9 ; year:2018 ; number:1 ; pages:11

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.1186/s13100-018-0136-1

Katalog-ID:	DOAJ016419987

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245	1	3	\|a An advanced enrichment method for rare somatic retroelement insertions sequencing
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520			\|a Abstract Background There is increasing evidence that the transpositional activity of retroelements (REs) is not limited to germ line cells, but often occurs in tumor and normal somatic cells. Somatic transpositions were found in several human tissues and are especially typical for the brain. Several computational and experimental approaches for detection of somatic retroelement insertions was developed in the past few years. These approaches were successfully applied to detect somatic insertions in clonally expanded tumor cells. At the same time, identification of somatic insertions presented in small proportion of cells, such as neurons, remains a considerable challenge. Results In this study, we developed a normalization procedure for library enrichment by DNA sequences corresponding to rare somatic RE insertions. Two rounds of normalization increased the number of fragments adjacent to somatic REs in the sequenced sample by more than 26-fold, and the number of identified somatic REs was increased by 8-fold. Conclusions The developed technique can be used in combination with vast majority of modern RE identification approaches and can dramatically increase their capacity to detect rare somatic RE insertions in different types of cells.
650		4	\|a Somatic retroelement insertions
650		4	\|a Genomic normalization
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700	0		\|a Anastasia A. Minervina \|e verfasserin \|4 aut
700	0		\|a Gaiaz A. Nugmanov \|e verfasserin \|4 aut
700	0		\|a Mariia V. Saliutina \|e verfasserin \|4 aut
700	0		\|a Konstantin V. Khodosevich \|e verfasserin \|4 aut
700	0		\|a Yuri B. Lebedev \|e verfasserin \|4 aut
700	0		\|a Ilgar Z. Mamedov \|e verfasserin \|4 aut
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allfields	10.1186/s13100-018-0136-1 doi (DE-627)DOAJ016419987 (DE-599)DOAJcf35768c383146e68c0de6bd418e038c DE-627 ger DE-627 rakwb eng QH426-470 Alexander Y. Komkov verfasserin aut An advanced enrichment method for rare somatic retroelement insertions sequencing 2018 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background There is increasing evidence that the transpositional activity of retroelements (REs) is not limited to germ line cells, but often occurs in tumor and normal somatic cells. Somatic transpositions were found in several human tissues and are especially typical for the brain. Several computational and experimental approaches for detection of somatic retroelement insertions was developed in the past few years. These approaches were successfully applied to detect somatic insertions in clonally expanded tumor cells. At the same time, identification of somatic insertions presented in small proportion of cells, such as neurons, remains a considerable challenge. Results In this study, we developed a normalization procedure for library enrichment by DNA sequences corresponding to rare somatic RE insertions. Two rounds of normalization increased the number of fragments adjacent to somatic REs in the sequenced sample by more than 26-fold, and the number of identified somatic REs was increased by 8-fold. Conclusions The developed technique can be used in combination with vast majority of modern RE identification approaches and can dramatically increase their capacity to detect rare somatic RE insertions in different types of cells. Somatic retroelement insertions Genomic normalization Kamchatka Crab duplex-specific nuclease Genetics Anastasia A. Minervina verfasserin aut Gaiaz A. Nugmanov verfasserin aut Mariia V. Saliutina verfasserin aut Konstantin V. Khodosevich verfasserin aut Yuri B. Lebedev verfasserin aut Ilgar Z. Mamedov verfasserin aut In Mobile DNA BMC, 2010 9(2018), 1, Seite 11 (DE-627)617812632 (DE-600)2536054-1 17598753 nnns volume:9 year:2018 number:1 pages:11 https://doi.org/10.1186/s13100-018-0136-1 kostenfrei https://doaj.org/article/cf35768c383146e68c0de6bd418e038c kostenfrei http://link.springer.com/article/10.1186/s13100-018-0136-1 kostenfrei https://doaj.org/toc/1759-8753 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_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_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 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 9 2018 1 11
spelling	10.1186/s13100-018-0136-1 doi (DE-627)DOAJ016419987 (DE-599)DOAJcf35768c383146e68c0de6bd418e038c DE-627 ger DE-627 rakwb eng QH426-470 Alexander Y. Komkov verfasserin aut An advanced enrichment method for rare somatic retroelement insertions sequencing 2018 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background There is increasing evidence that the transpositional activity of retroelements (REs) is not limited to germ line cells, but often occurs in tumor and normal somatic cells. Somatic transpositions were found in several human tissues and are especially typical for the brain. Several computational and experimental approaches for detection of somatic retroelement insertions was developed in the past few years. These approaches were successfully applied to detect somatic insertions in clonally expanded tumor cells. At the same time, identification of somatic insertions presented in small proportion of cells, such as neurons, remains a considerable challenge. Results In this study, we developed a normalization procedure for library enrichment by DNA sequences corresponding to rare somatic RE insertions. Two rounds of normalization increased the number of fragments adjacent to somatic REs in the sequenced sample by more than 26-fold, and the number of identified somatic REs was increased by 8-fold. Conclusions The developed technique can be used in combination with vast majority of modern RE identification approaches and can dramatically increase their capacity to detect rare somatic RE insertions in different types of cells. Somatic retroelement insertions Genomic normalization Kamchatka Crab duplex-specific nuclease Genetics Anastasia A. Minervina verfasserin aut Gaiaz A. Nugmanov verfasserin aut Mariia V. Saliutina verfasserin aut Konstantin V. Khodosevich verfasserin aut Yuri B. Lebedev verfasserin aut Ilgar Z. Mamedov verfasserin aut In Mobile DNA BMC, 2010 9(2018), 1, Seite 11 (DE-627)617812632 (DE-600)2536054-1 17598753 nnns volume:9 year:2018 number:1 pages:11 https://doi.org/10.1186/s13100-018-0136-1 kostenfrei https://doaj.org/article/cf35768c383146e68c0de6bd418e038c kostenfrei http://link.springer.com/article/10.1186/s13100-018-0136-1 kostenfrei https://doaj.org/toc/1759-8753 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_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_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 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 9 2018 1 11
allfields_unstemmed	10.1186/s13100-018-0136-1 doi (DE-627)DOAJ016419987 (DE-599)DOAJcf35768c383146e68c0de6bd418e038c DE-627 ger DE-627 rakwb eng QH426-470 Alexander Y. Komkov verfasserin aut An advanced enrichment method for rare somatic retroelement insertions sequencing 2018 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background There is increasing evidence that the transpositional activity of retroelements (REs) is not limited to germ line cells, but often occurs in tumor and normal somatic cells. Somatic transpositions were found in several human tissues and are especially typical for the brain. Several computational and experimental approaches for detection of somatic retroelement insertions was developed in the past few years. These approaches were successfully applied to detect somatic insertions in clonally expanded tumor cells. At the same time, identification of somatic insertions presented in small proportion of cells, such as neurons, remains a considerable challenge. Results In this study, we developed a normalization procedure for library enrichment by DNA sequences corresponding to rare somatic RE insertions. Two rounds of normalization increased the number of fragments adjacent to somatic REs in the sequenced sample by more than 26-fold, and the number of identified somatic REs was increased by 8-fold. Conclusions The developed technique can be used in combination with vast majority of modern RE identification approaches and can dramatically increase their capacity to detect rare somatic RE insertions in different types of cells. Somatic retroelement insertions Genomic normalization Kamchatka Crab duplex-specific nuclease Genetics Anastasia A. Minervina verfasserin aut Gaiaz A. Nugmanov verfasserin aut Mariia V. Saliutina verfasserin aut Konstantin V. Khodosevich verfasserin aut Yuri B. Lebedev verfasserin aut Ilgar Z. Mamedov verfasserin aut In Mobile DNA BMC, 2010 9(2018), 1, Seite 11 (DE-627)617812632 (DE-600)2536054-1 17598753 nnns volume:9 year:2018 number:1 pages:11 https://doi.org/10.1186/s13100-018-0136-1 kostenfrei https://doaj.org/article/cf35768c383146e68c0de6bd418e038c kostenfrei http://link.springer.com/article/10.1186/s13100-018-0136-1 kostenfrei https://doaj.org/toc/1759-8753 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_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_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 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 9 2018 1 11
allfieldsGer	10.1186/s13100-018-0136-1 doi (DE-627)DOAJ016419987 (DE-599)DOAJcf35768c383146e68c0de6bd418e038c DE-627 ger DE-627 rakwb eng QH426-470 Alexander Y. Komkov verfasserin aut An advanced enrichment method for rare somatic retroelement insertions sequencing 2018 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background There is increasing evidence that the transpositional activity of retroelements (REs) is not limited to germ line cells, but often occurs in tumor and normal somatic cells. Somatic transpositions were found in several human tissues and are especially typical for the brain. Several computational and experimental approaches for detection of somatic retroelement insertions was developed in the past few years. These approaches were successfully applied to detect somatic insertions in clonally expanded tumor cells. At the same time, identification of somatic insertions presented in small proportion of cells, such as neurons, remains a considerable challenge. Results In this study, we developed a normalization procedure for library enrichment by DNA sequences corresponding to rare somatic RE insertions. Two rounds of normalization increased the number of fragments adjacent to somatic REs in the sequenced sample by more than 26-fold, and the number of identified somatic REs was increased by 8-fold. Conclusions The developed technique can be used in combination with vast majority of modern RE identification approaches and can dramatically increase their capacity to detect rare somatic RE insertions in different types of cells. Somatic retroelement insertions Genomic normalization Kamchatka Crab duplex-specific nuclease Genetics Anastasia A. Minervina verfasserin aut Gaiaz A. Nugmanov verfasserin aut Mariia V. Saliutina verfasserin aut Konstantin V. Khodosevich verfasserin aut Yuri B. Lebedev verfasserin aut Ilgar Z. Mamedov verfasserin aut In Mobile DNA BMC, 2010 9(2018), 1, Seite 11 (DE-627)617812632 (DE-600)2536054-1 17598753 nnns volume:9 year:2018 number:1 pages:11 https://doi.org/10.1186/s13100-018-0136-1 kostenfrei https://doaj.org/article/cf35768c383146e68c0de6bd418e038c kostenfrei http://link.springer.com/article/10.1186/s13100-018-0136-1 kostenfrei https://doaj.org/toc/1759-8753 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_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_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 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 9 2018 1 11
allfieldsSound	10.1186/s13100-018-0136-1 doi (DE-627)DOAJ016419987 (DE-599)DOAJcf35768c383146e68c0de6bd418e038c DE-627 ger DE-627 rakwb eng QH426-470 Alexander Y. Komkov verfasserin aut An advanced enrichment method for rare somatic retroelement insertions sequencing 2018 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background There is increasing evidence that the transpositional activity of retroelements (REs) is not limited to germ line cells, but often occurs in tumor and normal somatic cells. Somatic transpositions were found in several human tissues and are especially typical for the brain. Several computational and experimental approaches for detection of somatic retroelement insertions was developed in the past few years. These approaches were successfully applied to detect somatic insertions in clonally expanded tumor cells. At the same time, identification of somatic insertions presented in small proportion of cells, such as neurons, remains a considerable challenge. Results In this study, we developed a normalization procedure for library enrichment by DNA sequences corresponding to rare somatic RE insertions. Two rounds of normalization increased the number of fragments adjacent to somatic REs in the sequenced sample by more than 26-fold, and the number of identified somatic REs was increased by 8-fold. Conclusions The developed technique can be used in combination with vast majority of modern RE identification approaches and can dramatically increase their capacity to detect rare somatic RE insertions in different types of cells. Somatic retroelement insertions Genomic normalization Kamchatka Crab duplex-specific nuclease Genetics Anastasia A. Minervina verfasserin aut Gaiaz A. Nugmanov verfasserin aut Mariia V. Saliutina verfasserin aut Konstantin V. Khodosevich verfasserin aut Yuri B. Lebedev verfasserin aut Ilgar Z. Mamedov verfasserin aut In Mobile DNA BMC, 2010 9(2018), 1, Seite 11 (DE-627)617812632 (DE-600)2536054-1 17598753 nnns volume:9 year:2018 number:1 pages:11 https://doi.org/10.1186/s13100-018-0136-1 kostenfrei https://doaj.org/article/cf35768c383146e68c0de6bd418e038c kostenfrei http://link.springer.com/article/10.1186/s13100-018-0136-1 kostenfrei https://doaj.org/toc/1759-8753 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_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_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 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 9 2018 1 11
language	English
source	In Mobile DNA 9(2018), 1, Seite 11 volume:9 year:2018 number:1 pages:11
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institution	findex.gbv.de
topic_facet	Somatic retroelement insertions Genomic normalization Kamchatka Crab duplex-specific nuclease Genetics
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container_title	Mobile DNA
authorswithroles_txt_mv	Alexander Y. Komkov @@aut@@ Anastasia A. Minervina @@aut@@ Gaiaz A. Nugmanov @@aut@@ Mariia V. Saliutina @@aut@@ Konstantin V. Khodosevich @@aut@@ Yuri B. Lebedev @@aut@@ Ilgar Z. Mamedov @@aut@@
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Komkov</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="245" ind1="1" ind2="3"><subfield code="a">An advanced enrichment method for rare somatic retroelement insertions sequencing</subfield></datafield><datafield tag="264" ind1=" " ind2="1"><subfield code="c">2018</subfield></datafield><datafield tag="336" ind1=" " ind2=" "><subfield code="a">Text</subfield><subfield code="b">txt</subfield><subfield code="2">rdacontent</subfield></datafield><datafield tag="337" ind1=" " ind2=" "><subfield code="a">Computermedien</subfield><subfield code="b">c</subfield><subfield code="2">rdamedia</subfield></datafield><datafield tag="338" ind1=" " ind2=" "><subfield code="a">Online-Ressource</subfield><subfield code="b">cr</subfield><subfield code="2">rdacarrier</subfield></datafield><datafield tag="520" ind1=" " ind2=" "><subfield code="a">Abstract Background There is increasing evidence that the transpositional activity of retroelements (REs) is not limited to germ line cells, but often occurs in tumor and normal somatic cells. Somatic transpositions were found in several human tissues and are especially typical for the brain. Several computational and experimental approaches for detection of somatic retroelement insertions was developed in the past few years. These approaches were successfully applied to detect somatic insertions in clonally expanded tumor cells. At the same time, identification of somatic insertions presented in small proportion of cells, such as neurons, remains a considerable challenge. Results In this study, we developed a normalization procedure for library enrichment by DNA sequences corresponding to rare somatic RE insertions. Two rounds of normalization increased the number of fragments adjacent to somatic REs in the sequenced sample by more than 26-fold, and the number of identified somatic REs was increased by 8-fold. 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callnumber-first	Q - Science
author	Alexander Y. Komkov
spellingShingle	Alexander Y. Komkov misc QH426-470 misc Somatic retroelement insertions misc Genomic normalization misc Kamchatka Crab duplex-specific nuclease misc Genetics An advanced enrichment method for rare somatic retroelement insertions sequencing
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topic_title	QH426-470 An advanced enrichment method for rare somatic retroelement insertions sequencing Somatic retroelement insertions Genomic normalization Kamchatka Crab duplex-specific nuclease
topic	misc QH426-470 misc Somatic retroelement insertions misc Genomic normalization misc Kamchatka Crab duplex-specific nuclease misc Genetics
topic_unstemmed	misc QH426-470 misc Somatic retroelement insertions misc Genomic normalization misc Kamchatka Crab duplex-specific nuclease misc Genetics
topic_browse	misc QH426-470 misc Somatic retroelement insertions misc Genomic normalization misc Kamchatka Crab duplex-specific nuclease misc Genetics
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title	An advanced enrichment method for rare somatic retroelement insertions sequencing
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title_full	An advanced enrichment method for rare somatic retroelement insertions sequencing
author_sort	Alexander Y. Komkov
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author_browse	Alexander Y. Komkov Anastasia A. Minervina Gaiaz A. Nugmanov Mariia V. Saliutina Konstantin V. Khodosevich Yuri B. Lebedev Ilgar Z. Mamedov
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title_sort	advanced enrichment method for rare somatic retroelement insertions sequencing
callnumber	QH426-470
title_auth	An advanced enrichment method for rare somatic retroelement insertions sequencing
abstract	Abstract Background There is increasing evidence that the transpositional activity of retroelements (REs) is not limited to germ line cells, but often occurs in tumor and normal somatic cells. Somatic transpositions were found in several human tissues and are especially typical for the brain. Several computational and experimental approaches for detection of somatic retroelement insertions was developed in the past few years. These approaches were successfully applied to detect somatic insertions in clonally expanded tumor cells. At the same time, identification of somatic insertions presented in small proportion of cells, such as neurons, remains a considerable challenge. Results In this study, we developed a normalization procedure for library enrichment by DNA sequences corresponding to rare somatic RE insertions. Two rounds of normalization increased the number of fragments adjacent to somatic REs in the sequenced sample by more than 26-fold, and the number of identified somatic REs was increased by 8-fold. Conclusions The developed technique can be used in combination with vast majority of modern RE identification approaches and can dramatically increase their capacity to detect rare somatic RE insertions in different types of cells.
abstractGer	Abstract Background There is increasing evidence that the transpositional activity of retroelements (REs) is not limited to germ line cells, but often occurs in tumor and normal somatic cells. Somatic transpositions were found in several human tissues and are especially typical for the brain. Several computational and experimental approaches for detection of somatic retroelement insertions was developed in the past few years. These approaches were successfully applied to detect somatic insertions in clonally expanded tumor cells. At the same time, identification of somatic insertions presented in small proportion of cells, such as neurons, remains a considerable challenge. Results In this study, we developed a normalization procedure for library enrichment by DNA sequences corresponding to rare somatic RE insertions. Two rounds of normalization increased the number of fragments adjacent to somatic REs in the sequenced sample by more than 26-fold, and the number of identified somatic REs was increased by 8-fold. Conclusions The developed technique can be used in combination with vast majority of modern RE identification approaches and can dramatically increase their capacity to detect rare somatic RE insertions in different types of cells.
abstract_unstemmed	Abstract Background There is increasing evidence that the transpositional activity of retroelements (REs) is not limited to germ line cells, but often occurs in tumor and normal somatic cells. Somatic transpositions were found in several human tissues and are especially typical for the brain. Several computational and experimental approaches for detection of somatic retroelement insertions was developed in the past few years. These approaches were successfully applied to detect somatic insertions in clonally expanded tumor cells. At the same time, identification of somatic insertions presented in small proportion of cells, such as neurons, remains a considerable challenge. Results In this study, we developed a normalization procedure for library enrichment by DNA sequences corresponding to rare somatic RE insertions. Two rounds of normalization increased the number of fragments adjacent to somatic REs in the sequenced sample by more than 26-fold, and the number of identified somatic REs was increased by 8-fold. Conclusions The developed technique can be used in combination with vast majority of modern RE identification approaches and can dramatically increase their capacity to detect rare somatic RE insertions in different types of cells.
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title_short	An advanced enrichment method for rare somatic retroelement insertions sequencing
url	https://doi.org/10.1186/s13100-018-0136-1 https://doaj.org/article/cf35768c383146e68c0de6bd418e038c http://link.springer.com/article/10.1186/s13100-018-0136-1 https://doaj.org/toc/1759-8753
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author2	Anastasia A. Minervina Gaiaz A. Nugmanov Mariia V. Saliutina Konstantin V. Khodosevich Yuri B. Lebedev Ilgar Z. Mamedov
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up_date	2024-07-03T20:54:52.650Z
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