CopywriteR: DNA copy number detection from off-target sequence data

Abstract Current methods for detection of copy number variants (CNV) and aberrations (CNA) from targeted sequencing data are based on the depth of coverage of captured exons. Accurate CNA determination is complicated by uneven genomic distribution and non-uniform capture efficiency of targeted exons...
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Autor*in:	Kuilman, Thomas [verfasserIn] Velds, Arno Kemper, Kristel Ranzani, Marco Bombardelli, Lorenzo Hoogstraat, Marlous Nevedomskaya, Ekaterina Xu, Guotai de Ruiter, Julian Lolkema, Martijn P Ylstra, Bauke Jonkers, Jos Rottenberg, Sven Wessels, Lodewyk F Adams, David J Peeper, Daniel S Krijgsman, Oscar

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2015

Schlagwörter:	Median Absolute Deviation Copy Number Aberration Copy Number State Copy Number Profile Copy Number Data

Anmerkung:	© Kuilman et al.; licensee BioMed Central. 2015. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (

Übergeordnetes Werk:	Enthalten in: Genome biology - London : BioMed Central, 2000, 16(2015), 1 vom: 27. Feb.
Übergeordnetes Werk:	volume:16 ; year:2015 ; number:1 ; day:27 ; month:02

Links:	Volltext

DOI / URN:	10.1186/s13059-015-0617-1

Katalog-ID:	SPR030022525

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allfields	10.1186/s13059-015-0617-1 doi (DE-627)SPR030022525 (SPR)s13059-015-0617-1-e DE-627 ger DE-627 rakwb eng Kuilman, Thomas verfasserin aut CopywriteR: DNA copy number detection from off-target sequence data 2015 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Kuilman et al.; licensee BioMed Central. 2015. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( Abstract Current methods for detection of copy number variants (CNV) and aberrations (CNA) from targeted sequencing data are based on the depth of coverage of captured exons. Accurate CNA determination is complicated by uneven genomic distribution and non-uniform capture efficiency of targeted exons. Here we present CopywriteR, which eludes these problems by exploiting ‘off-target’ sequence reads. CopywriteR allows for extracting uniformly distributed copy number information, can be used without reference, and can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. CopywriteR outperforms existing methods and constitutes a widely applicable alternative to available tools. Median Absolute Deviation (dpeaa)DE-He213 Copy Number Aberration (dpeaa)DE-He213 Copy Number State (dpeaa)DE-He213 Copy Number Profile (dpeaa)DE-He213 Copy Number Data (dpeaa)DE-He213 Velds, Arno aut Kemper, Kristel aut Ranzani, Marco aut Bombardelli, Lorenzo aut Hoogstraat, Marlous aut Nevedomskaya, Ekaterina aut Xu, Guotai aut de Ruiter, Julian aut Lolkema, Martijn P aut Ylstra, Bauke aut Jonkers, Jos aut Rottenberg, Sven aut Wessels, Lodewyk F aut Adams, David J aut Peeper, Daniel S aut Krijgsman, Oscar aut Enthalten in Genome biology London : BioMed Central, 2000 16(2015), 1 vom: 27. Feb. (DE-627)326173617 (DE-600)2040529-7 1474-760X nnns volume:16 year:2015 number:1 day:27 month:02 https://dx.doi.org/10.1186/s13059-015-0617-1 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA 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 16 2015 1 27 02
spelling	10.1186/s13059-015-0617-1 doi (DE-627)SPR030022525 (SPR)s13059-015-0617-1-e DE-627 ger DE-627 rakwb eng Kuilman, Thomas verfasserin aut CopywriteR: DNA copy number detection from off-target sequence data 2015 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Kuilman et al.; licensee BioMed Central. 2015. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( Abstract Current methods for detection of copy number variants (CNV) and aberrations (CNA) from targeted sequencing data are based on the depth of coverage of captured exons. Accurate CNA determination is complicated by uneven genomic distribution and non-uniform capture efficiency of targeted exons. Here we present CopywriteR, which eludes these problems by exploiting ‘off-target’ sequence reads. CopywriteR allows for extracting uniformly distributed copy number information, can be used without reference, and can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. CopywriteR outperforms existing methods and constitutes a widely applicable alternative to available tools. Median Absolute Deviation (dpeaa)DE-He213 Copy Number Aberration (dpeaa)DE-He213 Copy Number State (dpeaa)DE-He213 Copy Number Profile (dpeaa)DE-He213 Copy Number Data (dpeaa)DE-He213 Velds, Arno aut Kemper, Kristel aut Ranzani, Marco aut Bombardelli, Lorenzo aut Hoogstraat, Marlous aut Nevedomskaya, Ekaterina aut Xu, Guotai aut de Ruiter, Julian aut Lolkema, Martijn P aut Ylstra, Bauke aut Jonkers, Jos aut Rottenberg, Sven aut Wessels, Lodewyk F aut Adams, David J aut Peeper, Daniel S aut Krijgsman, Oscar aut Enthalten in Genome biology London : BioMed Central, 2000 16(2015), 1 vom: 27. Feb. (DE-627)326173617 (DE-600)2040529-7 1474-760X nnns volume:16 year:2015 number:1 day:27 month:02 https://dx.doi.org/10.1186/s13059-015-0617-1 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA 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 16 2015 1 27 02
allfields_unstemmed	10.1186/s13059-015-0617-1 doi (DE-627)SPR030022525 (SPR)s13059-015-0617-1-e DE-627 ger DE-627 rakwb eng Kuilman, Thomas verfasserin aut CopywriteR: DNA copy number detection from off-target sequence data 2015 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Kuilman et al.; licensee BioMed Central. 2015. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( Abstract Current methods for detection of copy number variants (CNV) and aberrations (CNA) from targeted sequencing data are based on the depth of coverage of captured exons. Accurate CNA determination is complicated by uneven genomic distribution and non-uniform capture efficiency of targeted exons. Here we present CopywriteR, which eludes these problems by exploiting ‘off-target’ sequence reads. CopywriteR allows for extracting uniformly distributed copy number information, can be used without reference, and can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. CopywriteR outperforms existing methods and constitutes a widely applicable alternative to available tools. Median Absolute Deviation (dpeaa)DE-He213 Copy Number Aberration (dpeaa)DE-He213 Copy Number State (dpeaa)DE-He213 Copy Number Profile (dpeaa)DE-He213 Copy Number Data (dpeaa)DE-He213 Velds, Arno aut Kemper, Kristel aut Ranzani, Marco aut Bombardelli, Lorenzo aut Hoogstraat, Marlous aut Nevedomskaya, Ekaterina aut Xu, Guotai aut de Ruiter, Julian aut Lolkema, Martijn P aut Ylstra, Bauke aut Jonkers, Jos aut Rottenberg, Sven aut Wessels, Lodewyk F aut Adams, David J aut Peeper, Daniel S aut Krijgsman, Oscar aut Enthalten in Genome biology London : BioMed Central, 2000 16(2015), 1 vom: 27. Feb. (DE-627)326173617 (DE-600)2040529-7 1474-760X nnns volume:16 year:2015 number:1 day:27 month:02 https://dx.doi.org/10.1186/s13059-015-0617-1 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA 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 16 2015 1 27 02
allfieldsGer	10.1186/s13059-015-0617-1 doi (DE-627)SPR030022525 (SPR)s13059-015-0617-1-e DE-627 ger DE-627 rakwb eng Kuilman, Thomas verfasserin aut CopywriteR: DNA copy number detection from off-target sequence data 2015 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Kuilman et al.; licensee BioMed Central. 2015. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( Abstract Current methods for detection of copy number variants (CNV) and aberrations (CNA) from targeted sequencing data are based on the depth of coverage of captured exons. Accurate CNA determination is complicated by uneven genomic distribution and non-uniform capture efficiency of targeted exons. Here we present CopywriteR, which eludes these problems by exploiting ‘off-target’ sequence reads. CopywriteR allows for extracting uniformly distributed copy number information, can be used without reference, and can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. CopywriteR outperforms existing methods and constitutes a widely applicable alternative to available tools. Median Absolute Deviation (dpeaa)DE-He213 Copy Number Aberration (dpeaa)DE-He213 Copy Number State (dpeaa)DE-He213 Copy Number Profile (dpeaa)DE-He213 Copy Number Data (dpeaa)DE-He213 Velds, Arno aut Kemper, Kristel aut Ranzani, Marco aut Bombardelli, Lorenzo aut Hoogstraat, Marlous aut Nevedomskaya, Ekaterina aut Xu, Guotai aut de Ruiter, Julian aut Lolkema, Martijn P aut Ylstra, Bauke aut Jonkers, Jos aut Rottenberg, Sven aut Wessels, Lodewyk F aut Adams, David J aut Peeper, Daniel S aut Krijgsman, Oscar aut Enthalten in Genome biology London : BioMed Central, 2000 16(2015), 1 vom: 27. Feb. (DE-627)326173617 (DE-600)2040529-7 1474-760X nnns volume:16 year:2015 number:1 day:27 month:02 https://dx.doi.org/10.1186/s13059-015-0617-1 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA 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 16 2015 1 27 02
allfieldsSound	10.1186/s13059-015-0617-1 doi (DE-627)SPR030022525 (SPR)s13059-015-0617-1-e DE-627 ger DE-627 rakwb eng Kuilman, Thomas verfasserin aut CopywriteR: DNA copy number detection from off-target sequence data 2015 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Kuilman et al.; licensee BioMed Central. 2015. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( Abstract Current methods for detection of copy number variants (CNV) and aberrations (CNA) from targeted sequencing data are based on the depth of coverage of captured exons. Accurate CNA determination is complicated by uneven genomic distribution and non-uniform capture efficiency of targeted exons. Here we present CopywriteR, which eludes these problems by exploiting ‘off-target’ sequence reads. CopywriteR allows for extracting uniformly distributed copy number information, can be used without reference, and can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. CopywriteR outperforms existing methods and constitutes a widely applicable alternative to available tools. Median Absolute Deviation (dpeaa)DE-He213 Copy Number Aberration (dpeaa)DE-He213 Copy Number State (dpeaa)DE-He213 Copy Number Profile (dpeaa)DE-He213 Copy Number Data (dpeaa)DE-He213 Velds, Arno aut Kemper, Kristel aut Ranzani, Marco aut Bombardelli, Lorenzo aut Hoogstraat, Marlous aut Nevedomskaya, Ekaterina aut Xu, Guotai aut de Ruiter, Julian aut Lolkema, Martijn P aut Ylstra, Bauke aut Jonkers, Jos aut Rottenberg, Sven aut Wessels, Lodewyk F aut Adams, David J aut Peeper, Daniel S aut Krijgsman, Oscar aut Enthalten in Genome biology London : BioMed Central, 2000 16(2015), 1 vom: 27. Feb. (DE-627)326173617 (DE-600)2040529-7 1474-760X nnns volume:16 year:2015 number:1 day:27 month:02 https://dx.doi.org/10.1186/s13059-015-0617-1 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA 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 16 2015 1 27 02
language	English
source	Enthalten in Genome biology 16(2015), 1 vom: 27. Feb. volume:16 year:2015 number:1 day:27 month:02
sourceStr	Enthalten in Genome biology 16(2015), 1 vom: 27. Feb. volume:16 year:2015 number:1 day:27 month:02
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	Median Absolute Deviation Copy Number Aberration Copy Number State Copy Number Profile Copy Number Data
isfreeaccess_bool	true
container_title	Genome biology
authorswithroles_txt_mv	Kuilman, Thomas @@aut@@ Velds, Arno @@aut@@ Kemper, Kristel @@aut@@ Ranzani, Marco @@aut@@ Bombardelli, Lorenzo @@aut@@ Hoogstraat, Marlous @@aut@@ Nevedomskaya, Ekaterina @@aut@@ Xu, Guotai @@aut@@ de Ruiter, Julian @@aut@@ Lolkema, Martijn P @@aut@@ Ylstra, Bauke @@aut@@ Jonkers, Jos @@aut@@ Rottenberg, Sven @@aut@@ Wessels, Lodewyk F @@aut@@ Adams, David J @@aut@@ Peeper, Daniel S @@aut@@ Krijgsman, Oscar @@aut@@
publishDateDaySort_date	2015-02-27T00:00:00Z
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spellingShingle	Kuilman, Thomas misc Median Absolute Deviation misc Copy Number Aberration misc Copy Number State misc Copy Number Profile misc Copy Number Data CopywriteR: DNA copy number detection from off-target sequence data
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topic_title	CopywriteR: DNA copy number detection from off-target sequence data Median Absolute Deviation (dpeaa)DE-He213 Copy Number Aberration (dpeaa)DE-He213 Copy Number State (dpeaa)DE-He213 Copy Number Profile (dpeaa)DE-He213 Copy Number Data (dpeaa)DE-He213
topic	misc Median Absolute Deviation misc Copy Number Aberration misc Copy Number State misc Copy Number Profile misc Copy Number Data
topic_unstemmed	misc Median Absolute Deviation misc Copy Number Aberration misc Copy Number State misc Copy Number Profile misc Copy Number Data
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title	CopywriteR: DNA copy number detection from off-target sequence data
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title_full	CopywriteR: DNA copy number detection from off-target sequence data
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author_browse	Kuilman, Thomas Velds, Arno Kemper, Kristel Ranzani, Marco Bombardelli, Lorenzo Hoogstraat, Marlous Nevedomskaya, Ekaterina Xu, Guotai de Ruiter, Julian Lolkema, Martijn P Ylstra, Bauke Jonkers, Jos Rottenberg, Sven Wessels, Lodewyk F Adams, David J Peeper, Daniel S Krijgsman, Oscar
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title_sort	copywriter: dna copy number detection from off-target sequence data
title_auth	CopywriteR: DNA copy number detection from off-target sequence data
abstract	Abstract Current methods for detection of copy number variants (CNV) and aberrations (CNA) from targeted sequencing data are based on the depth of coverage of captured exons. Accurate CNA determination is complicated by uneven genomic distribution and non-uniform capture efficiency of targeted exons. Here we present CopywriteR, which eludes these problems by exploiting ‘off-target’ sequence reads. CopywriteR allows for extracting uniformly distributed copy number information, can be used without reference, and can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. CopywriteR outperforms existing methods and constitutes a widely applicable alternative to available tools. © Kuilman et al.; licensee BioMed Central. 2015. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (
abstractGer	Abstract Current methods for detection of copy number variants (CNV) and aberrations (CNA) from targeted sequencing data are based on the depth of coverage of captured exons. Accurate CNA determination is complicated by uneven genomic distribution and non-uniform capture efficiency of targeted exons. Here we present CopywriteR, which eludes these problems by exploiting ‘off-target’ sequence reads. CopywriteR allows for extracting uniformly distributed copy number information, can be used without reference, and can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. CopywriteR outperforms existing methods and constitutes a widely applicable alternative to available tools. © Kuilman et al.; licensee BioMed Central. 2015. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (
abstract_unstemmed	Abstract Current methods for detection of copy number variants (CNV) and aberrations (CNA) from targeted sequencing data are based on the depth of coverage of captured exons. Accurate CNA determination is complicated by uneven genomic distribution and non-uniform capture efficiency of targeted exons. Here we present CopywriteR, which eludes these problems by exploiting ‘off-target’ sequence reads. CopywriteR allows for extracting uniformly distributed copy number information, can be used without reference, and can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. CopywriteR outperforms existing methods and constitutes a widely applicable alternative to available tools. © Kuilman et al.; licensee BioMed Central. 2015. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (
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title_short	CopywriteR: DNA copy number detection from off-target sequence data
url	https://dx.doi.org/10.1186/s13059-015-0617-1
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CopywriteR: DNA copy number detection from off-target sequence data

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