Associating somatic mutations to clinical outcomes: a pan-cancer study of survival time

Abstract We developed subclone multiplicity allocation and somatic heterogeneity (SMASH), a new statistical method for intra-tumor heterogeneity (ITH) inference. SMASH is tailored to the purpose of large-scale association studies with one tumor sample per patient. In a pan-cancer study of 14 cancer...
Ausführliche Beschreibung

Gespeichert in:

Autor*in:	Little, Paul [verfasserIn] Lin, Dan-Yu Sun, Wei

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2019

Schlagwörter:	Copy number alteration Intra-tumor heterogeneity Somatic mutations Subclone Tumor mutation burden

Anmerkung:	© The Author(s) 2019

Übergeordnetes Werk:	Enthalten in: Genome medicine - London : BioMed Central, 2009, 11(2019), 1 vom: 28. Mai
Übergeordnetes Werk:	volume:11 ; year:2019 ; number:1 ; day:28 ; month:05

Links:	Volltext

DOI / URN:	10.1186/s13073-019-0643-9

Katalog-ID:	SPR030672104

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allfields	10.1186/s13073-019-0643-9 doi (DE-627)SPR030672104 (SPR)s13073-019-0643-9-e DE-627 ger DE-627 rakwb eng Little, Paul verfasserin aut Associating somatic mutations to clinical outcomes: a pan-cancer study of survival time 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2019 Abstract We developed subclone multiplicity allocation and somatic heterogeneity (SMASH), a new statistical method for intra-tumor heterogeneity (ITH) inference. SMASH is tailored to the purpose of large-scale association studies with one tumor sample per patient. In a pan-cancer study of 14 cancer types, we studied the associations between survival time and ITH quantified by SMASH, together with other features of somatic mutations. Our results show that ITH is associated with survival time in several cancer types and its effect can be modified by other covariates, such as mutation burden. SMASH is available at https://github.com/Sun-lab/SMASH. Copy number alteration (dpeaa)DE-He213 Intra-tumor heterogeneity (dpeaa)DE-He213 Somatic mutations (dpeaa)DE-He213 Subclone (dpeaa)DE-He213 Tumor mutation burden (dpeaa)DE-He213 Lin, Dan-Yu aut Sun, Wei (orcid)0000-0002-6350-1107 aut Enthalten in Genome medicine London : BioMed Central, 2009 11(2019), 1 vom: 28. Mai (DE-627)594424275 (DE-600)2484394-5 1756-994X nnns volume:11 year:2019 number:1 day:28 month:05 https://dx.doi.org/10.1186/s13073-019-0643-9 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_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 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 11 2019 1 28 05
spelling	10.1186/s13073-019-0643-9 doi (DE-627)SPR030672104 (SPR)s13073-019-0643-9-e DE-627 ger DE-627 rakwb eng Little, Paul verfasserin aut Associating somatic mutations to clinical outcomes: a pan-cancer study of survival time 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2019 Abstract We developed subclone multiplicity allocation and somatic heterogeneity (SMASH), a new statistical method for intra-tumor heterogeneity (ITH) inference. SMASH is tailored to the purpose of large-scale association studies with one tumor sample per patient. In a pan-cancer study of 14 cancer types, we studied the associations between survival time and ITH quantified by SMASH, together with other features of somatic mutations. Our results show that ITH is associated with survival time in several cancer types and its effect can be modified by other covariates, such as mutation burden. SMASH is available at https://github.com/Sun-lab/SMASH. Copy number alteration (dpeaa)DE-He213 Intra-tumor heterogeneity (dpeaa)DE-He213 Somatic mutations (dpeaa)DE-He213 Subclone (dpeaa)DE-He213 Tumor mutation burden (dpeaa)DE-He213 Lin, Dan-Yu aut Sun, Wei (orcid)0000-0002-6350-1107 aut Enthalten in Genome medicine London : BioMed Central, 2009 11(2019), 1 vom: 28. Mai (DE-627)594424275 (DE-600)2484394-5 1756-994X nnns volume:11 year:2019 number:1 day:28 month:05 https://dx.doi.org/10.1186/s13073-019-0643-9 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_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 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 11 2019 1 28 05
allfields_unstemmed	10.1186/s13073-019-0643-9 doi (DE-627)SPR030672104 (SPR)s13073-019-0643-9-e DE-627 ger DE-627 rakwb eng Little, Paul verfasserin aut Associating somatic mutations to clinical outcomes: a pan-cancer study of survival time 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2019 Abstract We developed subclone multiplicity allocation and somatic heterogeneity (SMASH), a new statistical method for intra-tumor heterogeneity (ITH) inference. SMASH is tailored to the purpose of large-scale association studies with one tumor sample per patient. In a pan-cancer study of 14 cancer types, we studied the associations between survival time and ITH quantified by SMASH, together with other features of somatic mutations. Our results show that ITH is associated with survival time in several cancer types and its effect can be modified by other covariates, such as mutation burden. SMASH is available at https://github.com/Sun-lab/SMASH. Copy number alteration (dpeaa)DE-He213 Intra-tumor heterogeneity (dpeaa)DE-He213 Somatic mutations (dpeaa)DE-He213 Subclone (dpeaa)DE-He213 Tumor mutation burden (dpeaa)DE-He213 Lin, Dan-Yu aut Sun, Wei (orcid)0000-0002-6350-1107 aut Enthalten in Genome medicine London : BioMed Central, 2009 11(2019), 1 vom: 28. Mai (DE-627)594424275 (DE-600)2484394-5 1756-994X nnns volume:11 year:2019 number:1 day:28 month:05 https://dx.doi.org/10.1186/s13073-019-0643-9 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_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 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 11 2019 1 28 05
allfieldsGer	10.1186/s13073-019-0643-9 doi (DE-627)SPR030672104 (SPR)s13073-019-0643-9-e DE-627 ger DE-627 rakwb eng Little, Paul verfasserin aut Associating somatic mutations to clinical outcomes: a pan-cancer study of survival time 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2019 Abstract We developed subclone multiplicity allocation and somatic heterogeneity (SMASH), a new statistical method for intra-tumor heterogeneity (ITH) inference. SMASH is tailored to the purpose of large-scale association studies with one tumor sample per patient. In a pan-cancer study of 14 cancer types, we studied the associations between survival time and ITH quantified by SMASH, together with other features of somatic mutations. Our results show that ITH is associated with survival time in several cancer types and its effect can be modified by other covariates, such as mutation burden. SMASH is available at https://github.com/Sun-lab/SMASH. Copy number alteration (dpeaa)DE-He213 Intra-tumor heterogeneity (dpeaa)DE-He213 Somatic mutations (dpeaa)DE-He213 Subclone (dpeaa)DE-He213 Tumor mutation burden (dpeaa)DE-He213 Lin, Dan-Yu aut Sun, Wei (orcid)0000-0002-6350-1107 aut Enthalten in Genome medicine London : BioMed Central, 2009 11(2019), 1 vom: 28. Mai (DE-627)594424275 (DE-600)2484394-5 1756-994X nnns volume:11 year:2019 number:1 day:28 month:05 https://dx.doi.org/10.1186/s13073-019-0643-9 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_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 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 11 2019 1 28 05
allfieldsSound	10.1186/s13073-019-0643-9 doi (DE-627)SPR030672104 (SPR)s13073-019-0643-9-e DE-627 ger DE-627 rakwb eng Little, Paul verfasserin aut Associating somatic mutations to clinical outcomes: a pan-cancer study of survival time 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2019 Abstract We developed subclone multiplicity allocation and somatic heterogeneity (SMASH), a new statistical method for intra-tumor heterogeneity (ITH) inference. SMASH is tailored to the purpose of large-scale association studies with one tumor sample per patient. In a pan-cancer study of 14 cancer types, we studied the associations between survival time and ITH quantified by SMASH, together with other features of somatic mutations. Our results show that ITH is associated with survival time in several cancer types and its effect can be modified by other covariates, such as mutation burden. SMASH is available at https://github.com/Sun-lab/SMASH. Copy number alteration (dpeaa)DE-He213 Intra-tumor heterogeneity (dpeaa)DE-He213 Somatic mutations (dpeaa)DE-He213 Subclone (dpeaa)DE-He213 Tumor mutation burden (dpeaa)DE-He213 Lin, Dan-Yu aut Sun, Wei (orcid)0000-0002-6350-1107 aut Enthalten in Genome medicine London : BioMed Central, 2009 11(2019), 1 vom: 28. Mai (DE-627)594424275 (DE-600)2484394-5 1756-994X nnns volume:11 year:2019 number:1 day:28 month:05 https://dx.doi.org/10.1186/s13073-019-0643-9 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_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 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 11 2019 1 28 05
language	English
source	Enthalten in Genome medicine 11(2019), 1 vom: 28. Mai volume:11 year:2019 number:1 day:28 month:05
sourceStr	Enthalten in Genome medicine 11(2019), 1 vom: 28. Mai volume:11 year:2019 number:1 day:28 month:05
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	Copy number alteration Intra-tumor heterogeneity Somatic mutations Subclone Tumor mutation burden
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container_title	Genome medicine
authorswithroles_txt_mv	Little, Paul @@aut@@ Lin, Dan-Yu @@aut@@ Sun, Wei @@aut@@
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author	Little, Paul
spellingShingle	Little, Paul misc Copy number alteration misc Intra-tumor heterogeneity misc Somatic mutations misc Subclone misc Tumor mutation burden Associating somatic mutations to clinical outcomes: a pan-cancer study of survival time
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topic_title	Associating somatic mutations to clinical outcomes: a pan-cancer study of survival time Copy number alteration (dpeaa)DE-He213 Intra-tumor heterogeneity (dpeaa)DE-He213 Somatic mutations (dpeaa)DE-He213 Subclone (dpeaa)DE-He213 Tumor mutation burden (dpeaa)DE-He213
topic	misc Copy number alteration misc Intra-tumor heterogeneity misc Somatic mutations misc Subclone misc Tumor mutation burden
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title	Associating somatic mutations to clinical outcomes: a pan-cancer study of survival time
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title_full	Associating somatic mutations to clinical outcomes: a pan-cancer study of survival time
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author_browse	Little, Paul Lin, Dan-Yu Sun, Wei
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title_sort	associating somatic mutations to clinical outcomes: a pan-cancer study of survival time
title_auth	Associating somatic mutations to clinical outcomes: a pan-cancer study of survival time
abstract	Abstract We developed subclone multiplicity allocation and somatic heterogeneity (SMASH), a new statistical method for intra-tumor heterogeneity (ITH) inference. SMASH is tailored to the purpose of large-scale association studies with one tumor sample per patient. In a pan-cancer study of 14 cancer types, we studied the associations between survival time and ITH quantified by SMASH, together with other features of somatic mutations. Our results show that ITH is associated with survival time in several cancer types and its effect can be modified by other covariates, such as mutation burden. SMASH is available at https://github.com/Sun-lab/SMASH. © The Author(s) 2019
abstractGer	Abstract We developed subclone multiplicity allocation and somatic heterogeneity (SMASH), a new statistical method for intra-tumor heterogeneity (ITH) inference. SMASH is tailored to the purpose of large-scale association studies with one tumor sample per patient. In a pan-cancer study of 14 cancer types, we studied the associations between survival time and ITH quantified by SMASH, together with other features of somatic mutations. Our results show that ITH is associated with survival time in several cancer types and its effect can be modified by other covariates, such as mutation burden. SMASH is available at https://github.com/Sun-lab/SMASH. © The Author(s) 2019
abstract_unstemmed	Abstract We developed subclone multiplicity allocation and somatic heterogeneity (SMASH), a new statistical method for intra-tumor heterogeneity (ITH) inference. SMASH is tailored to the purpose of large-scale association studies with one tumor sample per patient. In a pan-cancer study of 14 cancer types, we studied the associations between survival time and ITH quantified by SMASH, together with other features of somatic mutations. Our results show that ITH is associated with survival time in several cancer types and its effect can be modified by other covariates, such as mutation burden. SMASH is available at https://github.com/Sun-lab/SMASH. © The Author(s) 2019
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title_short	Associating somatic mutations to clinical outcomes: a pan-cancer study of survival time
url	https://dx.doi.org/10.1186/s13073-019-0643-9
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up_date	2024-07-03T19:27:55.758Z
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Associating somatic mutations to clinical outcomes: a pan-cancer study of survival time

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Vorhandene Bände

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