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

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...

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Detalles Bibliográficos
Autores principales: Little, Paul, Lin, Dan-Yu, Sun, Wei
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6540540/
https://www.ncbi.nlm.nih.gov/pubmed/31138328
http://dx.doi.org/10.1186/s13073-019-0643-9
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author Little, Paul
Lin, Dan-Yu
Sun, Wei
author_facet Little, Paul
Lin, Dan-Yu
Sun, Wei
author_sort Little, Paul
collection PubMed
description 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13073-019-0643-9) contains supplementary material, which is available to authorized users.
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spelling pubmed-65405402019-06-03 Associating somatic mutations to clinical outcomes: a pan-cancer study of survival time Little, Paul Lin, Dan-Yu Sun, Wei Genome Med Method 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13073-019-0643-9) contains supplementary material, which is available to authorized users. BioMed Central 2019-05-28 /pmc/articles/PMC6540540/ /pubmed/31138328 http://dx.doi.org/10.1186/s13073-019-0643-9 Text en © The Author(s) 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Method
Little, Paul
Lin, Dan-Yu
Sun, Wei
Associating somatic mutations to clinical outcomes: a pan-cancer study of survival time
title Associating somatic mutations to clinical outcomes: a pan-cancer study of survival time
title_full Associating somatic mutations to clinical outcomes: a pan-cancer study of survival time
title_fullStr Associating somatic mutations to clinical outcomes: a pan-cancer study of survival time
title_full_unstemmed Associating somatic mutations to clinical outcomes: a pan-cancer study of survival time
title_short Associating somatic mutations to clinical outcomes: a pan-cancer study of survival time
title_sort associating somatic mutations to clinical outcomes: a pan-cancer study of survival time
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6540540/
https://www.ncbi.nlm.nih.gov/pubmed/31138328
http://dx.doi.org/10.1186/s13073-019-0643-9
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