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...
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| Format: | Article |
| Language: | English |
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BMC
2019-05-01
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| Series: | Genome Medicine |
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| Online Access: | http://link.springer.com/article/10.1186/s13073-019-0643-9 |
| _version_ | 1831520967425261568 |
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| author | Paul Little Dan-Yu Lin Wei Sun |
| author_facet | Paul Little Dan-Yu Lin Wei Sun |
| author_sort | Paul Little |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-13T17:42:40Z |
| format | Article |
| id | doaj.art-58bc8713fa84427185113a25f2f36757 |
| institution | Directory Open Access Journal |
| issn | 1756-994X |
| language | English |
| last_indexed | 2024-12-13T17:42:40Z |
| publishDate | 2019-05-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Medicine |
| spelling | doaj.art-58bc8713fa84427185113a25f2f367572022-12-21T23:36:41ZengBMCGenome Medicine1756-994X2019-05-0111111510.1186/s13073-019-0643-9Associating somatic mutations to clinical outcomes: a pan-cancer study of survival timePaul Little0Dan-Yu Lin1Wei Sun2Department of Biostatistics, University of North Carolina Chapel HillDepartment of Biostatistics, University of North Carolina Chapel HillPublic Health Sciences Division, Fred Hutchinson Cancer Research CenterAbstract 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.http://link.springer.com/article/10.1186/s13073-019-0643-9Copy number alterationIntra-tumor heterogeneitySomatic mutationsSubcloneTumor mutation burden |
| spellingShingle | Paul Little Dan-Yu Lin Wei Sun Associating somatic mutations to clinical outcomes: a pan-cancer study of survival time Genome Medicine Copy number alteration Intra-tumor heterogeneity Somatic mutations Subclone Tumor mutation burden |
| 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 | Copy number alteration Intra-tumor heterogeneity Somatic mutations Subclone Tumor mutation burden |
| url | http://link.springer.com/article/10.1186/s13073-019-0643-9 |
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