SUITOR: Selecting the number of mutational signatures through cross-validation.
For de novo mutational signature analysis, the critical first step is to decide how many signatures should be expected in a cancer genomics study. An incorrect number could mislead downstream analyses. Here we present SUITOR (Selecting the nUmber of mutatIonal signaTures thrOugh cRoss-validation), a...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2022-04-01
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| Series: | PLoS Computational Biology |
| Online Access: | https://doi.org/10.1371/journal.pcbi.1009309 |
| _version_ | 1828790242436448256 |
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| author | Donghyuk Lee Difei Wang Xiaohong R Yang Jianxin Shi Maria Teresa Landi Bin Zhu |
| author_facet | Donghyuk Lee Difei Wang Xiaohong R Yang Jianxin Shi Maria Teresa Landi Bin Zhu |
| author_sort | Donghyuk Lee |
| collection | DOAJ |
| description | For de novo mutational signature analysis, the critical first step is to decide how many signatures should be expected in a cancer genomics study. An incorrect number could mislead downstream analyses. Here we present SUITOR (Selecting the nUmber of mutatIonal signaTures thrOugh cRoss-validation), an unsupervised cross-validation method that requires little assumptions and no numerical approximations to select the optimal number of signatures without overfitting the data. In vitro studies and in silico simulations demonstrated that SUITOR can correctly identify signatures, some of which were missed by other widely used methods. Applied to 2,540 whole-genome sequenced tumors across 22 cancer types, SUITOR selected signatures with the smallest prediction errors and almost all signatures of breast cancer selected by SUITOR were validated in an independent breast cancer study. SUITOR is a powerful tool to select the optimal number of mutational signatures, facilitating downstream analyses with etiological or therapeutic importance. |
| first_indexed | 2024-12-12T01:26:59Z |
| format | Article |
| id | doaj.art-41e4e173ac624064b1f6a149222d6ed7 |
| institution | Directory Open Access Journal |
| issn | 1553-734X 1553-7358 |
| language | English |
| last_indexed | 2024-12-12T01:26:59Z |
| publishDate | 2022-04-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj.art-41e4e173ac624064b1f6a149222d6ed72022-12-22T00:43:04ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582022-04-01184e100930910.1371/journal.pcbi.1009309SUITOR: Selecting the number of mutational signatures through cross-validation.Donghyuk LeeDifei WangXiaohong R YangJianxin ShiMaria Teresa LandiBin ZhuFor de novo mutational signature analysis, the critical first step is to decide how many signatures should be expected in a cancer genomics study. An incorrect number could mislead downstream analyses. Here we present SUITOR (Selecting the nUmber of mutatIonal signaTures thrOugh cRoss-validation), an unsupervised cross-validation method that requires little assumptions and no numerical approximations to select the optimal number of signatures without overfitting the data. In vitro studies and in silico simulations demonstrated that SUITOR can correctly identify signatures, some of which were missed by other widely used methods. Applied to 2,540 whole-genome sequenced tumors across 22 cancer types, SUITOR selected signatures with the smallest prediction errors and almost all signatures of breast cancer selected by SUITOR were validated in an independent breast cancer study. SUITOR is a powerful tool to select the optimal number of mutational signatures, facilitating downstream analyses with etiological or therapeutic importance.https://doi.org/10.1371/journal.pcbi.1009309 |
| spellingShingle | Donghyuk Lee Difei Wang Xiaohong R Yang Jianxin Shi Maria Teresa Landi Bin Zhu SUITOR: Selecting the number of mutational signatures through cross-validation. PLoS Computational Biology |
| title | SUITOR: Selecting the number of mutational signatures through cross-validation. |
| title_full | SUITOR: Selecting the number of mutational signatures through cross-validation. |
| title_fullStr | SUITOR: Selecting the number of mutational signatures through cross-validation. |
| title_full_unstemmed | SUITOR: Selecting the number of mutational signatures through cross-validation. |
| title_short | SUITOR: Selecting the number of mutational signatures through cross-validation. |
| title_sort | suitor selecting the number of mutational signatures through cross validation |
| url | https://doi.org/10.1371/journal.pcbi.1009309 |
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