Dataset Information

Discovering novel mutation signatures by latent Dirichlet allocation with variational Bayes inference.

ABSTRACT:

Motivation

A cancer genome includes many mutations derived from various mutagens and mutational processes, leading to specific mutation patterns. It is known that each mutational process leads to characteristic mutations, and when a mutational process has preferences for mutations, this situation is called a 'mutation signature.' Identification of mutation signatures is an important task for elucidation of carcinogenic mechanisms. In previous studies, analyses with statistical approaches (e.g. non-negative matrix factorization and latent Dirichlet allocation) revealed a number of mutation signatures. Nonetheless, strictly speaking, these existing approaches employ an ad hoc method or incorrect approximation to estimate the number of mutation signatures, and the whole picture of mutation signatures is unclear.

Results

In this study, we present a novel method for estimating the number of mutation signatures-latent Dirichlet allocation with variational Bayes inference (VB-LDA)-where variational lower bounds are utilized for finding a plausible number of mutation patterns. In addition, we performed cluster analyses for estimated mutation signatures to extract novel mutation signatures that appear in multiple primary lesions. In a simulation with artificial data, we confirmed that our method estimated the correct number of mutation signatures. Furthermore, applying our method in combination with clustering procedures for real mutation data revealed many interesting mutation signatures that have not been previously reported.

Availability and implementation

All the predicted mutation signatures with clustering results are freely available at http://www.f.waseda.jp/mhamada/MS/index.html. All the C++ source code and python scripts utilized in this study can be downloaded on the Internet (https://github.com/qkirikigaku/MS_LDA).

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Matsutani T

PROVIDER: S-EPMC6853711 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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Publications

Discovering novel mutation signatures by latent Dirichlet allocation with variational Bayes inference.

Matsutani Taro T Ueno Yuki Y Fukunaga Tsukasa T Hamada Michiaki M

Bioinformatics (Oxford, England) 20191101 22

<h4>Motivation</h4>A cancer genome includes many mutations derived from various mutagens and mutational processes, leading to specific mutation patterns. It is known that each mutational process leads to characteristic mutations, and when a mutational process has preferences for mutations, this situation is called a 'mutation signature.' Identification of mutation signatures is an important task for elucidation of carcinogenic mechanisms. In previous studies, analyses with statistical approaches ...[more]

PMID: 30993319

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Dataset Information

Discovering novel mutation signatures by latent Dirichlet allocation with variational Bayes inference.

Motivation

Results

Availability and implementation

Supplementary information

Publications

Discovering novel mutation signatures by latent Dirichlet allocation with variational Bayes inference.

Similar Datasets

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