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

Taro Matsutani, Yuki Ueno, Tsukasa Fukunaga, Michiaki Hamada*

*この研究の対応する著者

研究成果: Article査読

4 被引用数 (Scopus)

抄録

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.

本文言語English
ページ(範囲)4543-4552
ページ数10
ジャーナルBioinformatics
35
22
DOI
出版ステータスPublished - 2019 11 1

ASJC Scopus subject areas

  • 統計学および確率
  • 生化学
  • 分子生物学
  • コンピュータ サイエンスの応用
  • 計算理論と計算数学
  • 計算数学

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