SignatureAnalyzer
GPU-accelerated Bayesian NMF for mutational and expression signatures
A fast, GPU-enabled implementation of Bayesian non-negative matrix factorization (NMF) for extracting mutational and gene-expression signatures from genomic data. SignatureAnalyzer is used across several large-scale cancer genomics efforts, including the PCAWG and CPTAC pan-cancer studies, to discover and assign de novo mutational signatures without specifying the number of signatures in advance, as described in (Taylor-Weiner et al., 2019).
Related publications
- PCAWG mutational signatures: Alexandrov, L. B., Kim, J., Haradhvala, N. J. et al. The repertoire of mutational signatures in human cancer. Nature 578, 94–101 (2020).
- SignatureAnalyzer-CPU source publications:
- Kim, J. et al. Somatic ERCC2 mutations are associated with a distinct genomic signature in urothelial tumors. Nature Genetics 48, 600–606 (2016).
- Kasar, S. et al. Whole-genome sequencing reveals activation-induced cytidine deaminase signatures during indolent chronic lymphocytic leukaemia evolution. Nature Communications 6, 8866 (2015).