Analysis of mutational signatures is becoming routine in cancer genomics, with implications for pathogenesis, classification, prognosis, and even treatment decisions. However, the field lacks a consensus on analysis and result interpretation. Using whole-genome sequencing of multiple myeloma (MM), chronic lymphocytic leukemia (CLL) and acute myeloid leukemia, we compare the performance of public signature analysis tools. We describe caveats and pitfalls of de novo signature extraction and fitting approaches, reporting on common inaccuracies: erroneous signature assignment, identification of localized hyper-mutational processes, overcalling of signatures. We provide reproducible solutions to solve these issues and use orthogonal approaches to validate our results. We show how a comprehensive mutational signature analysis may provide relevant biological insights, reporting evidence of c-AID activity among unmutated CLL cases or the absence of BRCA1/BRCA2-mediated homologous recombination deficiency in a MM cohort. Finally, we propose a general analysis framework to ensure production of accurate and reproducible mutational signature data.
A practical guide for mutational signature analysis in hematological malignancies / F. Maura, A. Degasperi, F. Nadeu, D. Leongamornlert, H. Davies, L. Moore, R. Royo, B. Ziccheddu, X.S. Puente, H. Avet-Loiseau, P.J. Cambell, S. Nik-Zainal, E. Campo, N. Munshi, N. Bolli. - In: NATURE COMMUNICATIONS. - ISSN 2041-1723. - 10:1(2019 Jul 05), pp. 2969.1-2969.12.
|Titolo:||A practical guide for mutational signature analysis in hematological malignancies|
MAURA, FRANCESCO (Corresponding)
BOLLI, NICCOLO' (Corresponding)
|Parole Chiave:||BRCA1 Protein; BRCA2 Protein; Computational Biology; DNA Mutational Analysis; Datasets as Topic; High-Throughput Nucleotide Sequencing; Humans; Leukemia, Lymphocytic, Chronic, B-Cell; Leukemia, Myeloid, Acute; Multiple Myeloma; Mutation; Practice Guidelines as Topic; Whole Genome Sequencing|
|Settore Scientifico Disciplinare:||Settore MED/06 - Oncologia Medica|
|Data di pubblicazione:||5-lug-2019|
|Digital Object Identifier (DOI):||http://dx.doi.org/10.1038/s41467-019-11037-8|
|Appare nelle tipologie:||01 - Articolo su periodico|