(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
Cancer gene identification from RNA variant allelic frequencies using RVdriver James R M Black · Thomas P Jones · Carlos Martínez-Ruiz · Maria Litovchenko · Clare Puttick · Charles Swanton · Nicholas McGranahan
Genome Biol. 2025 Jun 13;26(1):165. doi: 10.1186/s13059-025-03557-y.ABSTRACTExisting approaches to identifying cancer genes rely overwhelmingly on DNA sequencing data. Here, we introduce RVdriver, a computational tool that leverages paired bulk genomic and transcriptomic data to classify RNA variant allele frequencies (VAFs) of non-synonymous mutations relative to a synonymous mutation background. We analyze 7882 paired exomes and transcriptomes from 31 cancer types and identify novel, as well a
13 June 2025 at 18:00

Cancer gene identification from RNA variant allelic frequencies using RVdriver

(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)

By: James R M Black · Thomas P Jones · Carlos Martínez-Ruiz · Maria Litovchenko · Clare Puttick · Charles Swanton · Nicholas McGranahan

13 June 2025 at 18:00

Genome Biol. 2025 Jun 13;26(1):165. doi: 10.1186/s13059-025-03557-y.

ABSTRACT

Existing approaches to identifying cancer genes rely overwhelmingly on DNA sequencing data. Here, we introduce RVdriver, a computational tool that leverages paired bulk genomic and transcriptomic data to classify RNA variant allele frequencies (VAFs) of non-synonymous mutations relative to a synonymous mutation background. We analyze 7882 paired exomes and transcriptomes from 31 cancer types and identify novel, as well as known, cancer genes, complementing other DNA-based approaches. Furthermore, RNA VAFs of individual mutations are able to distinguish "driver" from "passenger" mutations within established cancer genes. This approach highlights the value of multi-omic approaches for cancer gene discovery.

PMID:40514689 | PMC:PMC12164115 | DOI:10.1186/s13059-025-03557-y

Cell
Embracing cancer complexity: Hallmarks of systemic disease Charles Swanton， Elsa Bernard， Chris Abbosh， Fabrice André， Johan Auwerx， Allan Balmain， Dafna Bar-Sagi， René Bernards， Susan Bullman， James DeGregori， Catherine Elliott， Ayelet Erez， Gerard Evan， Mark A. Febbraio， Andrés Hidalgo， Mariam Jamal-Hanjani， Johanna A. Joyce， Matthew Kaiser， Katja Lamia， Jason W. Locasale， Sherene Loi， Ilaria Malanchi， Miriam Merad， Kathryn Musgrave， Ketan J. Patel， Sergio Quezada， Jennifer A. Wargo， Ashani Weeraratna， Eileen White， Frank Winkler， John N. Wood， Karen H. Vousden， Douglas Hanahan
Cancer is a systemic disease in more than one dimension, in terms of its evolutionary course, direct crosstalk with the microenvironment, and intricate communication with the macro-environment. This broad perspective encompasses our understanding of cancer’s systemic features, mapping out the path for tackling its complexity to bridge what we can learn and who we need to help.
28 March 2024 at 08:00

Embracing cancer complexity: Hallmarks of systemic disease

Cell

By: Charles Swanton， Elsa Bernard， Chris Abbosh， Fabrice André， Johan Auwerx， Allan Balmain， Dafna Bar-Sagi， René Bernards， Susan Bullman， James DeGregori， Catherine Elliott， Ayelet Erez， Gerard Evan， Mark A. Febbraio， Andrés Hidalgo， Mariam Jamal-Hanjani， Johanna A. Joyce， Matthew Kaiser， Katja Lamia， Jason W. Locasale， Sherene Loi， Ilaria Malanchi， Miriam Merad， Kathryn Musgrave， Ketan J. Patel， Sergio Quezada， Jennifer A. Wargo， Ashani Weeraratna， Eileen White， Frank Winkler， John N. Wood， Karen H. Vousden， Douglas Hanahan

28 March 2024 at 08:00

Cancer is a systemic disease in more than one dimension, in terms of its evolutionary course, direct crosstalk with the microenvironment, and intricate communication with the macro-environment. This broad perspective encompasses our understanding of cancer’s systemic features, mapping out the path for tackling its complexity to bridge what we can learn and who we need to help.

Cell
Cancer biomarkers: Emerging trends and clinical implications for personalized treatment Antonio Passaro， Maise Al Bakir， Emily G. Hamilton， Maximilian Diehn， Fabrice André， Sinchita Roy-Chowdhuri， Giannis Mountzios， Ignacio I. Wistuba， Charles Swanton， Solange Peters
Cancer biomarkers have transformed oncology, enabling treatments tailored to each tumor’s unique profile. This review highlights the field’s progress due to advancements in understanding cancer biology, testing methods, and understanding of the immune microenvironment to advance precision oncology for improved patient outcomes.
28 March 2024 at 08:00

Cancer biomarkers: Emerging trends and clinical implications for personalized treatment

Cell

By: Antonio Passaro， Maise Al Bakir， Emily G. Hamilton， Maximilian Diehn， Fabrice André， Sinchita Roy-Chowdhuri， Giannis Mountzios， Ignacio I. Wistuba， Charles Swanton， Solange Peters

28 March 2024 at 08:00

Cancer biomarkers have transformed oncology, enabling treatments tailored to each tumor’s unique profile. This review highlights the field’s progress due to advancements in understanding cancer biology, testing methods, and understanding of the immune microenvironment to advance precision oncology for improved patient outcomes.

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