CHASMplus: predicting which missense mutations drive human cancers

_images/karchinlablogo.png
Author:

Collin Tokheim, Rachel Karchin

Contact:

ctokhei1 # alumni DOT jh DOT edu

Lab:

Karchin Lab

Source code:

GitHub

Q&A:

Biostars (tag: CHASMplus)

Large-scale DNA sequencing studies of patients’ tumors have revealed that most driver mutations occur only in a few patients, which presents a challenge for precision medicine. CHASMplus is a machine learning method that accurately distinguishes between driver and passenger missense mutations, even for those found at low frequencies or are cancer type-specific. Unlike previous approaches that focus on identifying driver genes, CHASMplus identifies whether individual mutations are cancer drivers. CHASMplus can be used by both bioinformaticians and biolgists by using a graphical user interface or a command line tool.

Note

You can run CHASMplus without installing anything by submitting your data to the OpenCRAVAT webserver (details here). After creating a user account, you’ll just need to check the box for CHASMplus and hit the annotate button (OpenCRAVAT webserver). Also, you can install locally a graphical user interface [see the Quick start (OpenCRAVAT & CHASMplus)]

Prominent papers using CHASMplus:

  • Reiter et al., Minimal functional driver gene heterogeneity among untreated metastases. Science

  • Anagnostou, Niknafs et al., Multimodal genomic features predict outcome of immune checkpoint blockade in non-small-cell lung cancer. Nature Cancer

  • Saito et al., Landscape and function of multiple mutations within individual oncogenes. Nature

  • Reiter et al., An analysis of genetic heterogeneity in untreated cancers. Nature Reviews Cancer

  • Hu et al., Multi-cancer analysis of clonality and the timing of systemic spread in paired primary tumors and metastases. Nature Genetics

  • Sakomoto et al., The Evolutionary Origins of Recurrent Pancreatic Cancer, Cancer Discovery

Contents:

Citation

Please cite our paper:

Tokheim and Karchin, CHASMplus Reveals the Scope of Somatic Missense Mutations Driving Human Cancers, Cell Systems (2019), https://doi.org/10.1016/j.cels.2019.05.005