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Mutations

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Mutations are changes in the sequence of DNA. These changes can occur spontaneously or they can be induced by exposure to environmental factors. Mutations can be characterized in a number of different ways: whether and how they alter the amino acid sequence of the protein, whether they occur over a small or large area of DNA, and whether they occur in somatic cells or germline cells.
Chromosomal Alterations Are Large-Scale Mutations
While point mutations are changes in a single nucleotide in...

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Cancer arises from mutations in the critical genes that allow healthy cells to escape cell cycle regulation and acquire the ability to proliferate indefinitely. Though originating from a single mutation event in one of the originator cells, cancer progresses when the mutant cell lines continue to gain more and more mutations, and finally, become malignant. For example, chronic myelogenous leukemia (CML) develops initially as a non-lethal increase in white blood cells, which progressively...

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A mutation is a change in the sequence of bases of DNA or RNA in a genome. Some mutations occur during replication of the genome due to errors made by the polymerase enzymes that replicate DNA or RNA. Unlike DNA polymerase, RNA polymerase is prone to errors because it is not capable of “proofreading” its work. Viruses with RNA-based genomes, like HIV, therefore accrue mutations faster than viruses with DNA-based genomes. Because mutation and recombination provide the raw material...

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Discovery of Driver Genes in Colorectal HT29-derived Cancer Stem-Like Tumorspheres

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An interpretable molecular framework for predicting cancer driver missense mutations.

Yan Yang^1,2, Weikang Sun^1,2, Yang Liu^1,2

¹Jiangsu Key Laboratory of Drug Discovery and Translational Research for Brain Diseases, School of Basic Medical Sciences, Soochow University, Suzhou, Jiangsu 215123, China.

Proceedings of the National Academy of Sciences of the United States of America

|February 3, 2026

Summary

Predicting the impact of missense mutations is challenging. A new framework, MutaPheno, uses molecular features to accurately identify disease-causing and cancer driver mutations, aiding targeted therapy development.

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Next Generation Sequencing for the Detection of Actionable Mutations in Solid and Liquid Tumors

Next Generation Sequencing for the Detection of Actionable Mutations in Solid and Liquid Tumors

Published on: September 20, 2016

Area of Science:

Genetics
Molecular Biology
Bioinformatics

Background:

Missense mutations are key contributors to inherited diseases and cancer.
Accurately predicting their functional impact, especially for cancer driver mutations, is difficult due to limited data and complex oncogenesis.
Understanding variant classes like pathogenic, benign, driver, and passenger mutations is crucial.

Purpose of the Study:

To systematically characterize missense variants using molecular features.
To develop an interpretable framework (MutaPheno) for predicting missense mutation functional consequences.
To assess MutaPheno's performance against existing tools for cancer driver mutation prediction.

Main Methods:

Systematic characterization of over 120,000 missense variants across multiple classes.
Utilized a comprehensive set of 34 mechanistically grounded molecular features (structural, functional, physicochemical, contextual).
Developed MutaPheno using a random forest algorithm, trained on pathogenic and benign variants.

Main Results:

Molecular features effectively discriminate between diverse variant classes, showing enrichment in pathogenic and driver mutations.
MutaPheno accurately predicts cancer driver mutations, outperforming other tools.
The model demonstrates robustness when tested on novel proteins.

Conclusions:

Shared molecular mechanisms exist between pathogenic and driver mutations.
Molecular features are vital for improving missense variant interpretation.
MutaPheno offers a transparent and generalizable tool for driver discovery and targeted therapy development.