Research Highlights

Algorithm estimates cancerous epigenetic changes

Published online 27 September 2013

Biplab Das

Inside the nucleus of a cell, DNA is wrapped around proteins known as histones within the structure of chromosomes. Enzymes can aberrantly modify these histones, silencing certain genes that produce proteins that suppress cancer. Now, an international research team has devised a computer-based model that can detect histone modifications in chromosomes of cancer cells, publishing their results in Bioinformatics1.

The model, known as Histone Modifications in Cancer (HMCan), is an algorithm that analyses and identifies histone modifications. It is used to estimate copy number alterations of genes in the genome of cancer cells using data from ChIP sequencing (ChIP-Seq), a method that analyses interactions between proteins and DNA.

To test the efficacy of HMCan, the researchers from King Abdullah University of Science and Technology (KAUST), in Thuwal, Saudi Arabia, and the Curie Institute in Paris and Mines ParisTech, compared it with three other tools already used to analyze data in normal genomes. HMCan was able to detect signs of histone modifications in simulated cancer genomes better than all three tools.

They then tested HMCan on cultured human bladder cancer cells, where it "provided better results than the three tools in identifying histone modifications," says study co-author Valentina Boeva.

This may allow physicians to detect histone modification, which could be useful in designing anticancer drugs to undo these cancerous changes.


  1. Ashoor, H. et al. HMCan: a method for detecting chromatin modifications in cancer samples using ChIP-seq data. Bioinformatics (2013) doi:10.1093/bioinformatics/btt524