Chordoma Foundation

Chordoma Genome Project

The Chordoma Genome Project is using the most advanced technologies to systematically reveal all of the genetic changes that drive chordoma and thereby identify new targets for treatment.

Chordoma Genome Project

Overview

All cancers are the result of abnormal changes (“mutations”) in DNA which cause uncontrolled growth of the cells in which the changes occur. Modern cancer drugs target and kill cells that harbor specific cancer-causing mutations, while sparing normal cells that don’t have these mutations. Therefore, knowing what mutations are present in the DNA of a tumor is critical to identifying and/or developing effective treatments.

Recently, powerful technologies have been developed that enable scientists to read  (“sequence”) all of the DNA in a cell (its “genome”), and identify all of the mutations it contains.  The Chordoma Genome Project (CGP) aims to catalog all the mutations present within chordoma in order to provide insight into which genes are responsible for driving the progression of the tumor, and thus how to most rationally and effectively treat it.

Partners

We are funding the Wellcome Trust Sanger Institute in the United Kingtom to analyze the DNA of chordoma tumors. The Sanger Institute is one of the worlds premier cancer genomics research centers and has an extensive track record of identifying cancer-causing mutations in other cancers. Chordoma tumor samples for this project are provided by Dr. Adrienne Flanagan at the University College London.

Open Data Sharing

We believe that disseminating the data generated from this project could enable important discoveries that would not otherwise be possible. Therefore, data is made freely available online so that all scientists interested in chordoma can bring their expertise to bear on this disease. Verified mutation data is accessible from the European Genome Archive.

Progress

Chromothripsis
Chromothripsis, a newly discovered way that cancer can form, was found in approximately 20% of chordomas

The Chordoma Foundation has been sponsoring genomic research on chordoma at the Sanger Institute since 2009. Thus far, over 400 mutations have been identified in several dozen genes, including some genes which fall in pathways that are therapeutically relevant. All of the mutations are being verified though a secondary sequencing method, and analysis is ongoing to determine the significance of the mutations that have been identified.

A Paradigm-shifting Discovery

Results of this project revealed unusual structural changes in the DNA of some chordoma tumors, which helped lead to the discovery of an entirely new way that cancer can form through the shattering of chromosomes – “chromothripsis”. This finding, which overturned conventional thinking about how cancer develops, was published in the journal Cell in January 2011 and was reported in the New York Times. Work to determine the role of chromothripsis in chordoma is ongoing.

Next Steps

The sequencing completed thus far has focused on the 2% of the human genome that contains genes – called the “exome.” The remaining 98% of the genome was once thought to be ‘junk DNA’. However, recent studies have revealed that up to 80% of this previously written-off DNA is actually functional, containing switches that regulate how genes work (see: Far From ‘Junk’, DNA Dark Matter Proves Crucial to Health – New York Times, 9/6/2012). Therefore it is crucial to develop a comprehensive catalogue of all the mutations present in the entire genome of chordoma tumors. The next step of the chordoma genome project will seek to develop this comprehensive catalogue by performing whole genome sequencing on 10 chordoma tumors.