The amount of information released more than doubles the volume of high-coverage, whole genome data currently available from all human genome sources combined. This information is valuable not just to cancer researchers, but also to scientists studying almost any disease. The release of this data was announced as a part of a perspective published on 29 May 2012 in Nature Genetics online.
Whole genome data from hundreds patients exceeds volume of all other sources combined
The 520 genome sequences released are matched sets of normal and tumour tissue samples from 260 paediatric cancer patients. The Paediatric Cancer Genome Project is expected to sequence more than 1200 genomes by year’s end. Each sample is sequenced at a quality control level known as 30-fold coverage, ensuring maximum accuracy. St. Jude researchers are analysing the genomic sequences to determine the differences between each child’s normal and cancerous cells to pinpoint the causes of more than a half-dozen of the most deadly childhood cancers, an effort which has already produced a number of key discoveries reported in top scientific journals.
Dr James Downing, St. Jude scientific director who leads the project at St. Jude, said that they want to make this information available to the broader scientific community so that, collectively, researchers can explore new treatment options for these children. By sharing the information even before they analyse it themselves, they are hoping that other researchers can use this rich resource for insights into many other types of diseases in children and adults.
Launched in early 2010, the Paediatric Cancer Genome Project is the world’s largest effort and investment to date to understand the genetic origins of childhood cancers. The three-year project will cost an estimated 65 million USD. St. Jude is covering 55 million USD of the cost, including a 20 million USD commitment from Kay Jewelers, a long-standing partner of St. Jude. This is the first major privately funded human genome sequencing project to share its data as soon as it becomes available. To date, this type of open access has largely been restricted to government-funded efforts. Non-government efforts are typically treated as proprietary.
Researchers worldwide will be able to access the sequence data via the Web-based European Genome-Phenome Archive, which provides large datasets for free access by researchers on request.
Marked differences between paediatric and adult cancers
While most cancer genome initiatives focus only on genes, which make up a small portion of the genome, the Paediatric Cancer Genome Project researchers have taken a different approach. They are sequencing the entire genome – all the DNA – in each patient’s tumour. This provides a richer, more complete picture of the DNA changes underlying the development and progression of each patient’s disease.
According to Richard Wilson, PhD, director of The Genome Institute at Washington University School of Medicine in St. Louis, this approach has been more valuable than anyone could have predicted. They have identified unusual, ’cryptic’ changes in many patients’ cancer cells that they would not have found using other methods.
The Paediatric Cancer Genome Project has already yielded significant insights into aggressive childhood cancers of the retina, brainstem and blood published in leading international scientific journals. Project researchers working on the retinoblastoma discovered clues to the tumour’s rapid development that enabled them identify a promising new anti-cancer agent. Investigators studying an early T-precursor acute lymphoblastic leukaemia (ETP-ALL) found unexpected genetic alterations that could change diagnosis and treatment for patients with this disease. Efforts to understand the genetic changes underlying a brainstem tumour, diffuse intrinsic pontine glioma, found that a startling 78% of the tumours carried changes in two genes not previously tied to cancer. Most recently, project researchers identified a gene mutation associated with a chronic and often fatal form of neuroblastoma—a discovery that provides the first clue about the genetic basis of the long-recognised but poorly understood link between treatment outcome and age at diagnosis.
These findings would not have been possible without the Paediatric Cancer Genome Project. These results offer new strategies for finding and treating these high-risk cancers. The project has also demonstrated the marked differences between paediatric and adult cancers, underscoring the importance of developing therapies specifically for childhood cancers.