"Big Data" and a supercomputer used to create a new Pathology Atlas for cancer researchers

Personalised medicine requires in-depth knowledge of genetic and metabolic processes in cancers in order to discover techniques to attack specific cancers.

Swedish researchers at the KTH Royal Institute of Technology have recently published a new Pathology Atlas that contains an analysis of all human genes in most major cancers showing the consequence of their corresponding protein levels for overall patient survival. The Atlas is based on the analysis of 17 main cancer types using data from 8,000 patients.

A national supercomputer centre was used to analyse more than 2.5 petabytes of underlying publicly available data from the Cancer Genome Atlas (TCGA) to generate more than 900,000 survival plots describing the consequence of RNA and protein levels on clinical survival. Professor Mathias Uhlen, Director of the Human Protein Atlas consortium and leader of the Pathology Atlas effort says: "This study differs from earlier cancer investigations, since it is not focused on the mutations in cancers, but the downstream effects of such mutations across all protein-coding genes.

The research was published in the prestigious journal Science. Some of the important findings of the research were that a large fraction of genes is differentially expressed in cancers -- and in many cases -- have an impact on overall patient survival. The research also showed that gene expression patterns of individual tumours varied considerably, and could exceed the variation observed between different cancer types. Shorter patient survival was generally associated with up-regulation of genes involved in mitosis and cell growth, and down-regulation of genes involved in cellular differentiation. The data allowed the researchers to generate personalised genome-scale metabolic models for cancer patients to identify key genes involved in tumour growth.

Fredrik Ponten, Professor in Pathology of Uppsala University said, "we are pleased to provide a stand-alone open-access resource for cancer researchers worldwide, which we hope will help accelerate their efforts to find the biomarkers needed to develop personalised cancer treatments."

Further reading:
Science - journal abstract
Science Daily - summary
 



« Back to News
"Big Data" and a supercomputer used to create a new Pathology Atlas for cancer researchers Latest "Big Data" and a supercomputer used to create a new Pathology Atlas for cancer researchers RSS