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Supercomputing reveals the genetic code of cancer

Cancer researchers must use one of the world’s fastest computers to detect which versions of genes are only found in cancer cells. Every form of cancer, even every tumour, has its own distinct variants.

“This charting may help tailor the treatment to each patient,” says Associate Professor Rolf Skotheim, who is affiliated with the Centre for Cancer Biomedicine and the Research Group for Biomedical Informatics at the University of Oslo in Norway, as well as the Department of Molecular Oncology at Radiumhospitalet, Oslo University Hospital.

His research group is working to identify the genes that cause bowel and prostate cancer, which are both common diseases. There are 4,000 new cases of bowel cancer in Norway every year. Only six out of ten patients survive the first five years. Prostate cancer affects 5,000 Norwegians every year. Nine out of ten survive.

Comparisons between healthy and diseased cells

In order to identify the genes that lead to cancer, Skotheim and his research group are comparing the genetic material in tumours with the genetic material in healthy cells. In order to understand this process, a fast introduction to our genetic material is needed.

Our genetic material consists of just over 20,000 genes. Each gene consists of thousands of base pairs, represented by a specific sequence of the four building blocks adenine, thymine, guanine, and cytosine, popularly abbreviated to A, T, G, and C. The sequence of these building blocks is the very recipe for the gene. Our whole DNA consists of some six billion base pairs.

The DNA strand carries the molecular instructions for activity in the cells. In other words, DNA contains the recipe for proteins, which perform the tasks in the cells. DNA, nevertheless, does not actually produce proteins. First a copy of DNA is made. This transcript is called RNA, and it is this molecule that is read when proteins are produced.

RNA is only a small component of DNA, and is made up of its active constituents. Most of DNA is inactive. Only 1-2 % of the DNA strand is active.

In cancer cells, something goes wrong with the RNA-transcription. There is either too much RNA, which means that far too many proteins of a specific type are formed, or the composition of base pairs in RNA is wrong. The latter is precisely the area being studied by the UiO researchers.

Wrong combinatorics

All genes can be divided into active and inactive parts. A single gene may consist of tens of active stretches of nucleotides (exons).