Structural variations in genomes can arise from deleting, amplifying, or reordering genomic segments ranging from a few thousand letters of the genetic code to whole chromosomes. These variations have previously been difficult to classify and catalog due to the complex mechanisms of their formation.
Jan Korbel, group leader at EMBL and one of the initiators and coordinators of the Pan-Cancer project, explains:
In this study we have uncovered and classified different ways by which the cancer genome can rearrange. We performed the first detailed classification of structure variation mechanisms in cancer genomes."
The researchers uncovered several new processes that can lead to cancer, for instance a complex process in which some fractions of the genome are duplicated more than once. This can lead to cancer genes becoming active, because they are copied in high number and then brought to a region in which they can be switched on. Linking events to mutations
"Most previous studies have been conducted on the coding 1-2% of the genome," says Joachim Weischenfeldt, group leader in the Biotech Research & Innovation Centre in Copenhagen and a former postdoc in EMBL's Korbel group. "Structural variations have been largely ignored, because most of them are situated in the non-coding part of the genome and are much more complex to comprehend."
Along with colleagues Weischenfeldt developed methods to identify structural variants and the mechanisms of their formation by performing a whole genome sequencing analysis on the Pan-Cancer data. "This paper is one of the first ones to systematically classify very complex types of structural variants that occur in cancer genomes and link them to mechanisms of formation," says Weischenfeldt. "It now gives us a handle to distinguish the different types of structural variants that occur in cancer genomes. We can potentially use these as biomarkers in different cancers, because mutations in certain very potent driver genes give rise to specific types of structural variants." Biomarkers are biological indicators, such as specific molecules or genetic sequences, that can be used to identify certain conditions - in this case cancer. Related Stories
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