Using next-generation sequencing, researchers found a variant in the human genome that carries a six-fold higher risk for developing some brain tumors—a discovery they say could lead to better diagnosis and treatment of the cancers.
The team of researchers from the University of California, San Francisco, and Mayo Clinic found that the presence of a “G” instead of an “A” at a specific spot in the sequence of patients’ genetic codes was strongly associated with increased risk of certain subtypes of gliomas. Results from the study were published online Sunday in the journal Nature Genetics.
The study began with the research team seeking out regions of the genome that might be associated with glioma development. They observed that a portion of chromosome 8 contained single nucleotide polymorphisms (SNPs) associated with brain tumors.
Researchers centered their search on seven candidates, including the SNP called rs55705857, which confers a relative risk for glioma approaching that observed in changes in the BRCA1 gene for breast cancer. The team found a “highly significant” association between slower growing gliomas and the “G” or guanine version of the SNP, rather than the more common “A” or adenine version.
As part of their work, the team compared the sequence of the gene variant throughout mammalian evolution. They found the variant to have been conserved as far back as the platypus. Computer modeling placed the SNP within the functional part of the microRNA, though the research team is investigating whether the microRNA actually exists and what its functional implications might be.
“The altered microRNA might target tumor suppressor genes, it might activate a cancer gene, it might be involved in regulating the stability of the genome, or there might be something else going on altogether,” said corresponding author Robert Jenkins, MD, Ph.D., professor of laboratory medicine in Mayo’s Department of Laboratory Medicine and Pathology and Division of Laboratory Genetics, in a statement.
Dr. Jenkins co-led the study along with geneticists Margaret Wrensch, Ph.D., and John Wiencke, Ph.D., professors in UCSF’s Department of Neurological Surgery.
Discovery of the variation through next-gen sequencing suggests that easier-to-apply experimental and mathematical methods may miss such rare, highly potent gene variants, the researchers added.
[The study can be read here (subscription required): http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.2388.html, “A low-frequency variant at 8q24.21 is strongly associated with risk of oligodendroglial tumors and astrocytomas with IDH1 or IDH2 mutation.”]