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Big Data analysis identifies new cancer risk genes Posted on Jul 10 - 2018

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There are many genetic causes of cancer: while some mutations are inherited from your parents, others are acquired all throughout your life due to external factors or due to mistakes in copying DNA. Large-scale genome sequencing has revolutionised the identification of cancers driven by the latter group of mutations - somatic mutations - but it has not been as effective in the identification of the inherited genetic variants that predispose to cancer. The main source for identifying these inherited mutations is still family studies.

Now, three researchers at the Centre for Genomic Regulation (CRG) in Barcelona, led by the ICREA Research Professor Ben Lehner, have developed a new statistical method to identify cancer predisposition genes from tumour sequencing data. "Our computational method uses an old idea that cancer genes often require 'two hits' before they cause cancer. We developed a method that allows us to systematically identify these genes from existing cancer genome datasets" explains Solip Park, first author of the study and Juan de la Cierva postdoctoral researcher at the CRG.

The method allows researchers to find risk variants without a control sample, meaning that they do not need to compare cancer patients to groups of healthy people, "Now we have a powerful tool to detect new cancer predisposition genes and, consequently, to contribute to improving cancer diagnosis and prevention in the future," adds Park.

The work, which is published in Nature Communications, presents their statistical method ALFRED and identifies 13 candidate cancer predisposition genes, of which 10 are new. "We applied our method to the genome sequences of more than 10,000 cancer patients with 30 different tumour types and identified known and new possible cancer predisposition genes that have the potential to contribute substantially to cancer risk," says Ben Lehner, principal investigator of the study.

"Our results show that the new cancer predisposition genes may have an important role in many types of cancer. For example, they were associated with 14% of ovarian tumours, 7% of breast tumours and to about 1 in 50 of all cancers. For example, inherited variants in one of the newly-proposed risk genes - NSD1 - may be implicated in at least 3 out of 1,000 cancer patients." explains Fran Supek, CRG alumnus and currently group leader of the Genome Data Science laboratory at the Institute for Reseach in Biomedicine (IRB Barcelona). View More

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