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Some of the most harmful genetic changes in cancer are also the hardest to see. These structural alterations, deep within a tumor’s DNA, can fuel aggressive growth and evade standard testing, especially when tissue samples are small or degraded.<\/p>\n
To address this challenge, Mayo Clinic researchers have developed a new computational tool called BACDAC that shines a light on these elusive genomic patterns. The tool helps researchers identify signs of genomic instability using DNA sequencing that reads the entire genome<\/a>, even in low-purity or low-coverage samples.<\/p>\n The tool could help clinicians better predict how a tumor will behave and guide more personalized treatment choices.<\/p>\n Detecting chromosome changes<\/p>\n At the core of BACDAC’s approach is the concept of ploidy, which refers to the number of complete sets of chromosomes in a cell. While normal human cells have two sets (46 chromosomes total), cancer cells<\/a> often show large-scale gains or losses, disrupting this balance and enabling unchecked growth.<\/p>\n In a study published<\/a> in Genome Biology, the research team used BACDAC to analyze more than 650 tumors across 12 cancer types. The tool helped researchers detect signs of whole-genome doubling, where a tumor duplicates all of its DNA. This type of abnormal ploidy is often linked to aggressive behavior<\/a> and treatment resistance.<\/p>\n “This tool lets us see a layer of the genome that’s been invisible until now,” says George Vasmatzis, Ph.D., a lead author of the study and co-director of Mayo Clinic’s Biomarker Discovery Program. “We’ve spent decades studying the biology of genomic instability. This is the first time we’ve been able to translate that knowledge into a tool that works at scale.”<\/p>\n BACDAC also provides a visual summary of a tumor’s genomic landscape. A custom output called the Constellation Plot offers an intuitive view of whether the tumor’s chromosomes are stable or disrupted. This may help researchers and pathologists interpret results more easily.<\/p>\n Next, the Mayo Clinic team plans to further validate BACDAC and develop it into a clinically deployable diagnostic tool. It may help inform treatment decisions by providing a clearer view of a tumor’s structural changes.<\/p>\n