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Science Studies Describe Approach to Improve Detection of Circulating Tumor DNA, Emergence of Measles Virus

The ability to detect low levels of circulating tumor DNA (ctDNA) can be significantly improved by first analyzing mutations identified through tumor genotyping, according to a new study in Science Translational Medicine. While ctDNA has proven useful for noninvasive cancer monitoring, detecting this genetic material in patients with low-volume or residual disease remains challenging. To address this issue, a team led by University of Cambridge scientists developed a pipeline — called integration of variant reads, or INVAR — that combines custom error-suppression methods and signal-enrichment approaches based on biological features of ctDNA. Using this method, the investigators write, the detection limit in each sample can be estimated independently based on the number of informative reads sequenced across multiple patient-specific loci. Using 176 plasma samples from 105 patients with melanoma, lung, renal, glioma, and breast cancer across both early and advanced disease, they show INVAR routinely quantified ctDNA to one mutant molecule per 100,000 and, in one case, ctDNA was detected to an integrated mutant allele fraction of 2.5 parts per million. "As tumor tissue sequencing becomes increasingly routine in personalized oncology, patient-specific mutation lists may be increasingly leveraged for individualized monitoring from a variety of sequencing data types for sensitive monitoring," the researchers say.

By comparing the genomes of measles viruses from various time points over the past 100 years, a Robert Koch Institute-led team shows that measles emerged in human populations, likely spilling over from cattle, hundreds of years earlier than previously thought. As they report in Science, the scientists sequenced the genome of a 1912 measles virus using preserved lung samples from infected patients, then compared the findings to the genome of a 1960 measles virus and modern measles genomes. They also analyzed the now-eradicated cattle virus rinderpest, which is the closest relative to measles, and the related PPRV virus. The researchers find that measles potentially arose as early as the sixth century BC, possibly coinciding with the time humans began forming cities large enough to support continuous disease transmission. GenomeWeb has more on this here.