A study comparing the performance of five circulating tumor DNA (ctDNA) sequencing assays is presented in Nature Biotechnology this week, providing a resource for precision oncology decision making. In the report, members of the international SEQC2 Oncopanel Sequencing Working Group evaluated hybrid capture assays from Roche Sequencing Solutions, Illumina, Integrated DNA Technologies, and Burning Rock Dx and an amplicon sequencing panel from Thermo Fisher Scientific. While all the assays detected ctDNA mutations with high sensitivity, precision, and reproducibility above 0.5 percent variant allele frequency, "below this limit, detection became unreliable and varied widely between assays, especially when input material was limited," the study's authors write. "Missed mutations were more common than erroneous candidates, indicating that the reliable sampling of rare ctDNA fragments is the key challenge for ctDNA assays." The work, they add, helps lay an analytical framework for standardized proficiency testing on ctDNA assays.
By resequencing hundreds of lettuce accessions, a team led by scientists from BGI-Shenzhen have uncovered new details about the domestication of this key vegetable crop. In the study, which appears in Nature Genetics, the researchers resequenced 445 Lactuca sativa accessions, including major lettuce crop types and wild relative species, to generate a comprehensive map of lettuce genome variations. They use this map to analyze population structure and demography, finding that lettuce was first domesticated near the Caucasus with the loss of seed shattering marking a key milestone in the domestication process. They also identify the genetics underlying other key domestication traits and wild introgressions in major resistance clusters in the plant's genome.
A genomic analysis of Pacific region populations is published in Nature this week, offering new details about human evolution, archaic hominin interactions, and natural selection processes at work in island environments. A team led by Institut Pasteur investigators analyzed the genomes of 317 individuals from 20 populations from the Pacific region. They find that the ancestors of Papuan-related groups underwent a strong bottleneck before the settlement of the region, eventually separating around 20,000 to 40,000 years ago. Then, following the arrival of Taiwanese Indigenous peoples around 5,000 years ago, there were recurrent episodes of genetic interactions with the Near Oceanian populations. Other findings include evidence of DNA in Pacific populations from both Neanderthals and Denisovans, including genes related to the immune system.