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Nature Studies Present Six Bat Genomes, Approach to Prioritize Cells in Single-Cell Analyses, More

Members of the international Bat1K initiative report in Nature this week high-quality reference genomes for six bat species, providing details about a number of the animals' adaptations including ones related to longevity, echolocation, and disease resistance. The researchers combined long-read sequencing and state-of-the-art scaffolding protocols to generate the genomes of Rhinolophus ferrumequinum, Rousettus aegyptiacus, Phyllostomus discolor, Myotis myotis, Pipistrellus kuhlii, and Molossus molossus. In analyzing the genomes, they find evidence of positive selection on hearing-related genes in the ancestral branch of bats, suggesting that laryngeal echolocation was an ancestral trait in this group, and discover a basal origin for bats within the Scrotifera clade of placental mammals. Other discoveries include selection and loss of immunity-related genes and expansions of anti-viral APOBEC3 genes, as well as bat-specific variation in microRNAs, which may regulate bat-specific gene-expression programs.

A method for prioritizing cell types most responsive to biological perturbations in single-cell data is presented in Nature Biotechnology this week. Developed by scientists at the École Polytechnique Fédérale de Lausanne in Switzerland, the technique — called Augur — uses machine learning to quantify the separability of perturbed and unperturbed cells within a high-dimensional space. The investigators validate the method using single-cell RNA sequencing, chromatin accessibility, and imaging transcriptomics datasets, showing that it outperforms existing methods based on differential gene expression.

A blood test that analyzes circulating tumor DNA methylation for the early detection of cancer is reported in Nature Communications this week. Developed by scientists from Fudan University and collaborators, the test — called PanSeer — was evaluated using plasma samples from 605 asymptomatic participants in the Taizhou Longitudinal Study, 191 of whom were diagnosed with stomach, esophageal, colorectal, lung, or liver cancer up to four years later. The researchers also tested plasma samples from an additional 223 cancer patients, plus 200 primary tumor and normal tissues. They show that PanSeer could detect the different cancers in 88 percent of post-diagnosis patients with a specificity of 96 percent. PanSeer also detected cancer in 95 percent of asymptomatic individuals who were later diagnosed. The researchers state that they aim to validate PanSeer in a large prospective study of healthy individuals to establish its clinical utility.