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Genome Research Studies on Primate Evolution, Gene Fusions, Expression Prediction

Investigators at the University of Paris and the University of Montreal point to positive selection for cognition-related genes in the brain during primate evolution. By bringing together conservation, central nervous system expression, selection, and other data for nearly 11,700 orthologous genes in modern humans, archaic humans, and other primates, the team saw pronounced conservation for protein-coding genes involved in human brain function, along with signs of positive selection on genes suspected of contributing to human cognition. While gene conservation "applied to genes functionally associated with the synapse and expressed in brain structures such as the prefrontal cortex and the cerebellum," the authors write, "several genes presenting signatures commonly associated with positive selection appear as causing brain diseases or conditions, such as micro/macrocephaly, Joubert syndrome, dyslexia, and autism."

A German team describes an algorithm known as Arriba, designed for picking up gene fusions based on RNA-sequencing data. After benchmarking the algorithm and comparing it with half a dozen other fusion detection algorithms, the researchers applied Arriba to available RNA-seq profiles for more than 800 pancreatic cancer samples, uncovering apparent driver fusions involving genes such as ALK, BRAF, and ROS1. Those fusions appeared to be particularly common in pancreatic tumors with wild type versions of the KRAS gene, the authors report, and included potential therapeutic targets. "In view of the therapeutic relevance of these fusions and the overall high incidence of oncogenic fusions in KRAS wild-type pancreatic tumors," they note, "we recommend systematic testing of the KRAS mutation status and screening for gene fusions in the absence of KRAS mutations."

Finally, researchers from Johns Hopkins University explore ties between mitochondrial DNA copy number changes and gene expression in tissue samples from hundreds of individuals, uncovering mtDNA copy number features neurodegenerative disease traits. The team analyzed copy number and expression data generated for dozens tissue types in 419 participants in the Genotype-Tissue Expression project, leading to 700 genes with expression profiles linked to mtDNA copy number in whole blood and additional associations between mtDNA copy number (mtDNA-CN) and expression in 30 more tissue types. "Neurodegenerative disease pathways were significantly associated in multiple tissues, and in an independent data set, the UK Biobank, we observed that higher mtDNA-CN was significantly associated with lower rates of both prevalent … and incident neurodegenerative disease," the authors report, noting that results so far hint that "blood-derived mtDNA-CN can reflect metabolic health across multiple tissues."