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Genome Biology Papers Include Giant Panda Chromosome Clues, Healthy Tissue Mutation Patterns

Researchers from the Chinese Academy of Sciences and the Wellcome Sanger Institute present a chromosome evolution analysis of the giant panda, centered on a new 2.3 billion base, chromosome-level genome generated for a male panda from a Beijing zoo with the help of 10x Genomics linked reads. By comparing the giant panda genome to available dog and cat genomes, for example, the team was able to identify breakpoint similarities and differences between the animals. Among them: evolutionary breakpoint regions falling near smell genes or pathways in each of the animals, as well as a rearrangement and pseudogene near another evolutionary breakpoint that may have altered cats' ability to enjoy sweets. 

A team from Sweden and Spain takes a look at the somatic mutations that arise in healthy adult tissues. After clonally expanding normal cells from six healthy donor biopsies — focusing on kidney tubule, epidermis, sub-cutaneous and visceral fat — the researchers used sequencing to search for tissue-specific somatic mutation signatures. Together with available sequence data from healthy and cancer-affected tissues, the analysis highlighted a potentially risky mutation signature in a kidney proximal tubule population, the authors report., noting that "the "unique pattern is characterized by [a] high rate of mutation accumulation during adult life and specific targeting of expressed genes and regulatory regions."

For their own analysis of somatic mutations in healthy tissues, researchers from Stanford University turn to available transcriptomic data spanning three dozen healthy tissue types. Based on RNA sequence data on 7,584 samples from nearly 550 seemingly healthy participants in the dbGAP GTEx project, that team unearthed almost 281,000 mutations, including tissue-specific alterations that seem to influence gene expression and regulation. "Our findings paint a complex landscape of somatic mutation across the human body, highlighting their tissue-specific distributions and functional associations," they write, explaining that the "prevalence of cancer mutations and positive selection of cancer driver genes in non-diseased tissues suggests the possibility of a poised pre-cancerous state, which could also contribute to aging."

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