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Nature Papers on Goal of Human Pangenome Reference Consortium, Cycas Panzhihuaensis Genome, More

The Human Pangenome Reference Consortium, an international alliance of researchers aiming to build a reference genome that reflects human diversity, lays out its mission in Nature this week. In its piece, the consortium members highlight the lack of diversity within the existing human reference genome — currently a linear composite of merged haplotypes from more than 20 people, with a single individual comprising most of the sequence — and cite the need for a "more sophisticated and complete human reference genome with a graph-based, telomere-to-telomere representation of global genomic diversity." To achieve this, the group said it will work with scientists and bioethicists across the world to create a human pangenome reference and resource that represents genomic diversity across human populations. It will also work to improve assembly technology and develop an ecosystem of tools for analyses of graph-based genome sequences. Such a resource, they say, will "contain a more accurate and diverse representation of global genomic variation, improve gene-disease association studies across populations, expand the scope of genomics research to the most repetitive and polymorphic regions of the genome, and serve as the ultimate genetic resource for future biomedical research and precision medicine."

The reference genome for Cycas panzhihuaensis, a member of one of the most ancient lineages of living seed plants and the last major lineage of such plants for which a high-quality genome assembly was lacking, is presented in Nature Plants this week. Built by a team led by scientists from the Chinese Academy of Sciences, the assembly "closes an important gap in our understanding of genome structure and evolution in seed plants" and enables comparative genomics and phylogenomic analyses that could help "unravel the genetic control of important traits in cycads and other gymnosperms."

A study linking a gut microbial metabolite to colorectal cancer (CRC) progression is published in Nature Metabolism this week, adding to the body of data linking the microbiome to the disease. While it is known that different gut-derived bacteria can induce tumor growth, the crosstalk between the gut microbiome and the host in relation to tumor cell metabolism remains largely unexplored. To investigate, a group led by researchers from the University of Luxembourg used RNA sequencing to analyze stool samples from CRC patients and healthy individuals, finding elevated levels of Fusobacterium nucleatum among cancer patients. Additional analysis revealed that formate, a metabolite produced by the bacterium, promoted tumor development. The scientists also identify molecular signatures linking CRC phenotypes with Fusobacterium abundance and show that treating mice with either the bacterium or the metabolite leads to increased tumor incidence or size.

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The Scan

Cancer Survival Linked to Mutational Burden in Pan-Cancer Analysis

A pan-cancer paper appearing in JCO Precision Oncology suggests tumor mutation patterns provide clues for predicting cancer survival that are independent of other prognostic factors.

Australian Survey Points to Public Support for Genetic Risk Disclosure in Relatives of At-Risk Individuals

A survey in the European Journal of Human Genetics suggests most adult Australians are in favor of finding out if a relative tests positive for a medically actionable genetic variant.

Study Links Evolution of Stony Coral Skeleton to Bicarbonate Transporter Gene

A PNAS paper focuses on a skeleton-related bicarbonate transporter gene introduced to stony coral ancestors by tandem duplication.

Hormone-Based Gene Therapy to Sterilize Domestic Cat

A new paper in Nature Communication suggests that gene therapy could be a safer alternative to spaying domestic cats.