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Tomàs Marquès-Bonet, Alejandro Valenzuela, David Juan, Esther Lizano and Arcadi Navarro. Credit: IBE and UPF.

The most complete catalogue of primate DNA ever produced opens new lines of study of human disease

Researchers from the Institute of Evolutionary Biology (IBE), Pompeu Fabra University (UPF), Illumina and Baylor College of Medicine have published in the journal Science the genome of more than 800 individuals from 233 species of primates from around the world, the largest sequencing ever produced of this species. 80% of the genomes in the project have been sequenced at the National Centre for Genomic Analysis (CNAG-CRG), located at the Barcelona Science Park. The study can help identify genetic causes of human diseases.

The new work has sequenced the genome of 233 species of primates, nearly half of all existing species. Combined with the study of fossil remains, this multiplies by four the number of primate genomes available to date. From these genomes, the new work has identified 4.3 million mutations that will be used for comparative studies with human variants and to identify those key variants in many human diseases for which the genetic causes are currently unknown.

This information has enabled the creation of a new artificial intelligence algorithm with clinical applications to identify new ideas about the genetic causes of human disease through the genomic data of primates. The new algorithm, called PrimateAI-3D and developed by Illumina, is a kind of ChatGPT for genetics that uses genome sequences instead of human language.

8 out of every 10 genomes in the study have been sequenced at the CNAG-CRG, which offers the latest generation methods from the Barcelona Science Park for massive parallel sequencing and data analysis. “This project has been one of the most important we have worked on in the last few years at CNAG. We have developed a new sequencing methodology, analysing more than 600 primate genomes. No doubt, a key study that has enabled us to obtain a more complete vision of the genetic variation of primates and also of the human genome”, explains Ivo Gut, director of the CNAG-CRG.

The study provides new information on the genetic diversity and phylogeny of primates. “Humans are primates,” reminds Tomàs Marquès-Bonet, ICREA researcher at IBE and CNAG, Professor of Genetics at UPF and one of the co-leaders of the study, “the study of hundreds of non-human primate genomes, given their phylogenetic position, is highly valuable for human evolutionary studies, to better understand the human genome and the bases of our singularity, including the bases of human diseases, and for their future conservation.”

The project has been published in one of the new special editions of the journal Science directed from Spain. Among other conclusions, the project has halved the number of genomic innovations that were thought to be exclusively human. This helps identify mutations that are not shared with primates that may be exclusive to human evolution and the characteristics that make us human. The studies also indicate that the genetics of primates does not always correspond to their taxonomy, and that during the evolution of baboons there have been several episodes of hybridisation and gene flow between species that had not been previously recognised.

 » Reference articles:

Kuderna, L.F.K et al. “A global catalog of whole-genome diversity from 233 primate species”. Science (2023). DOI: 10.1126/science.abn7829

Sorensen, E, et al. “Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons”. Science (2023). DOI: 10.1126/science.abn8153

Gao, H, et al. “The landscape of tolerated genetic variation in humans and primates”. Science (2023). DOI: 10.1126/science.abn8197

» Link to the news: CNAG website [+]