Meet a cancer genomicist uncovering the determinants of health disparities in patients with cancer

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In this issue of Cell Genomics, Huguet et al. present an article focused on the interpretation of the effect size of CNVs on cognitive ability across different gene sets related to brain and non-brain functions. The cover image represents this article. The human genomic sequence is depicted in the background, with blue and red parentheses indicating genomic duplications and deletions, respectively. Circles of corresponding colors show which organ-associated gene sets affect cognitive ability when duplicated or deleted. Therefore, the scale depicts the resulting changes of cognitive ability for a given individual, with the left part showing a decreased cognitive ability. Artist credit: Guillaume Huguet and Thomas Renne, authors on this article, jointly produced the conceptual design of this cover, with Guillaume Huguet completing the graphic illustration.

N ⁶-methyladenosine (m6A), the most prevalent internal mRNA modification in higher eukaryotes, plays diverse roles in cellular regulation. By incorporating both sequence- and genome-derived features, Fan et al. designed a novel Transformer-BiGRU framework that achieves superior performance in computational m6A identification, thus demonstrating the potential of AI in genomic studies.

De Jonghe et al. present a comprehensive review of current commercial single-cell and spatial omic technologies, outlining key platforms, methodologies, and trends shaping the field—from microfluidics and plate-based approaches to combinatorial indexing, highlighting their applications in drug discovery. The authors discuss emerging engineering and computational advancements that are enabling more efficient data generation and interpretation. Finally, they explore new tools and techniques that promise to expand the scope of omic analyses, driving innovation and understanding in biomedical research.

Fan et al. devised a hybrid neural network architecture that integrates sequence and genomic features to predict RNA m6A modification sites. This framework significantly enhanced the precision of m6A prediction and enabled the identification of m6A sites at the isoform level.

Chiang et al. used polymer modeling to predict the panoply of 3D structures of all active genes in human lymphoblastoid cells, depositing the information in a database: 3DGene. Mining these data, they showed that the structural diversity of genes is dependent on influential nodes—chromatin sites that frequently interact.

Zhang et al. constructed a comprehensive genome-wide map of VNTR polymorphisms both in length and repeat composition across 8,222 high-coverage genomes, with over 2.5 M VNTR length and 11 M VNTR motif polymorphisms identified. This study will expand our knowledge of VNTR polymorphisms and their functional implications in human genetics.

Yao et al. develop a computational pipeline integrating a robust Mendelian randomization method with AlphaFold3 to select valid pQTL instruments, identify causal protein biomarkers, and predict 3D structural alterations. Seven plasma proteins have been identified as linked to Alzheimer’s disease and may aid future drug development.

Popp et al. generate dozens of cell types from 53 human iPSC lines in order to characterize the dynamic genetic regulation of gene expression across early stages of cellular differentiation. Accessing these understudied contexts can clarify the functional impact of disease loci with unknown mechanisms of action.

Yuan et al. conducted cross-species single-nucleus analyses of transcription and chromatin accessibility of the anterior cingulate cortex (ACC). They discovered novel primate-shared and human-specific VEN marker genes acting on cell morphogenesis during brain development, and they delineated the genetic basis of cellular and functional innovations in the ACC during evolution.

St. Ange et al. provide a single-nucleus RNA sequencing atlas of adult wild-type and IIS mutant Caenorhabditis elegans neurons, identifying genes that turn on from L4 to adulthood, including GPCRs. Functional behavior experiments revealed the roles of genes expressed in single neurons, including previously unidentified IIS targets.

Copy-number variants are major contributors to neurodevelopmental disorders and are associated with lower cognition. Huguet et al. identified a duplication increasing cognitive ability. They highlighted that genes of many biological processes had unbalanced gene-dosage sensitivity toward deletions or duplications for both brain and non-brain functions.

Sadowski et al. propose a framework to study the genetics of response to commonly prescribed drugs in large biobanks. They quantify the heritability of response to statins, metformin, warfarin, and methotrexate, and identify associated genes. Their analysis also shows the importance of accounting for drug use in genetic risk prediction.

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