ArticleGenome medicine2025
Whole-genome sequencing reveals individual and cohort level insights into chromosome 9p syndromes.
Article in Genome medicine, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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8 citing papers in PubMed.
- Optical mapping reveals a higher level of large-scale structural variants in a family with paternally transmitted myotonic dystrophy and independent Parkinson's disease.The Journal of pathology · 2026Article
- Sex-aware genome-wide assessment of de novo variants in autism across coding and noncoding regions.Human genomics · 2026Article
- Prenatal diagnosis of 9p distal deletion associated with subependymal cysts: A case report and literature review.Medicine · 2026Review
- Whole Genome Sequencing Reveals amedRxiv : the preprint server for health sciences · 2026Article
- Multi-omics Differential Inference for Functional Interpretation (MoDIFI): A Statistical Framework to Prioritize Cell Lines for Neurodevelopmental Variants.bioRxiv : the preprint server for biology · 2026Article
- De Novo Variation in Autism by Sex and Diagnostic Status in 41,367 Parent-Child Trios.medRxiv : the preprint server for health sciences · 2026Article
- CNPI: Rapid Analyses of Human Copy Number Data.Journal of molecular biology · 2025Article
- Interferon Epsilon Loss Is Elusive 9p21 Link to Immune-Cold Tumors, Resistant to Immune Checkpoint Therapy, and Endogenous CXCL9/10 Induction.Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer · 2025Review
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Abstract
backgroundPrevious genomic efforts on chromosome 9p deletion and duplication syndromes have utilized low-resolution strategies (i.e., karyotypes, chromosome microarrays). These studies have provided important initial insights into these syndromes. This current study is the first large-scale whole-genome sequencing (WGS) study of 100 individuals from families with chromosome 9p syndromes.
methodsThrough the newly formed 9P-ARCH (Advanced Research in Chromosomal Health: Genomic, Phenotypic, and Functional Aspects of 9p-Related syndromes) research network, we assembled a cohort of individuals from families with chromosome 9p syndromes. WGS was applied to 100 individuals, and other genomic technologies were applied to a subset of individuals. To prioritize genes on 9p, we utilized two independent approaches: statistical analyses of genomic data and spatial transcriptomic profiling of embryonic mouse tissue. To assess the enrichment of DNVs within genomic regions, we developed a computational tool, DiamondsDenovo ( https://github.com/TNTurnerLab/DiamondsDenovo ).
resultsUnlike previous low-resolution studies, we analyzed the genomic architecture of chromosome 9p syndromes, highlighting fundamental features and their commonalities and differences across individuals. A machine-learning model was developed to predict 9p deletion syndrome based on gene copy number estimates using WGS data. We identified two late-replicating regions containing most structural variant breakpoints in 9p deletion syndrome, pointing to replication-based issues as a potential cause of structural variant formation in most individuals and structural rearrangements in some individuals. Genes on 9p were prioritized based on statistical assessment of human genomic variation and through spatial transcriptomics, with 24 genes (AK3, BRD10, CD274, CDC37L1, DMRT1, DMRT2, DMRT3, DOCK8, GLIS3, JAK2, KANK1, KDM4C, PLPP6, PTPRD, PUM3, RANBP6, RCL1, RFX3, RIC1, SLC1A1, SMARCA2, UHRF2, VLDLR, and ZNG1A) identified as important for the majority (83%) of individuals with 9p deletion syndrome. Testing of the mitochondrial genome revealed excess copy number in individuals with 9p deletion syndrome.
conclusionsThis study introduces the 9P-ARCH research network that is actively pursuing genomic, phenotypic, and functional aspects of 9p-related syndromes. We advanced the study of 9p-related syndromes both at the individual level and across the cohort through the largest, most comprehensive genomic analysis of 9p-related syndromes to date.
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