Structural genetic variants, from detection to phenotype

Articles

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  Global DNA methylation differences involving germline structural variation impact gene expression in pediatric brain tumors

  The role of germline variation in cancer remains underexplored. Here, the authors investigate the landscape of germline structural variants on tumour DNA methylation across pediatric brain and central nervous system tumour patients and suggest disease implications.

  • Fengju Chen
  • Yiqun Zhang
  • Chad J. Creighton

  ArticleOpen Access21 May 2025 Nature Communications
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  Long-read sequencing of 945 Han individuals identifies structural variants associated with phenotypic diversity and disease susceptibility

  Genetic studies of Chinese individuals have been performed, but mostly with short read sequencing, limiting the types of variants that can be identified. Here, the authors perform long read sequencing of 945 han Chinese individuals, finding structural variants under natural selection and those associated with human traits and evolutionary history.

  • Jiao Gong
  • Huiru Sun
  • Shaohua Fan

  ArticleOpen Access10 Feb 2025 Nature Communications
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  3D genome landscape of primary and metastatic colorectal carcinoma reveals the regulatory mechanism of tumorigenic and metastatic gene expression

  Multi-omics profiling of matched normal colon, primary tumor, and liver metastasis from colorectal carcinoma patients based on Hi-C, ATAC-seq and RNA-seq technologies sheds light on the changes and regulatory mechanisms of 3D genomics during the tumorigenesis and metastasis of colorectal carcinoma.

  • Xiang Xu
  • Jingbo Gan
  • Jin Gu

  ArticleOpen Access4 Mar 2025 Communications Biology
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  Common mitochondrial deletions in RNA-Seq: evaluation of bulk, single-cell, and spatial transcriptomic datasets

  A methods application study demonstrates that the Splice-Break2 pipeline can detect large mitochondrial DNA deletions in RNA-Seq data. Analyses includes GTEx and GEO datasets and demonstrate differences across tissues, brain regions, and age.

  • Audrey A. Omidsalar
  • Carmel G. McCullough
  • Brooke E. Hjelm

  ArticleOpen Access17 Feb 2024 Communications Biology