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DNA-GPS: A theoretical framework for optics-free spatial genomics and synthesis of current methods.
Greenstreet, Laura; Afanassiev, Anton; Kijima, Yusuke; Heitz, Matthieu; Ishiguro, Soh; King, Samuel; Yachie, Nozomu; Schiebinger, Geoffrey.
Afiliação
  • Greenstreet L; Department of Mathematics, The University of British Columbia, Vancouver, BC, Canada.
  • Afanassiev A; Department of Mathematics, The University of British Columbia, Vancouver, BC, Canada.
  • Kijima Y; School of Biomedical Engineering, The University of British Columbia, Vancouver, BC, Canada; Department of Aquatic Bioscience, The University of Tokyo, Tokyo, Japan.
  • Heitz M; Department of Mathematics, The University of British Columbia, Vancouver, BC, Canada.
  • Ishiguro S; School of Biomedical Engineering, The University of British Columbia, Vancouver, BC, Canada.
  • King S; School of Biomedical Engineering, The University of British Columbia, Vancouver, BC, Canada.
  • Yachie N; School of Biomedical Engineering, The University of British Columbia, Vancouver, BC, Canada; Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan; Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), Osaka University, Suita, Osaka, Japan; Graduat
  • Schiebinger G; Department of Mathematics, The University of British Columbia, Vancouver, BC, Canada; School of Biomedical Engineering, The University of British Columbia, Vancouver, BC, Canada. Electronic address: geoff@math.ubc.ca.
Cell Syst ; 14(10): 844-859.e4, 2023 10 18.
Article em En | MEDLINE | ID: mdl-37751737
While single-cell sequencing technologies provide unprecedented insights into genomic profiles at the cellular level, they lose the spatial context of cells. Over the past decade, diverse spatial transcriptomics and multi-omics technologies have been developed to analyze molecular profiles of tissues. In this article, we categorize current spatial genomics technologies into three classes: optical imaging, positional indexing, and mathematical cartography. We discuss trade-offs in resolution and scale, identify limitations, and highlight synergies between existing single-cell and spatial genomics methods. Further, we propose DNA-GPS (global positioning system), a theoretical framework for large-scale optics-free spatial genomics that combines ideas from mathematical cartography and positional indexing. DNA-GPS has the potential to achieve scalable spatial genomics for multiple measurement modalities, and by eliminating the need for optical measurement, it has the potential to position cells in three-dimensions (3D).
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Perfilação da Expressão Gênica / Genômica Idioma: En Revista: Cell Syst Ano de publicação: 2023 Tipo de documento: Article País de afiliação: Canadá País de publicação: Estados Unidos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Perfilação da Expressão Gênica / Genômica Idioma: En Revista: Cell Syst Ano de publicação: 2023 Tipo de documento: Article País de afiliação: Canadá País de publicação: Estados Unidos