title: Microdissection of spatially identified single nuclei in a solid tumor for single cell whole genome sequencing.
abstract: The relative spatial distribution of cells in a solid tumor contributes to development of malignancy, yet the details of this process remain poorly understood. To elucidate these mechanisms, the ability to extract and analyze the entire DNA content of individual cells whose precise location in the tumor is known is required, yet such methodology has not yet been described. Here we detail a procedure to directly extract complete individual nuclei from fixed-frozen tissue sections using through-focus analysis coupled with laser microdissection, followed by whole genome amplification. We show that this technique is suitable for routine evaluation of genomic variation such as SNP analyses of the specifically selected nuclei. Our method should provide a means for whole genome variation studies of single cells from spatially defined positions within tumor tissues.
authors: Ministry of Education Key Laboratory of Systems Biomedicine.|State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai, P R China.
authors: Yan
authors: Y
authors: Guo
authors: Ministry of Education Key Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, P R China.
authors: Yi
authors: Y
authors: Yang
authors: Ministry of Education Key Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, P R China.
authors: Juan
authors: J
authors: Zhou
authors: Ministry of Education Key Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, P R China.
authors: Daniel M
authors: DM
authors: Czajkowsky
authors: Ministry of Education Key Laboratory of Systems Biomedicine.|Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Shanghai Jiao Tong University, Shanghai, P R China.
authors: Bingya
authors: B
authors: Liu
authors: Ministry of Education Key Laboratory of Systems Biomedicine.|State Key Laboratory of Oncogenes and Related Genes.|Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Shanghai Jiao Tong University, Shanghai, P R China.
authors: Zhifeng
authors: Z
authors: Shao
mesh_terms: D002467:Cell Nucleus / Q000235:genetics*; D016678:Genome / Q000235:genetics*; D006801:Humans; D061346:Laser Capture Microdissection / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D059010:Single-Cell Analysis / Q000379:methods*; D013270:Stomach / Q000737:chemistry / Q000166:cytology; D013274:Stomach Neoplasms / Q000737:chemistry / Q000473:pathology
keywords: isolation; laser microdissection; single nucleus; tissue; whole genome amplification