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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.

Microdissection of spatially identified single nuclei in a solid tumor for single cell whole genome sequencing