Fluorescence-activated cell or nuclei sorting (FACS/FANS) can be used to isolate specific neural populations (e.g., NeuN+ neurons versus NeuN− cells or cortical inhibitory interneurons versus excitatory principal neurons). Analysis of sorted nuclei populations (e.g., 5000 or 500,000 cells) from specific brain regions increases the power to detect somatic mosaicism that arises in one lineage, because these genomes are no longer diluted by genomes derived from other lineages. Independent pools of sorted nuclei can then be subjected to RNA sequencing (RNA-seq) and quantitative reverse transcription polymerase chain reaction (qRT-PCR) to confirm cell type–specific gene expression profiles (75). In addition to increasing the power for detecting a somatic mutation, cell sorting before DNA extraction could yield information about the embryological origin and developmental trajectory of somatic variation across the brain. Large pools of sorted cells can yield enough DNA for the direct examination of somatic variants by WGS or WES. However, smaller pool sizes will only generate small amounts of DNA; thus, they are best suited for generating PCR amplicon libraries (e.g., as used in MEI detection and other targeted sequencing) or for subsequent whole-genome amplification (WGA).
