Summary
A major unanswered question in neuroscience is whether there exists genomic variability between individual neurons of the brain, contributing to functional diversity or to an unexplained burden of neurological disease. To address this question, we developed a method to amplify genomes of single neurons from human brains. Since recent reports suggest frequent LINE-1 (L1) retrotransposition in human brains, we performed genome-wide L1 insertion profiling of 300 single neurons from cerebral cortex and caudate nucleus of 3 normal individuals, recovering >80% of germline insertions from single neurons. While we find somatic L1 insertions, we estimate <0.6 unique somatic insertions per neuron and most neurons lack detectable somatic insertions, suggesting that L1 is not a major generator of neuronal diversity in cortex and caudate. We then genotyped single cortical cells to characterize the mosaicism of a somatic AKT3 mutation identified in a child with hemimegalencephaly. Single-neuron sequencing allows systematic assessment of genomic diversity in the human brain.
Summary
Somatic mutations occur during brain development and are increasingly
implicated as a cause of neurogenetic disease. However, the patterns in which
somatic mutations distribute in the human brain are unknown. We used
high-coverage whole-genome sequencing of single neurons from a normal individual
to identify spontaneous somatic mutations as clonal marks to track cell lineages
in human brain. Somatic mutation analyses in >30 locations throughout the
nervous system identified multiple lineages and sub-lineages of cells marked by
different LINE-1 (L1) retrotransposition events and subsequent mutation of
poly-A microsatellites within L1. One clone contained thousands of cells limited
to the left middle frontal gyrus, whereas a second distinct clone contained
millions of cells distributed over the entire left hemisphere. These patterns
mirror known somatic mutation disorders of brain development, and suggest that
focally distributed mutations are also prevalent in normal brains. Single-cell
analysis of somatic mutation enables tracing of cell lineage clones in human
brain.
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