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The Brain Culls Most of Its Genetically Damaged Neurons Around Birth, a Nature Study Finds

Sequencing 2,357 single neurons from donors aged 14 weeks' gestation to the 90s, Harvard and Boston Children's researchers saw the share with scrambled chromosomes fall from 26 to 6 percent.

Outspoken Digest Science Desk

Friday, October 30, 2026/2 min read

A fluorescence micrograph of a single cortical neuron glowing red against a black background, its cell body at the centre and branching dendrites covered in fine spines, published on 6 April 2017, an illustrative image of a cortical neuron and not from the Nature study
Photo: Sergb95 via Wikimedia Commons (CC BY-SA 4.0)

More than a quarter of the neurons in a developing human cortex carry chromosomes that have gained or lost large chunks of DNA. By the time a baby is born, most of those cells are gone. That is the finding of a study published in Nature on 28 October by researchers at Harvard Medical School and Boston Children's Hospital, who argue the brain runs a quality-control purge around the time of birth.

The team, led by paediatric neurogeneticist Diane Shao with Peter Park and Christopher Walsh as senior authors, sequenced the genomes of 2,357 individual cortical neurons from postmortem donors ranging from fetuses at 14 weeks' gestation to people in their 90s, according to the institutions' release. In prenatal samples an average of 25.9 percent of neurons had widespread copy number variants across several chromosomes, with a range of 12.7 to 46 percent between specimens. In the neonatal period that figure dropped roughly 4.5-fold to about 6.2 percent.

What did the researchers actually measure?

Copy number variants, large deletions or duplications of DNA that arise in a single cell rather than being inherited. Two different single-cell whole-genome sequencing methods were used, one on 1,526 neurons from 16 donors and the other on 831 neurons from 12 donors, and both showed the same post-birth decline. The group also profiled 44,861 nuclei for chromatin accessibility and gene expression. Nature's news report said Shao's team spent years checking the result was real before publishing.

Neurons with heavy CNV burdens tended to show abnormal expression of genes involved in building synapses. The authors' interpretation is that neurons compete for connections as circuits form, and cells carrying damaged genomes lose that contest and are eliminated, roughly in parallel with the wave of programmed cell death already known from animal studies. Walsh said the team was unprepared for how common the damaged cells were in early development.

Why does it matter for autism, epilepsy and ageing?

Because the checkpoint can presumably fail. The surviving neurons were depleted for CNVs hitting dosage-sensitive genes and genes linked to neurodevelopmental disorders, which fits a selection process. If that process is disrupted by genetic or environmental factors, more faulty neurons might persist, and the authors raise childhood-onset conditions such as autism and epilepsy as areas where the finding could eventually matter. Cells with smaller CNV burdens declined more slowly across life, and a small fraction persist into old age even in healthy brains; the group is now testing whether that has any bearing on Alzheimer's disease.

What the study does not show

How the brain detects a faulty neuron remains unknown; the synapse-gene link is described as one possible clue, not a mechanism. The data are snapshots from deceased donors, not cells tracked over time, and the single-cell CNV work rests on 16 and 12 individuals. Christos Proukakis, a University College London neurologist not involved in the work, told Nature that the survivors may simply be the neurons that kept the most intact genomes. Park and Walsh sit on the scientific advisory board of a single-cell genomics company, the release disclosed.

The next step the authors describe is finding the molecular signal that marks a neuron for removal. If it exists and can be measured, it would give developmental neuroscience something it has lacked: a way to ask, cell by cell, which neurons a brain decided to keep.

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