Single-Neuron Sequencing Analysis of L1 Retrotransposition and Somatic Mutation in the Human Brain
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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. Because 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 three 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.
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Retrotransposition during development or adulthood leads to somatic mosaicism and has been estimated in adult neurons at varying but generally low frequencies.
“Retrotransposition during development or adulthood would lead to somatic mosaicism, and has been estimated to occur in adult neurons by qPCR or single-cell genomic studies at varying (but generally low) frequencies (events/cell): < 0.04–0.680, 13.781, 0.58–182, 0.283 and 0.63–1.6684.”
From The role of retrotransposable elements in ageing and age-associated diseases (2021) · cites this paper as [80]
Reanalysis of Upton et al.'s data while filtering artifacts generates a consensus that retrotransposition occurs in developing brain but at a much lower rate consistent with prior single-cell studies.
“Reanalysis of their data while filtering these artifacts generates a consensus that retrotransposition does occur in developing brain but at a much lower rate consistent with prior single-cell studies (Evrony et al., 2012; Evrony et al., 2015), thereby constraining the range of possible functional roles for retrotransposition in the brain.”
From Resolving rates of mutation in the brain using single-neuron genomics (2016) · cites this paper as Evrony et al., 2012
These RC-seq somatic insertion rates are quite consistent with rates previously estimated by L1-IP in single cortical and caudate neurons (0.07 ± 0.15 SD; p = 0.54, ANOVA) and using single-neuron whole-genome sequencing (0.18 ± 0.47 SD; p = 0.37, ANOVA), suggesting a notable consensus by three methods confirming that somatic L1 insertions are present in human brain, but fewer than one per average.
“These RC-seq somatic insertion rates are quite consistent with rates previously estimated by L1 insertion profiling (L1-IP) in single cortical and caudate neurons (0.07 ± 0.15 (SD); p = 0.54, ANOVA) (Evrony et al., 2012), and using single-neuron whole-genome sequencing (0.18 ± 0.47 (SD); p = 0.37, ANOVA) (Evrony et al., 2015), suggesting a notable consensus by three methods confirming that somatic”
From Resolving rates of mutation in the brain using single-neuron genomics (2016) · cites this paper as Evrony et al., 2012
The 2 remaining cells in which L1 #1 was detected (neurons 2 and 77) were excluded from the rate estimate because they were a priori chosen for whole-genome sequencing as positive controls known to harbor somatic L1 insertions previously detected by the L1-IP method in Evrony et al. (2012).
“The 2 remaining cells in which L1 #1 was detected (neurons 2 and 77) (Evrony et al., 2015) were excluded from the rate estimate, because they were a priori chosen for whole-genome sequencing as positive controls known to harbor somatic L1 insertions previously detected by the L1-IP method in Evrony et al. (2012).”
From Resolving rates of mutation in the brain using single-neuron genomics (2016) · cites this paper as Evrony et al. (2012)
Levels of mosaicism as low as 8% are sufficient to disrupt the normal architecture and function of the neocortex in HMG.
“Surprisingly, levels of mosaicism as low as 8% are sufficient to disrupt the normal architecture and function of the neocortex in HMG (Evrony et al., 2012; Lee et al., 2012; Poduri et al., 2012; Riviere et al., 2012).”
From Genetic Changes Shaping the Human Brain (2015) · cites this paper as Evrony et al., 2012
In the human brain, single-cell sequencing has been successfully used to detect somatic mosaicism in HMG.
“In the human brain, single-cell sequencing has been successfully used to detect somatic mosaicism in HMG and to evaluate the rate of somatic long interspersed nuclear element-1 (LINE1) retrotransposition (Evrony et al., 2012).”
From Genetic Changes Shaping the Human Brain (2015) · cites this paper as Evrony et al., 2012
LINE1 retrotransposition is not a major generator of neuronal diversity in the brain.
“Fewer than one unique insertion was detected per neuron, suggesting that LINE1 retrotransposition is not a major generator of neuronal diversity in the brain.”
From Genetic Changes Shaping the Human Brain (2015) · cites this paper as Evrony et al., 2012
Single-cell sequencing has been used to evaluate the rate of somatic LINE1 retrotransposition in the human brain.
“In the human brain, single-cell sequencing has been successfully used to detect somatic mosaicism in HMG and to evaluate the rate of somatic long interspersed nuclear element-1 (LINE1) retrotransposition (Evrony et al., 2012).”
From Genetic Changes Shaping the Human Brain (2015) · cites this paper as Evrony et al., 2012
Fewer than one unique insertion was detected per neuron.
“Fewer than one unique insertion was detected per neuron, suggesting that LINE1 retrotransposition is not a major generator of neuronal diversity in the brain.”
From Genetic Changes Shaping the Human Brain (2015) · cites this paper as Evrony et al., 2012
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- Authors
- Evrony, G. D., Cai, X., Lee, E., Hills, L. B., Elhosary, P. C., Lehmann, H. S., Parker, J. J., Atabay, K. D., Gilmore, E. C., Poduri, A., Park, P. J., & Walsh, C. A.
- Affiliations
- Boston Children's Hospital (US)
- Brigham and Women's Hospital (US)
- Case Western Reserve University (US)
- Corresponding author
- Walsh, Christopher A.
- ORCID
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2012-10
- Volume
- 151
- Issue
- 3
- Pages
- 483-496
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC3567441
- OpenAlex
- W2123490990
- Cited by
- 548
- References
- 66
- Citations by year
- 2026: 16 · 2025: 26 · 2024: 23 · 2023: 28 · 2022: 29 · 2021: 36 · 2020: 45 · 2019: 41 · 2018: 45 · 2017: 56 · 2016: 49 · 2015: 55 · 2014: 48 · 2013: 47 · 2012: 4
- FWCI
- 29.39
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Science Foundation
- Howard Hughes Medical Institute
- Manton Center for Orphan Disease Research, Boston Children's Hospital
- National Institute of General Medical Sciences (T32GM007726, T32GM007753)
- National Institute of Neurological Disorders and Stroke (R01NS035129, R01NS079277)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Keywords
- LINE-1 retrotransposition, somatic mutations, somatic mosaicism, hemimegalencephaly, cerebral cortex, caudate nucleus, single-cell genotyping
- MeSH terms
- Caudate Nucleus, Cerebral Cortex, Child, Chromosomes, Human, Pair 18, Humans, Male, Mosaicism, Mutation, Neurons, Trisomy, Long Interspersed Nucleotide Elements, Proto-Oncogene Proteins c-akt, Malformations of Cortical Development, Genome-Wide Association Study, Single-Cell Analysis
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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