ArticleCell reports2025
Combined somatic mutation and transcriptome analysis reveals region-specific differences in clonal architecture in human cortex.
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Article in Cell reports, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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6citing papers in PubMed
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Who cites it
6 citing papers in PubMed.
- Origins and timing of somatic variants in the brain.Current opinion in genetics & development · 2026Review
- Somatic mosaicism in the brain: linking development, ageing and neurodegeneration.Nature reviews. Neurology · 2026Review
- Molecular signatures and lineage diversification of neurogenic and gliogenic radial glia in the gyrencephalic ferret cortex.Communications biology · 2026Article
- A recurrent sequencing artifact on Illumina sequencers with two-color fluorescent dye chemistry and its impact on somatic variant detection.Genome biology · 2026Article
- Article
- DeepGene-BC: Deep Learning-Based Breast Cancer Subtype Prediction via Somatic Point Mutation Profiles.Cancers · 2026Article
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Authors and funding
25 authors.
Vinayak V ViswanadhamDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Bioinformatics and Integrative Genomics Program, Harvard Medical School, Boston, MA, USA.
Sonia N KimDivision of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Program in Biological and Biomedical Sciences, Harvard University, Boston, MA, USA.
Emre CaglayanDivision of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Ryan N DoanDivision of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA.
Yanmei DouDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
Sara BizzottoDivision of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Sattar KhoshkhooDivision of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA.
August Yue HuangDivision of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Rebecca YehDivision of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA.
Brian H ChhoukDivision of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA.
Alex TruongResearch Computing, Harvard Medical School, Boston, MA, USA.
Kathleen M ChappellResearch Computing, Harvard Medical School, Boston, MA, USA.
Marc BeaudinDivision of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA.
Alison BartonDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Bioinformatics and Integrative Genomics Program, Harvard Medical School, Boston, MA, USA.
Shyam K AkulaDivision of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA.
Yifan ZhaoDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Program in Health Sciences & Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA, USA.
Lariza RentoDivision of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA.
Michael LodatoDivision of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Ryan A SzetoProgram in Biological and Biomedical Sciences, Harvard University, Boston, MA, USA.
Javier GanzDivision of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Pengpeng LiDivision of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Jessica W TsaiDivision of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA.
Robert Sean HillDivision of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Peter J ParkDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA. Electronic address: peter_park@hms.harvard.edu.
Christopher A WalshDivision of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Program in Biological and Biomedical Sciences, Harvard University, Boston, MA, USA. Electronic address: christopher.walsh@childrens.harvard.edu.
Funding
RESEARCH TRAINING-MEDICAL INFORMATICS 90T15LM007092 · NLM · HARVARD UNIVERSITY (SCH OF PUBLIC HLTH) · PI Nils Gehlenborg · 1992 to 2026
$32.8MCell Identity Determination In Human Brain: Somatic Mutation and Cell LineageR01NS032457 · NINDS · BOSTON CHILDREN'S HOSPITAL · PI Alice Eunjung Lee, Christopher A. Walsh · 1995 to 2026
$12.7M1/2-Somatic mosaicism and autism spectrum disorderU01MH106883 · NIMH · BOSTON CHILDREN'S HOSPITAL · PI PARK, PETER J, WALSH, CHRISTOPHER A. · 2015 to 2019
$9.2MRole of clonal somatic mutations in microglia and Alzheimer’s diseaseR01AG088082 · NIA · BOSTON CHILDREN'S HOSPITAL · PI Yue Huang · 2024 to 2026
$4.4MSpatial single-cell analysis of somatic mutation in human brain during aging and neurodegenerationDP2AG086139 · NIA · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI Michael Anthony Lodato · 2023 to 2026
$2.5MDetection and Characterization of Somatic Mutations in Human Tissue Utilizing Duplex-Consensus SequencingUH3NS132144 · NINDS · BOSTON CHILDREN'S HOSPITAL · PI Sangita Choudhury, Alice Eunjung Lee · 2025 to 2026
$1.5MGenetic and Cellular Mechanisms of Temporal Lobe EpilepsyK08NS128272 · NINDS · BRIGHAM AND WOMEN'S HOSPITAL · PI Sattar Khoshkhoo · 2022 to 2026
$1.2MRole of clonal somatic mutations in microglia activation and Alzheimer’s diseaseR56AG079857 · NIA · BOSTON CHILDREN'S HOSPITAL · PI HUANG, YUE, LEE, EUNJUNG ALICE · 2023 to 2023
$883kCharacterizing mechanisms and consequences of intergenic transcription in human cancersF31CA264958 · NCI · HARVARD MEDICAL SCHOOL · PI VISWANADHAM, VINAYAK VENKATASESHA · 2021 to 2022
$60kHoward Hughes Medical InstituteNCI NIH HHS F31 CA264958NIA NIH HHS DP2 AG086139NIA NIH HHS R01 AG088082NIA NIH HHS R56 AG079857NIMH NIH HHS U01 MH106883NINDS NIH HHS K08 NS128272NINDS NIH HHS L30 NS118655NINDS NIH HHS R01 NS032457NINDS NIH HHS UH3 NS132144NLM NIH HHS T15 LM007092
Abstract
The human cerebral cortex is specialized into regions, but little is known about how human cellular lineages shape cortical regional variation and neuronal cell-type distribution during development. Here, we map single-cell lineages of human cortical regions and neuronal subtypes using >1,000 somatic single-nucleotide variants (sSNVs) identified from deep bulk whole-genome sequencing and analyzed over 25 regions and >72,000 single cells. In the fronto-parietal cortex, sSNVs are rarely restricted, marking neuron-generating clones that disperse into neighboring regions. In contrast, the primary visual cortex harbors 30%-70% more sSNVs than the neighboring secondary visual cortex. Clones at this border exhibit more restricted dispersion, suggesting late developmental lineage segregation. Single-nucleus sSNV and whole-transcriptome analysis reveal glutamatergic neuron clones with modest regional restrictions that share low-mosaic sSNVs with some GABAergic neurons, suggesting a recent dorsal cortical progenitor. Our analysis reveals human-specific cortical lineage patterns, regional differences in clonal patterns, and late divergence of some glutamatergic/GABAergic lineages.
Indexed as
Cerebral CortexGene Expression ProfilingMutationTranscriptomeCell LineageClone CellsHumansNeuronsPolymorphism, Single NucleotideSingle-Cell Analysiscortical developmentCP: genomicsCP: neuroscienceglutamatergic neuronsinterneuronslineage tracingsingle-cell transcriptomicssomatic mutationsspatial genomicsvisual cortex
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.