title: Cell lineage analysis in human brain using endogenous retroelements.
abstract: 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 sublineages 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.
authors.affiliation: Division of Genetics and Genomics, Manton Center for Orphan Disease Research, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Gilad D
authors.initials: GD
authors.lastname: Evrony
authors.affiliation: Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA.
authors.forename: Eunjung
authors.initials: E
authors.lastname: Lee
authors.affiliation: Division of Genetics and Genomics, Manton Center for Orphan Disease Research, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Bhaven K
authors.initials: BK
authors.lastname: Mehta
authors.affiliation: Department of Statistics, Stanford University, Stanford, CA 94305, USA.
authors.forename: Yuval
authors.initials: Y
authors.lastname: Benjamini
authors.affiliation: NIH NeuroBioBank, University of Maryland, Baltimore, MD 21201, USA.
authors.forename: Robert M
authors.initials: RM
authors.lastname: Johnson
authors.affiliation: Division of Genetics and Genomics, Manton Center for Orphan Disease Research, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Xuyu
authors.initials: X
authors.lastname: Cai
authors.affiliation: Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA.
authors.forename: Lixing
authors.initials: L
authors.lastname: Yang
authors.affiliation: Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA.
authors.forename: Psalm
authors.initials: P
authors.lastname: Haseley
authors.affiliation: Division of Genetics and Genomics, Manton Center for Orphan Disease Research, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Hillel S
authors.initials: HS
authors.lastname: Lehmann
authors.affiliation: Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA. Electronic address: peter_park@hms.harvard.edu.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Park
authors.affiliation: Division of Genetics and Genomics, Manton Center for Orphan Disease Research, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Electronic address: christopher.walsh@childrens.harvard.edu.
authors.forename: Christopher A
authors.initials: CA
authors.lastname: Walsh
mesh_terms: D000293:Adolescent; D001921:Brain / Q000166:cytology / Q000378:metabolism; D019070:Cell Lineage / Q000235:genetics*; D002465:Cell Movement; D002540:Cerebral Cortex / Q000166:cytology* / Q000378:metabolism; D002999:Clone Cells / Q000166:cytology / Q000378:metabolism; D004252:DNA Mutational Analysis; D006801:Humans; D020084:Long Interspersed Nucleotide Elements / Q000235:genetics*; D008297:Male; D018895:Microsatellite Repeats / Q000235:genetics; D009154:Mutation / Q000235:genetics; D009474:Neurons / Q000166:cytology* / Q000378:metabolism; D011061:Poly A / Q000235:genetics; D016133:Polymerase Chain Reaction; D018626:Retroelements / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D018626:Retroelements; D011061:Poly A