Building a lineage from single cells: genetic techniques for cell lineage tracking

Assessment of megabase-scale somatic copy number variation using single-cell sequencing

(2016) Kristin A. Knouse et al.   GENOME RESEARCH

Monovar: single-nucleotide variant detection in single cells

(2016) Hamim Zafar et al.   NATURE METHODS

Highly multiplexed targeted DNA sequencing from single nuclei

(2016) Marco L Leung et al.   Nature Protocols

Single-cell genome sequencing: current state of the science

(2016) Charles Gawad et al.   NATURE REVIEWS GENETICS

Ctip1 Controls Acquisition of Sensory Area Identity and Establishment of Sensory Input Fields in the Developing Neocortex

(2016) Luciano C. Greig et al.   NEURON

The Complete Genome Sequences, Unique Mutational Spectra, and Developmental Potency of Adult Neurons Revealed by Cloning

(2016) Jennifer L. Hazen et al.   NEURON

Whole-organism lineage tracing by combinatorial and cumulative genome editing

(2016) Aaron McKenna et al.   SCIENCE

A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages

(2016) Robert J. Kimmerling et al.   Nature Communications

Resolving rates of mutation in the brain using single-neuron genomics

(2016) Gilad D Evrony et al.   eLife

Digital Droplet Multiple Displacement Amplification (ddMDA) for Whole Genome Sequencing of Limited DNA Samples

(2016) Minsoung Rhee et al.   PLoS One

Design and Analysis of Single-Cell Sequencing Experiments

(2015) Dominic Grün et al.   CELL

Ubiquitous L1 Mosaicism in Hippocampal Neurons

(2015) Kyle R. Upton et al.   CELL

Embryonic Origin of Postnatal Neural Stem Cells

(2015) Luis C. Fuentealba et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Optimizing sparse sequencing of single cells for highly multiplex copy number profiling

(2015) Timour Baslan et al.   GENOME RESEARCH

Advances and Applications of Single-Cell Sequencing Technologies

(2015) Yong Wang et al.   MOLECULAR CELL

In situ single-cell analysis identifies heterogeneity for PIK3CA mutation and HER2 amplification in HER2-positive breast cancer

(2015) Michalina Janiszewska et al.   NATURE GENETICS

Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues

(2015) Je Hyuk Lee et al.   Nature Protocols

Using tumour phylogenetics to identify the roots of metastasis in humans

(2015) Kamila Naxerova et al.   Nature Reviews Clinical Oncology

Genomic integrity and the ageing brain

(2015) Hei-man Chow et al.   NATURE REVIEWS NEUROSCIENCE

Clonally Related Forebrain Interneurons Disperse Broadly across Both Functional Areas and Structural Boundaries

(2015) Christian Mayer et al.   NEURON

Cell Lineage Analysis in Human Brain Using Endogenous Retroelements

(2015) Gilad D. Evrony et al.   NEURON

Wide Dispersion and Diversity of Clonally Related Inhibitory Interneurons

(2015) Corey C. Harwell et al.   NEURON

Enhanced sequencing coverage with digital droplet multiple displacement amplification

(2015) Angus M. Sidore et al.   NUCLEIC ACIDS RESEARCH

Uniform and accurate single-cell sequencing based on emulsion whole-genome amplification

(2015) Yusi Fu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Somatic mutation in single human neurons tracks developmental and transcriptional history

(2015) M. A. Lodato et al.   SCIENCE

High burden and pervasive positive selection of somatic mutations in normal human skin

(2015) I. Martincorena et al.   SCIENCE

Quantitative assessment of single-cell whole genome amplification methods for detecting copy number variation using hippocampal neurons

(2015) Luwen Ning et al.   Scientific Reports

SNES: single nucleus exome sequencing

(2015) Marco L Leung et al.   GENOME BIOLOGY

Single-Cell Genetic Analysis Using Automated Microfluidics to Resolve Somatic Mosaicism

(2015) Keith E. Szulwach et al.   PLoS One

Development and Applications of CRISPR-Cas9 for Genome Engineering

(2014) Patrick D. Hsu et al.   CELL

Diverse Behaviors of Outer Radial Glia in Developing Ferret and Human Cortex

(2014) C. C. Gertz et al.   JOURNAL OF NEUROSCIENCE

Clonal evolution in breast cancer revealed by single nucleus genome sequencing

(2014) Yong Wang et al.   NATURE

Genome sequencing of normal cells reveals developmental lineages and mutational processes

(2014) Sam Behjati et al.   NATURE

Spatially resolved transcriptomics and beyond

(2014) Nicola Crosetto et al.   NATURE REVIEWS GENETICS

Mobile DNA elements in the generation of diversity and complexity in the brain

(2014) Jennifer A. Erwin et al.   NATURE REVIEWS NEUROSCIENCE

Multiplex Cell and Lineage Tracking with Combinatorial Labels

(2014) Karine Loulier et al.   NEURON

Multiplexing clonality: combining RGB marking and genetic barcoding

(2014) Kerstin Cornils et al.   NUCLEIC ACIDS RESEARCH

Single cell sequencing reveals low levels of aneuploidy across mammalian tissues

(2014) Kristin A. Knouse et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dissecting the clonal origins of childhood acute lymphoblastic leukemia by single-cell genomics

(2014) Charles Gawad et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Highly Multiplexed Subcellular RNA Sequencing in Situ

(2014) J. H. Lee et al.   SCIENCE

Single-Cell, Genome-wide Sequencing Identifies Clonal Somatic Copy-Number Variation in the Human Brain

(2014) Xuyu Cai et al.   Cell Reports

In situ sequencing for RNA analysis in preserved tissue and cells

(2013) Rongqin Ke et al.   NATURE METHODS

Improved tools for the Brainbow toolbox

(2013) Dawen Cai et al.   NATURE METHODS

Single-cell sequencing-based technologies will revolutionize whole-organism science

(2013) Ehud Shapiro et al.   NATURE REVIEWS GENETICS

Precursor Diversity and Complexity of Lineage Relationships in the Outer Subventricular Zone of the Primate

(2013) Marion Betizeau et al.   NEURON

Single-cell paired-end genome sequencing reveals structural variation per cell cycle

(2013) Thierry Voet et al.   NUCLEIC ACIDS RESEARCH

Mosaic Copy Number Variation in Human Neurons

(2013) M. J. McConnell et al.   SCIENCE

Cell lineage analysis of acute leukemia relapse uncovers the role of replication-rate heterogeneity and microsatellite instability

(2012) L. I. Shlush et al.   BLOOD

Single-Neuron Sequencing Analysis of L1 Retrotransposition and Somatic Mutation in the Human Brain

(2012) Gilad D. Evrony et al.   CELL

Single-Cell Exome Sequencing Reveals Single-Nucleotide Mutation Characteristics of a Kidney Tumor

(2012) Xun Xu et al.   CELL

Single-Cell Exome Sequencing and Monoclonal Evolution of a JAK2-Negative Myeloproliferative Neoplasm

(2012) Yong Hou et al.   CELL

Genome-wide Single-Cell Analysis of Recombination Activity and De Novo Mutation Rates in Human Sperm

(2012) Jianbin Wang et al.   CELL

Fate Mapping by PiggyBac Transposase Reveals That Neocortical GLAST+ Progenitors Generate More Astrocytes Than Nestin+ Progenitors in Rat Neocortex

(2012) F. Siddiqi et al.   CEREBRAL CORTEX

A method for stable transgenesis of radial glia lineage in rat neocortex by piggyBac mediated transposition

(2012) Fuyi Chen et al.   JOURNAL OF NEUROSCIENCE METHODS

Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells

(2012) Alexej Abyzov et al.   NATURE

Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing

(2012) Li Ding et al.   NATURE

Genome-Wide Detection of Single-Nucleotide and Copy-Number Variations of a Single Human Cell

(2012) C. Zong et al.   SCIENCE

Cell Lineage Analysis of the Mammalian Female Germline

(2012) Yitzhak Reizel et al.   PLoS Genetics

Single-cell sequencing analysis characterizes common and cell-lineage-specific mutations in a muscle-invasive bladder cancer

(2012) Yingrui Li et al.   GigaScience

Cell of Origin of Small Cell Lung Cancer: Inactivation of Trp53 and Rb1 in Distinct Cell Types of Adult Mouse Lung

(2011) Kate D. Sutherland et al.   CANCER CELL

In Vivo Clonal Analysis Reveals Self-Renewing and Multipotent Adult Neural Stem Cell Characteristics

(2011) Michael A. Bonaguidi et al.   CELL

Conditional expression of the TVA receptor allows clonal analysis of descendents from Cre-expressing progenitor cells

(2011) Kevin T. Beier et al.   DEVELOPMENTAL BIOLOGY

Identification of a retina-specific Otx2 enhancer element active in immature developing photoreceptors

(2011) Mark M. Emerson et al.   DEVELOPMENTAL BIOLOGY

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

Somatic retrotransposition alters the genetic landscape of the human brain

(2011) J. Kenneth Baillie et al.   NATURE

Tracking single hematopoietic stem cells in vivo using high-throughput sequencing in conjunction with viral genetic barcoding

(2011) Rong Lu et al.   NATURE BIOTECHNOLOGY

Clonal Production and Organization of Inhibitory Interneurons in the Neocortex

(2011) K. N. Brown et al.   SCIENCE

Colon Stem Cell and Crypt Dynamics Exposed by Cell Lineage Reconstruction

(2011) Yitzhak Reizel et al.   PLoS Genetics

Cellular barcoding tool for clonal analysis in the hematopoietic system

(2010) A. Gerrits et al.   BLOOD

Intestinal Crypt Homeostasis Results from Neutral Competition between Symmetrically Dividing Lgr5 Stem Cells

(2010) Hugo J. Snippert et al.   CELL

Phylogenetic analysis of developmental and postnatal mouse cell lineages

(2010) Stephen J. Salipante et al.   EVOLUTION & DEVELOPMENT

Distant metastasis occurs late during the genetic evolution of pancreatic cancer

(2010) Shinichi Yachida et al.   NATURE

In situ detection and genotyping of individual mRNA molecules

(2010) Chatarina Larsson et al.   NATURE METHODS

Genetic Mosaic Dissection of Lis1 and Ndel1 in Neuronal Migration

(2010) Simon Hippenmeyer et al.   NEURON

Emerging potential of transposons for gene therapy and generation of induced pluripotent stem cells

(2009) T. VandenDriessche et al.   BLOOD

New and Improved Tools for In Utero Electroporation Studies of Developing Cerebral Cortex

(2009) J. LoTurco et al.   CEREBRAL CORTEX

A multifunctional reporter mouse line for Cre- and FLP-dependent lineage analysis

(2009) Masakazu Yamamoto et al.   GENESIS

L1 retrotransposition in human neural progenitor cells

(2009) Nicole G. Coufal et al.   NATURE

piggyBac transposition reprograms fibroblasts to induced pluripotent stem cells

(2009) Knut Woltjen et al.   NATURE

Somatic evolutionary genomics: Mutations during development cause highly variable genetic mosaicism with risk of cancer and neurodegeneration

(2009) S. A. Frank   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cell Lineage Analysis of a Mouse Tumor

(2008) D. Frumkin et al.   CANCER RESEARCH

Analysis of the clonal architecture of the human small intestinal epithelium establishes a common stem cell for all lineages and reveals a mechanism for the fixation and spread of mutations

(2008) Lydia Gutierrez-Gonzalez et al.   JOURNAL OF PATHOLOGY