Single Cell Genomics: Advances and Future Perspectives

SAMstrt: statistical test for differential expression in single-cell transcriptome with spike-in normalization

(2013) Shintaro Katayama et al.   BIOINFORMATICS

Direct sequencing of small genomes on the Pacific Biosciences RS without library preparation

(2013) Paul Coupland et al.   BIOTECHNIQUES

Complex Tumor Genomes Inferred from Single Circulating Tumor Cells by Array-CGH and Next-Generation Sequencing

(2013) E. Heitzer et al.   CANCER RESEARCH

Genome Analyses of Single Human Oocytes

(2013) Yu Hou et al.   CELL

Criteria for Inference of Chromothripsis in Cancer Genomes

(2013) Jan O. Korbel et al.   CELL

Chromothripsis in congenital disorders and cancer: similarities and differences

(2013) Wigard P Kloosterman et al.   CURRENT OPINION IN CELL BIOLOGY

Cell-free fetal DNA and maternal serum analytes for monitoring embryonic and fetal status

(2013) Joe Leigh Simpson   FERTILITY AND STERILITY

Sequencing of isolated sperm cells for direct haplotyping of a human genome

(2013) E. F. Kirkness et al.   GENOME RESEARCH

Single-cell mutational profiling and clonal phylogeny in cancer

(2013) N. E. Potter et al.   GENOME RESEARCH

Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing

(2013) H. Guo et al.   GENOME RESEARCH

Evolution of aneuploidy up to Day 4 of human preimplantation development

(2013) A. Mertzanidou et al.   HUMAN REPRODUCTION

Familial haplotyping and embryo analysis for Preimplantation Genetic Diagnosis (PGD) using DNA microarrays: a proof of principle study

(2013) G. Altarescu et al.   JOURNAL OF ASSISTED REPRODUCTION AND GENETICS

Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing

(2013) Zhigang Xue et al.   NATURE

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

(2013) Takashi Nagano et al.   NATURE

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

(2013) Alex K. Shalek et al.   NATURE

Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells

(2013) Jeff Gole et al.   NATURE BIOTECHNOLOGY

Association between large detectable clonal mosaicism and type 2 diabetes with vascular complications

(2013) Amélie Bonnefond et al.   NATURE GENETICS

Quantitative assessment of single-cell RNA-sequencing methods

(2013) Angela R Wu et al.   NATURE METHODS

Accounting for technical noise in single-cell RNA-seq experiments

(2013) Philip Brennecke et al.   NATURE METHODS

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

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

(2013) Ehud Shapiro et al.   NATURE REVIEWS GENETICS

A genomic view of mosaicism and human disease

(2013) Leslie G. Biesecker et al.   NATURE REVIEWS GENETICS

Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells

(2013) Liying Yan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2013) Thierry Voet et al.   NUCLEIC ACIDS RESEARCH

Genome-wide copy number profiling of single cells in S-phase reveals DNA-replication domains

(2013) Niels Van der Aa et al.   NUCLEIC ACIDS RESEARCH

A Robust Method to Analyze Copy Number Alterations of Less than 100 kb in Single Cells Using Oligonucleotide Array CGH

(2013) Birte Möhlendick et al.   PLoS One

RNA-sequencing from single nuclei

(2013) R. V. Grindberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reproducible copy number variation patterns among single circulating tumor cells of lung cancer patients

(2013) X. Ni et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-Cell DNA-Methylation Analysis Reveals Epigenetic Chimerism in Preimplantation Embryos

(2013) C. Lorthongpanich et al.   SCIENCE

Mosaic Copy Number Variation in Human Neurons

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

Somatic Mutation, Genomic Variation, and Neurological Disease

(2013) A. Poduri et al.   SCIENCE

Strand-seq: A unifying tool for studies of chromosome segregation

(2013) Ester Falconer et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

BAIT: Organizing genomes and mapping rearrangements in single cells

(2013) Mark Hills et al.   Genome Medicine

Efficiency of whole genome amplification of single circulating tumor cells enriched by CellSearch and sorted by FACS

(2013) Joost F Swennenhuis et al.   Genome Medicine

Preimplantation genetic diagnosis guided by single-cell genomics

(2013) Niels Van der Aa et al.   Genome Medicine

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

Microfluidic single cell analysis: from promise to practice

(2012) Véronique Lecault et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Multiple meiotic errors caused by predivision of chromatids in women of advanced maternal age undergoing in vitro fertilisation

(2012) Alan H Handyside et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

SNP array-based copy number and genotype analyses for preimplantation genetic diagnosis of human unbalanced translocations

(2012) Chris MJ van Uum et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Nonallelic homologous recombination between retrotransposable elements is a driver of de novo unbalanced translocations

(2012) C. Robberecht et al.   GENOME RESEARCH

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

(2012) Alexej Abyzov et al.   NATURE

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

Detectable clonal mosaicism and its relationship to aging and cancer

(2012) Kevin B Jacobs et al.   NATURE GENETICS

Detectable clonal mosaicism from birth to old age and its relationship to cancer

(2012) Cathy C Laurie et al.   NATURE GENETICS

DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution

(2012) Ester Falconer et al.   NATURE METHODS

Genome-wide copy number analysis of single cells

(2012) Timour Baslan et al.   Nature Protocols

Microarray analysis of copy number variation in single cells

(2012) Peter Konings et al.   Nature Protocols

Highly multiplexed and strand-specific single-cell RNA 5′ end sequencing

(2012) Saiful Islam et al.   Nature Protocols

Human aneuploidy: mechanisms and new insights into an age-old problem

(2012) So I. Nagaoka et al.   NATURE REVIEWS GENETICS

Detection of ≥1 Mb microdeletions and microduplications in a single cell using custom oligonucleotide arrays

(2012) Weimin Bi et al.   PRENATAL DIAGNOSIS

Extensive genetic variation in somatic human tissues

(2012) M. O'Huallachain et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Two methods for full-length RNA sequencing for low quantities of cells and single cells

(2012) X. Pan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detection of ultra-rare mutations by next-generation sequencing

(2012) M. W. Schmitt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) C. Zong et al.   SCIENCE

Probing Meiotic Recombination and Aneuploidy of Single Sperm Cells by Whole-Genome Sequencing

(2012) S. Lu et al.   SCIENCE

CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification

(2012) Tamar Hashimshony et al.   Cell Reports

Embryos of Robertsonian Translocation Carriers Exhibit a Mitotic Interchromosomal Effect That Enhances Genetic Instability during Early Development

(2012) Samer Alfarawati 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

The Human Cleavage Stage Embryo Is a Cradle of Chromosomal Rearrangements

(2011) T. Voet et al.   CYTOGENETIC AND GENOME RESEARCH

Limiting dilution bisulfite (pyro)sequencing reveals parent-specific methylation patterns in single early mouse embryos and bovine oocytes

(2011) Nady El Hajj et al.   Epigenetics

Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq

(2011) S. Islam et al.   GENOME RESEARCH

Synthetic spike-in standards for RNA-seq experiments

(2011) L. Jiang et al.   GENOME RESEARCH

Chromothripsis as a mechanism driving complex de novo structural rearrangements in the germline†

(2011) Wigard P. Kloosterman et al.   HUMAN MOLECULAR GENETICS

Breakage-fusion-bridge cycles leading to inv dup del occur in human cleavage stage embryos

(2011) Thierry Voet et al.   HUMAN MUTATION

First births after preimplantation genetic diagnosis of structural chromosome abnormalities using comparative genomic hybridization and microarray analysis

(2011) S. Alfarawati et al.   HUMAN REPRODUCTION

PGD for reciprocal and Robertsonian translocations using array comparative genomic hybridization

(2011) F. Fiorentino et al.   HUMAN REPRODUCTION

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

Single-cell dissection of transcriptional heterogeneity in human colon tumors

(2011) Piero Dalerba et al.   NATURE BIOTECHNOLOGY

Variation in genome-wide mutation rates within and between human families

(2011) Donald F Conrad et al.   NATURE GENETICS

Counting absolute numbers of molecules using unique molecular identifiers

(2011) Teemu Kivioja et al.   NATURE METHODS

Direct, genome-wide assessment of DNA mutations in single cells

(2011) Michael Gundry et al.   NUCLEIC ACIDS RESEARCH

Deterministic and Stochastic Allele Specific Gene Expression in Single Mouse Blastomeres

(2011) Fuchou Tang et al.   PLoS One

Somatic mosaicism in healthy human tissues

(2011) Subhajyoti De   TRENDS IN GENETICS

Future medical applications of single-cell sequencing in cancer

(2011) Nicholas Navin et al.   Genome Medicine

Telomere DNA Deficiency Is Associated with Development of Human Embryonic Aneuploidy

(2011) Nathan R. Treff et al.   PLoS Genetics

Resolution of Cell Fate Decisions Revealed by Single-Cell Gene Expression Analysis from Zygote to Blastocyst

(2010) Guoji Guo et al.   DEVELOPMENTAL CELL

Accurate single cell 24 chromosome aneuploidy screening using whole genome amplification and single nucleotide polymorphism microarrays

(2010) Nathan R. Treff et al.   FERTILITY AND STERILITY

Validation of microarray comparative genomic hybridization for comprehensive chromosome analysis of embryos

(2010) Cristina Gutiérrez-Mateo et al.   FERTILITY AND STERILITY

Preclinical validation of a microarray method for full molecular karyotyping of blastomeres in a 24-h protocol

(2010) D.S. Johnson et al.   HUMAN REPRODUCTION

SNP microarray-based 24 chromosome aneuploidy screening is significantly more consistent than FISH

(2010) N. R. Treff et al.   MOLECULAR HUMAN REPRODUCTION

Single-cell whole-genome amplification technique impacts the accuracy of SNP microarray-based genotyping and copy number analyses

(2010) Nathan R. Treff et al.   MOLECULAR HUMAN REPRODUCTION

Whole-genome molecular haplotyping of single cells

(2010) H Christina Fan et al.   NATURE BIOTECHNOLOGY

RNA-Seq analysis to capture the transcriptome landscape of a single cell

(2010) Fuchou Tang et al.   Nature Protocols

Non-genetic heterogeneity of cells in development: more than just noise

(2009) S. Huang   DEVELOPMENT

What next for preimplantation genetic screening? High mitotic chromosome instability rate provides the biological basis for the low success rate

(2009) E. Vanneste et al.   HUMAN REPRODUCTION

Karyomapping: a universal method for genome wide analysis of genetic disease based on mapping crossovers between parental haplotypes

(2009) A. H. Handyside et al.   JOURNAL OF MEDICAL GENETICS

Direct RNA sequencing

(2009) Fatih Ozsolak et al.   NATURE

The cancer genome

(2009) Michael R. Stratton et al.   NATURE

Chromosome instability is common in human cleavage-stage embryos

(2009) Evelyne Vanneste et al.   NATURE MEDICINE

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Identification of small gains and losses in single cells after whole genome amplification on tiling oligo arrays

(2009) Jochen B. Geigl et al.   NUCLEIC ACIDS RESEARCH

The impact of ovarian stimulation for IVF on the developing embryo

(2009) Margarida Avo Santos et al.   REPRODUCTION

Amplification of multiple genomic loci from single cells isolated by laser micro-dissection of tissues

(2008) Dan Frumkin et al.   BMC BIOTECHNOLOGY

Modelling and measuring single cell RNA expression levels find considerable transcriptional differences among phenotypically identical cells

(2008) Tatiana Subkhankulova et al.   BMC GENOMICS