Single-cell analysis of structural variations and complex rearrangements with tri-channel processing

Multi-platform discovery of haplotype-resolved structural variation in human genomes

(2019) Mark J. P. Chaisson et al.   Nature Communications

Chemoresistance Evolution in Triple-Negative Breast Cancer Delineated by Single-Cell Sequencing

(2018) Charissa Kim et al.   CELL

Tracking Cancer Evolution Reveals Constrained Routes to Metastases: TRACERx Renal

(2018) Samra Turajlic et al.   CELL

Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data

(2018) Jean Fan et al.   GENOME RESEARCH

Detecting Somatic Mutations in Normal Cells

(2018) Yanmei Dou et al.   TRENDS IN GENETICS

Unexpected CRISPR on-target effects

(2018) Hyunji Lee et al.   NATURE BIOTECHNOLOGY

PDX models recapitulate the genetic and epigenetic landscape of pediatric T‐cell leukemia

(2018) Paulina Richter‐Pechańska et al.   EMBO Molecular Medicine

Chromothripsis is linked to TP53 alteration, cell cycle impairment, and dismal outcome in acute myeloid leukemia with complex karyotype

(2017) Frank G. Rücker et al.   HAEMATOLOGICA

The whole-genome landscape of medulloblastoma subtypes

(2017) Paul A. Northcott et al.   NATURE

Copy number alterations unmasked as enhancer hijackers

(2017) Rameen Beroukhim et al.   NATURE GENETICS

The genomic landscape of pediatric and young adult T-lineage acute lymphoblastic leukemia

(2017) Yu Liu et al.   NATURE GENETICS

Genomic consequences of aberrant DNA repair mechanisms stratify ovarian cancer histotypes

(2017) Yi Kan Wang et al.   NATURE GENETICS

Scalable whole-genome single-cell library preparation without preamplification

(2017) Hans Zahn et al.   NATURE METHODS

Single-cell template strand sequencing by Strand-seq enables the characterization of individual homologs

(2017) Ashley D Sanders et al.   Nature Protocols

Dense and accurate whole-chromosome haplotyping of individual genomes

(2017) David Porubsky et al.   Nature Communications

Genome-wide mapping of sister chromatid exchange events in single yeast cells using Strand-seq

(2017) Clémence Claussin et al.   eLife

Chromothripsis is linked to TP53 alteration, cell cycle impairment, and dismal outcome in acute myeloid leukemia with complex karyotype

(2017) Frank G. Rücker et al.   HAEMATOLOGICA

Characterizing polymorphic inversions in human genomes by single-cell sequencing

(2016) Ashley D. Sanders et al.   GENOME RESEARCH

Direct chromosome-length haplotyping by single-cell sequencing

(2016) David Porubský et al.   GENOME RESEARCH

Mosaicism in health and disease — clones picking up speed

(2016) Lars A. Forsberg et al.   NATURE REVIEWS GENETICS

Single-cell genome sequencing: current state of the science

(2016) Charles Gawad et al.   NATURE REVIEWS GENETICS

Bromodeoxyuridine does not contribute to sister chromatid exchange events in normal or Bloom syndrome cells

(2016) Niek van Wietmarschen et al.   NUCLEIC ACIDS RESEARCH

Genomic Instability of iPSCs: Challenges Towards Their Clinical Applications

(2016) Masahito Yoshihara et al.   Stem Cell Reviews and Reports

Genomic Instability of iPSCs: Challenges Towards Their Clinical Applications

(2016) Masahito Yoshihara et al.   Stem Cell Reviews and Reports

Chromothripsis: A New Mechanism for Rapid Karyotype Evolution

(2015) Mitchell L. Leibowitz et al.   Annual Review of Genetics

Chromothripsis and Kataegis Induced by Telomere Crisis

(2015) John Maciejowski et al.   CELL

Pediatric T-cell lymphoblastic leukemia evolves into relapse by clonal selection, acquisition of mutations and promoter hypomethylation

(2015) J. B. Kunz et al.   HAEMATOLOGICA

Chromothripsis in cancer cells: An update

(2015) Agata Rode et al.   INTERNATIONAL JOURNAL OF CANCER

A cell-based model system links chromothripsis with hyperploidy

(2015) B. R. Mardin et al.   Molecular Systems Biology

Chromothripsis from DNA damage in micronuclei

(2015) Cheng-Zhong Zhang et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

A Big Bang model of human colorectal tumor growth

(2015) Andrea Sottoriva et al.   NATURE GENETICS

Somatic mosaicism: implications for disease and transmission genetics

(2015) Ian M. Campbell et al.   TRENDS IN GENETICS

Pediatric T-cell lymphoblastic leukemia evolves into relapse by clonal selection, acquisition of mutations and promoter hypomethylation

(2015) J. B. Kunz et al.   HAEMATOLOGICA

The mitotic origin of chromosomal instability

(2014) Samuel F. Bakhoum et al.   CURRENT BIOLOGY

Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma

(2014) Paul A. Northcott et al.   NATURE

Constitutional and somatic rearrangement of chromosome 21 in acute lymphoblastic leukaemia

(2014) Yilong Li et al.   NATURE

LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

A far downstream enhancer for murine Bcl11b controls its T-cell specific expression

(2013) L. Li et al.   BLOOD

Diverse Mechanisms of Somatic Structural Variations in Human Cancer Genomes

(2013) Lixing Yang et al.   CELL

Criteria for Inference of Chromothripsis in Cancer Genomes

(2013) Jan O. Korbel et al.   CELL

Chromothripsis and beyond: rapid genome evolution from complex chromosomal rearrangements

(2013) C.-Z. Zhang et al.   GENES & DEVELOPMENT

Emerging landscape of oncogenic signatures across human cancers

(2013) Giovanni Ciriello et al.   NATURE GENETICS

The Implications of Clonal Genome Evolution for Cancer Medicine

(2013) Samuel Aparicio et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

(2013) Thierry Voet et al.   NUCLEIC ACIDS RESEARCH

BAIT: Organizing genomes and mapping rearrangements in single cells

(2013) Mark Hills et al.   Genome Medicine

DELLY: structural variant discovery by integrated paired-end and split-read analysis

(2012) T. Rausch et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Inactivation of ribosomal protein L22 promotes transformation by induction of the stemness factor, Lin28B

(2012) S. Rao et al.   BLOOD

Genome Sequencing of Pediatric Medulloblastoma Links Catastrophic DNA Rearrangements with TP53 Mutations

(2012) Tobias Rausch et al.   CELL

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

(2012) Ester Falconer et al.   NATURE METHODS

cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate

(2012) Günter Klambauer et al.   NUCLEIC ACIDS RESEARCH

The consequences of uniparental disomy and copy number neutral loss-of-heterozygosity during human development and cancer

(2011) Pablo Lapunzina et al.   BIOLOGY OF THE CELL

Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development

(2011) Philip J. Stephens et al.   CELL

Mutations of PHF6 are associated with mutations of NOTCH1, JAK1 and rearrangement of SET-NUP214 in T-cell acute lymphoblastic leukemia

(2011) Q. Wang et al.   HAEMATOLOGICA

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

(2011) Thierry Voet et al.   HUMAN MUTATION

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

Exploring the Genomes of Cancer Cells: Progress and Promise

(2011) M. R. Stratton   SCIENCE

Chromosome Segregation Errors as a Cause of DNA Damage and Structural Chromosome Aberrations

(2011) A. Janssen et al.   SCIENCE

Mechanisms of Chromosomal Instability

(2010) Sarah L. Thompson et al.   CURRENT BIOLOGY

Tracing the tumor lineage

(2010) Nicholas E. Navin et al.   Molecular Oncology

The patterns and dynamics of genomic instability in metastatic pancreatic cancer

(2010) Peter J. Campbell et al.   NATURE