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Single cell tri-channel-processing reveals structural variation landscapes and complex rearrangement processes

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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

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

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Criteria for Inference of Chromothripsis in Cancer Genomes

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Diverse Mechanisms of Somatic Structural Variations in Human Cancer Genomes

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Chromothripsis and Kataegis Induced by Telomere Crisis

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

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Tracking Cancer Evolution Reveals Constrained Routes to Metastases: TRACERx Renal

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Mechanisms of Chromosomal Instability

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The mitotic origin of chromosomal instability

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Somatic mosaicism: implications for disease and transmission genetics

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Detecting Somatic Mutations in Normal Cells

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Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma

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Chromothripsis from DNA damage in micronuclei

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A global reference for human genetic variation

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The whole-genome landscape of medulloblastoma subtypes

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Unexpected CRISPR on-target effects

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Emerging landscape of oncogenic signatures across human cancers

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A Big Bang model of human colorectal tumor growth

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Copy number alterations unmasked as enhancer hijackers

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Genomic consequences of aberrant DNA repair mechanisms stratify ovarian cancer histotypes

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

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

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Scalable whole-genome single-cell library preparation without preamplification

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

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The emerging complexity of gene fusions in cancer

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Single-cell genome sequencing: current state of the science

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Mosaicism in health and disease — clones picking up speed

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Genome structural variation discovery and genotyping

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Dense and accurate whole-chromosome haplotyping of individual genomes

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A new recurrent and specific cryptic translocation, t(5;14)(q35;q32), is associated with expression of the Hox11L2 gene in T acute lymphoblastic leukemia

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

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The Implications of Clonal Genome Evolution for Cancer Medicine

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Chromosomal breakage-fusion-bridge events cause genetic intratumor heterogeneity

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Deregulated expression of TCL1 causes T cell leukemia in mice

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Transcript mapping with high-density oligonucleotide tiling arrays

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

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STAR: ultrafast universal RNA-seq aligner

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THE STABILITY OF BROKEN ENDS OF CHROMOSOMES IN ZEA MAYS

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

inferredcites →https://doi.org/10.1093/nar/gkt345openalex-snapshot

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

inferredcites →https://doi.org/10.1093/nar/gkw422openalex-snapshot

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

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Patterns of structural variation in human cancer

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Chromothripsis and beyond: rapid genome evolution from complex chromosomal rearrangements

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Characterizing polymorphic inversions in human genomes by single-cell sequencing

inferredcites →https://doi.org/10.1101/gr.209841.116openalex-snapshot

Direct chromosome-length haplotyping by single-cell sequencing

inferredcites →https://doi.org/10.1101/gr.228080.117openalex-snapshot

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Paired-End Mapping Reveals Extensive Structural Variation in the Human Genome

inferredcites →https://doi.org/10.1126/science.1204040openalex-snapshot

Exploring the Genomes of Cancer Cells: Progress and Promise

inferredcites →https://doi.org/10.1126/science.1210214openalex-snapshot

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

inferredcites →https://doi.org/10.1136/esmoopen-2015-000023openalex-snapshot

NTRK gene fusions as novel targets of cancer therapy across multiple tumour types

inferredcites →https://doi.org/10.1146/annurev-genet-120213-092228openalex-snapshot

Chromothripsis: A New Mechanism for Rapid Karyotype Evolution

inferredcites →https://doi.org/10.1158/0008-5472.can-06-2615openalex-snapshot

Activation of TLX3 and NKX2-5 in t(5;14)(q35;q32) T-Cell Acute Lymphoblastic Leukemia by Remote 3′- BCL11B Enhancers and Coregulation by PU.1 and HMGA1

inferredcites →https://doi.org/10.1182/blood-2012-03-415349openalex-snapshot

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

inferredcites →https://doi.org/10.1182/blood-2012-08-447839openalex-snapshot

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

inferredcites →https://doi.org/10.1182/blood-2016-09-738070openalex-snapshot

Ex vivo drug response profiling detects recurrent sensitivity patterns in drug-resistant acute lymphoblastic leukemia

inferredcites →https://doi.org/10.1182/blood-2016-10-706465openalex-snapshot

The genetics and molecular biology of T-ALL

inferredcites →https://doi.org/10.1186/gb-2014-15-6-r84openalex-snapshot

LUMPY: a probabilistic framework for structural variant discovery

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Cancer genomics: one cell at a time

inferredcites →https://doi.org/10.1186/s13059-014-0550-8openalex-snapshot

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

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Single-cell sequencing reveals karyotype heterogeneity in murine and human malignancies

inferredcites →https://doi.org/10.15252/emmm.201809443openalex-snapshot

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

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A cell‐based model system links chromothripsis with hyperploidy

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Neoplastic Transformation and Cytogenetic Changes after Gamma Irradiation of Human Epithelial Cells Expressing Telomerase

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

inferredcites →https://doi.org/10.3324/haematol.2015.129692openalex-snapshot

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

inferredcites →https://doi.org/10.3324/haematol.2017.180497openalex-snapshot

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

inferredcites →https://doi.org/10.48550/arxiv.1207.3907openalex-snapshot

Haplotype-based variant detection from short-read sequencing

inferredcites →https://doi.org/10.7554/elife.30560openalex-snapshot

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

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1007/978-1-0716-2655-9_11openalex-snapshot

Somatic CNV Detection by Single-Cell Whole-Genome Sequencing in Postmortem Human Brain

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