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Novel patterns of complex structural variation revealed across thousands of cancer genome graphs

https://doi.org/10.1101/836296
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What this work says

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

inferredcites →https://doi.org/10.1002/cncr.30259openalex-snapshot
The efficacy of anti‐PD‐1 agents in acral and mucosal melanoma
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Roles of FHIT and WWOX fragile genes in cancer
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The molecular basis of common and rare fragile sites
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The Architecture and Evolution of Cancer Neochromosomes
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Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development
inferredcites →https://doi.org/10.1016/j.cell.2012.04.024openalex-snapshot
Mutational Processes Molding the Genomes of 21 Breast Cancers
inferredcites →https://doi.org/10.1016/j.cell.2013.02.023openalex-snapshot
Criteria for Inference of Chromothripsis in Cancer Genomes
inferredcites →https://doi.org/10.1016/j.cell.2013.03.021openalex-snapshot
Punctuated Evolution of Prostate Cancer Genomes
inferredcites →https://doi.org/10.1016/j.cell.2013.09.053openalex-snapshot
Super-Enhancers in the Control of Cell Identity and Disease
inferredcites →https://doi.org/10.1016/j.cell.2016.12.025openalex-snapshot
Insertions and Deletions Target Lineage-Defining Genes in Human Cancers
inferredcites →https://doi.org/10.1016/j.cell.2018.05.036openalex-snapshot
Structural Alterations Driving Castration-Resistant Prostate Cancer Revealed by Linked-Read Genome Sequencing
inferredcites →https://doi.org/10.1016/j.cell.2019.05.013openalex-snapshot
Tracing Oncogene Rearrangements in the Mutational History of Lung Adenocarcinoma
inferredcites →https://doi.org/10.1016/j.celrep.2019.05.014openalex-snapshot
Breakage-Fusion-Bridge Events Trigger Complex Genome Rearrangements and Amplifications in Developmentally Arrested T Cell Lymphomas
inferredcites →https://doi.org/10.1016/j.cels.2016.05.007openalex-snapshot
Allele-Specific Quantification of Structural Variations in Cancer Genomes
inferredcites →https://doi.org/10.1016/j.coisb.2016.12.005openalex-snapshot
Modeling cancer rearrangement landscapes
inferredcites →https://doi.org/10.1016/s0092-8674(00)81034-xopenalex-snapshot
The FHIT Gene, Spanning the Chromosome 3p14.2 Fragile Site and Renal Carcinoma–Associated t(3;8) Breakpoint, Is Abnormal in Digestive Tract Cancers
inferredcites →https://doi.org/10.1038/nature08768openalex-snapshot
Signatures of mutation and selection in the cancer genome
inferredcites →https://doi.org/10.1038/nature08822openalex-snapshot
The landscape of somatic copy-number alteration across human cancers
inferredcites →https://doi.org/10.1038/nature11003openalex-snapshot
The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity
inferredcites →https://doi.org/10.1038/nature12477openalex-snapshot
Signatures of mutational processes in human cancer
inferredcites →https://doi.org/10.1038/nature17676openalex-snapshot
Landscape of somatic mutations in 560 breast cancer whole-genome sequences
inferredcites →https://doi.org/10.1038/nature18964openalex-snapshot
The Simons Genome Diversity Project: 300 genomes from 142 diverse populations
inferredcites →https://doi.org/10.1038/nature22071openalex-snapshot
Whole-genome landscapes of major melanoma subtypes
inferredcites →https://doi.org/10.1038/nature24477openalex-snapshot
Mechanism of tandem duplication formation in BRCA1-mutant cells
inferredcites →https://doi.org/10.1038/ng.2702openalex-snapshot
An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers
inferredcites →https://doi.org/10.1038/ng.2760openalex-snapshot
Pan-cancer patterns of somatic copy number alteration
inferredcites →https://doi.org/10.1038/nmeth.1276openalex-snapshot
High-resolution mapping of copy-number alterations with massively parallel sequencing
inferredcites →https://doi.org/10.1038/nmeth.3394openalex-snapshot
CONSERTING: integrating copy-number analysis with structural-variation detection
inferredcites →https://doi.org/10.1038/nmeth.4366openalex-snapshot
Genome-wide reconstruction of complex structural variants using read clouds
inferredcites →https://doi.org/10.1038/nrc3891openalex-snapshot
Therapeutic opportunities within the DNA damage response
inferredcites →https://doi.org/10.1038/s41467-017-01355-0openalex-snapshot
Pan-cancer analysis of homozygous deletions in primary tumours uncovers rare tumour suppressors
inferredcites →https://doi.org/10.1038/s41568-018-0060-1openalex-snapshot
The COSMIC Cancer Gene Census: describing genetic dysfunction across all human cancers
inferredcites →https://doi.org/10.1038/s41568-019-0128-6openalex-snapshot
Extrachromosomal oncogene amplification in tumour pathogenesis and evolution
inferredcites →https://doi.org/10.1038/s41576-018-0003-4openalex-snapshot
Piercing the dark matter: bioinformatics of long-range sequencing and mapping
inferredcites →https://doi.org/10.1038/s41586-019-1186-3openalex-snapshot
Next-generation characterization of the Cancer Cell Line Encyclopedia
inferredcites →https://doi.org/10.1038/s41586-019-1670-9openalex-snapshot
Somatic mutations and clonal dynamics in healthy and cirrhotic human liver
inferredcites →https://doi.org/10.1038/s41586-019-1672-7openalex-snapshot
The landscape of somatic mutation in normal colorectal epithelial cells
inferredcites →https://doi.org/10.1038/s41588-018-0179-8openalex-snapshot
Copy number signatures and mutational processes in ovarian carcinoma
inferredcites →https://doi.org/10.1038/s41588-018-0331-5openalex-snapshot
The landscape of selection in 551 esophageal adenocarcinomas defines genomic biomarkers for the clinic
inferredcites →https://doi.org/10.1038/s41592-018-0051-xopenalex-snapshot
Strelka2: fast and accurate calling of germline and somatic variants
inferredcites →https://doi.org/10.1073/pnas.090013497openalex-snapshot
Chromosomal breakage-fusion-bridge events cause genetic intratumor heterogeneity
inferredcites →https://doi.org/10.1073/pnas.1110574108openalex-snapshot
Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion
inferredcites →https://doi.org/10.1073/pnas.1220977110openalex-snapshot
An algorithmic approach for breakage-fusion-bridge detection in tumor genomes
inferredcites →https://doi.org/10.1073/pnas.1520010113openalex-snapshot
The tandem duplicator phenotype as a distinct genomic configuration in cancer
inferredcites →https://doi.org/10.1093/annonc/mdu479openalex-snapshot
Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data
inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btr670openalex-snapshot
Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data
inferredcites →https://doi.org/10.1093/bioinformatics/btr708openalex-snapshot
ART: a next-generation sequencing read simulator
inferredcites →https://doi.org/10.1093/biostatistics/kxh008openalex-snapshot
Circular binary segmentation for the analysis of array-based DNA copy number data
inferredcites →https://doi.org/10.1093/nar/gkw520openalex-snapshot
FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing
inferredcites →https://doi.org/10.1093/nar/gky1015openalex-snapshot
COSMIC: the Catalogue Of Somatic Mutations In Cancer
inferredcites →https://doi.org/10.1101/181339openalex-snapshot
Patterns of structural variation in human cancer
inferredcites →https://doi.org/10.1101/gr.106344.110openalex-snapshot
Detecting copy number variation with mated short reads
inferredcites →https://doi.org/10.1101/gr.118414.110openalex-snapshot
Estimation of rearrangement phylogeny for cancer genomes
inferredcites →https://doi.org/10.1101/gr.134395.111openalex-snapshot
A genome-wide analysis of common fragile sites: What features determine chromosomal instability in the human genome?
inferredcites →https://doi.org/10.1101/gr.180281.114openalex-snapshot
TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data
inferredcites →https://doi.org/10.1101/gr.221028.117openalex-snapshot
SvABA: genome-wide detection of structural variants and indels by local assembly
inferredcites →https://doi.org/10.1101/gr.222109.117openalex-snapshot
GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly
inferredcites →https://doi.org/10.1126/science.aau3879openalex-snapshot
Somatic mutant clones colonize the human esophagus with age
inferredcites →https://doi.org/10.1186/1471-2105-13-s6-s10openalex-snapshot
Reconstructing cancer genomes from paired-end sequencing data
inferredcites →https://doi.org/10.1186/s13059-016-0893-4openalex-snapshot
deconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution
inferredcites →https://doi.org/10.1186/s13059-017-1267-2openalex-snapshot
ReMixT: clone-specific genomic structure estimation in cancer
inferredcites →https://doi.org/10.1371/journal.pcbi.1006799openalex-snapshot
Integrated structural variation and point mutation signatures in cancer genomes using correlated topic models
inferredcites →https://doi.org/10.3892/ijo_00000572openalex-snapshot
Global screening and extended nomenclature for 230 aphidicolin-inducible fragile sites, including 61 yet unreported ones

What points at this work

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

inferred← citeshttps://doi.org/10.1016/j.cell.2021.03.009openalex-snapshot
Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes
inferred← citeshttps://doi.org/10.1016/j.xgen.2022.100112openalex-snapshot
Unscrambling cancer genomes via integrated analysis of structural variation and copy number
inferred← citeshttps://doi.org/10.1038/s41467-021-21933-7openalex-snapshot
Structural variant evolution after telomere crisis
inferred← citeshttps://doi.org/10.1038/s41588-020-0678-2openalex-snapshot
Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers
inferred← citeshttps://doi.org/10.1038/s41591-020-0915-3openalex-snapshot
Genome-wide cell-free DNA mutational integration enables ultra-sensitive cancer monitoring
inferred← citeshttps://doi.org/10.1101/2019.12.18.881086openalex-snapshot
Revealing the impact of recurrent and rare structural variants in multiple myeloma
inferred← citeshttps://doi.org/10.1101/2019.12.20.875807openalex-snapshot
Enhancer hijacking determines intra- and extrachromosomal circular MYCN amplicon architecture in neuroblastoma
inferred← citeshttps://doi.org/10.1101/833590openalex-snapshot
Nanopore sequencing of DNA concatemers reveals higher-order features of chromatin structure
inferred← citeshttps://doi.org/10.1111/pcmr.12885openalex-snapshot
Acral lentiginous melanoma: Basic facts, biological characteristics and research perspectives of an understudied disease
inferred← citeshttps://doi.org/10.1158/1078-0432.c.6530273openalex-snapshot
Data from Designing Evolutionary-based Interception Strategies to Block the Transition from Precursor Phases to Multiple Myeloma
inferred← citeshttps://doi.org/10.1158/1078-0432.c.6530273.v1openalex-snapshot
Data from Designing Evolutionary-based Interception Strategies to Block the Transition from Precursor Phases to Multiple Myeloma
inferred← citeshttps://doi.org/10.1158/1078-0432.ccr-20-1395openalex-snapshot
Designing Evolutionary-based Interception Strategies to Block the Transition from Precursor Phases to Multiple Myeloma
inferred← citeshttps://doi.org/10.1158/2643-3230.bcd-20-0132openalex-snapshot
Revealing the Impact of Structural Variants in Multiple Myeloma
inferred← citeshttps://doi.org/10.3389/fped.2020.00189openalex-snapshot
Developmental Mutators and Early Onset Cancer
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