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BreakCA, a method to discover indels using ChIP-seq and ATAC-seq reads, finds recurrent indels in regulatory regions of neuroblastoma genomes

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1 of the 61 references listed on this page is in the Retraction Watch database as retracted (export 2026-11-04): 10.3892/ijmm.2016.2614 (notice 2024-09-16).

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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.26145openalex-snapshot

Retinoic acid induces REST degradation and neuronal differentiation by modulating the expression of SCFβ‐TRCP in neuroblastoma cells

inferredcites →https://doi.org/10.1002/j.1460-2075.1996.tb00416.xopenalex-snapshot

Ral‐GTPases mediate a distinct downstream signaling pathway from Ras that facilitates cellular transformation.

inferredcites →https://doi.org/10.1007/978-1-4939-8666-8_7openalex-snapshot

Split-Read Indel and Structural Variant Calling Using PINDEL

inferredcites →https://doi.org/10.1016/j.cell.2010.06.004openalex-snapshot

NF1 Is a Tumor Suppressor in Neuroblastoma that Determines Retinoic Acid Response and Disease Outcome

inferredcites →https://doi.org/10.1016/j.molonc.2015.10.020openalex-snapshot

Transcription factor activating protein 2 beta (TFAP2B) mediates noradrenergic neuronal differentiation in neuroblastoma

inferredcites →https://doi.org/10.1016/j.ydbio.2011.04.011openalex-snapshot

The transcription factors AP-2β and AP-2α are required for survival of sympathetic progenitors and differentiated sympathetic neurons

inferredcites →https://doi.org/10.1038/nature09906openalex-snapshot

Mapping and analysis of chromatin state dynamics in nine human cell types

inferredcites →https://doi.org/10.1038/nature11154openalex-snapshot

Sequence analysis of mutations and translocations across breast cancer subtypes

inferredcites →https://doi.org/10.1038/nature11247openalex-snapshot

An integrated encyclopedia of DNA elements in the human genome

inferredcites →https://doi.org/10.1038/nature11329openalex-snapshot

Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations

inferredcites →https://doi.org/10.1038/nature11404openalex-snapshot

Comprehensive genomic characterization of squamous cell lung cancers

inferredcites →https://doi.org/10.1038/nature14666openalex-snapshot

Non-coding recurrent mutations in chronic lymphocytic leukaemia

inferredcites →https://doi.org/10.1038/nature15540openalex-snapshot

Genetic predisposition to neuroblastoma mediated by a LMO1 super-enhancer polymorphism

inferredcites →https://doi.org/10.1038/nature18910openalex-snapshot

Non-coding recurrent mutations in chronic lymphocytic leukaemia

inferredcites →https://doi.org/10.1038/nature19057openalex-snapshot

Analysis of protein-coding genetic variation in 60,706 humans

inferredcites →https://doi.org/10.1038/nbt.1754openalex-snapshot

Integrative genomics viewer

inferredcites →https://doi.org/10.1038/ncomms14385openalex-snapshot

Small genomic insertions form enhancers that misregulate oncogenes

inferredcites →https://doi.org/10.1038/ncomms3185openalex-snapshot

Frequency of TERT promoter mutations in human cancers

inferredcites →https://doi.org/10.1038/ng.2529openalex-snapshot

The genetic landscape of high-risk neuroblastoma

inferredcites →https://doi.org/10.1038/ng.2653openalex-snapshot

The Genotype-Tissue Expression (GTEx) project

inferredcites →https://doi.org/10.1038/ng.3101openalex-snapshot

Genome-wide analysis of noncoding regulatory mutations in cancer

inferredcites →https://doi.org/10.1038/ng.3333openalex-snapshot

Relapsed neuroblastomas show frequent RAS-MAPK pathway mutations

inferredcites →https://doi.org/10.1038/ng.3921openalex-snapshot

Heterogeneity of neuroblastoma cell identity defined by transcriptional circuitries

inferredcites →https://doi.org/10.1038/nmeth.2688openalex-snapshot

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

inferredcites →https://doi.org/10.1038/nmeth.4267openalex-snapshot

Genome-wide profiling of heritable and de novo STR variations

inferredcites →https://doi.org/10.1038/nmeth.4396openalex-snapshot

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

inferredcites →https://doi.org/10.1038/s41588-018-0044-9openalex-snapshot

Enhancer invasion shapes MYCN-dependent transcriptional amplification in neuroblastoma

inferredcites →https://doi.org/10.1073/pnas.0700735104openalex-snapshot

JARID1B is a histone H3 lysine 4 demethylase up-regulated in prostate cancer

inferredcites →https://doi.org/10.1073/pnas.112008599openalex-snapshot

A core–BRAF35 complex containing histone deacetylase mediates repression of neuronal-specific genes

inferredcites →https://doi.org/10.1073/pnas.79.24.7824openalex-snapshot

Human c-myc onc gene is located on the region of chromosome 8 that is translocated in Burkitt lymphoma cells.

inferredcites →https://doi.org/10.1073/pnas.94.3.1041openalex-snapshot

Relative mutation rates at di-, tri-, and tetranucleotide microsatellite loci

inferredcites →https://doi.org/10.1086/302905openalex-snapshot

Characteristics and Frequency of Germline Mutations at Microsatellite Loci from the Human Y Chromosome, as Revealed by Direct Observation in Father/Son Pairs

inferredcites →https://doi.org/10.1086/338997openalex-snapshot

Mutation Patterns at Dinucleotide Microsatellite Loci in Humans

inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot

The Sequence Alignment/Map format and SAMtools

inferredcites →https://doi.org/10.1093/bioinformatics/btp616openalex-snapshot

edgeR : a Bioconductor package for differential expression analysis of digital gene expression data

inferredcites →https://doi.org/10.1093/bioinformatics/bts378openalex-snapshot

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

inferredcites →https://doi.org/10.1093/bioinformatics/btt656openalex-snapshot

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

inferredcites →https://doi.org/10.1093/bioinformatics/btu168openalex-snapshot

VariantAnnotation : a Bioconductor package for exploration and annotation of genetic variants

inferredcites →https://doi.org/10.1093/bioinformatics/btv710openalex-snapshot

Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications

inferredcites →https://doi.org/10.1093/bioinformatics/btw024openalex-snapshot

TFBSTools: an R/bioconductor package for transcription factor binding site analysis

inferredcites →https://doi.org/10.1093/nar/gkv1176openalex-snapshot

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

inferredcites →https://doi.org/10.1101/531210openalex-snapshot

The mutational constraint spectrum quantified from variation in 141,456 humans

inferredcites →https://doi.org/10.1101/gr.129684.111openalex-snapshot

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

inferredcites →https://doi.org/10.1101/gr.210500.116openalex-snapshot

A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree

inferredcites →https://doi.org/10.1126/science.1229259openalex-snapshot

Highly Recurrent TERT Promoter Mutations in Human Melanoma

inferredcites →https://doi.org/10.1126/science.1259037openalex-snapshot

An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element

inferredcites →https://doi.org/10.1126/science.1260200openalex-snapshot

TERT promoter mutations and telomerase reactivation in urothelial cancer

inferredcites →https://doi.org/10.1182/blood-2009-03-212191openalex-snapshot

Lymphomas with concurrent BCL2 and MYC translocations: the critical factors associated with survival

inferredcites →https://doi.org/10.1186/1748-7188-2-15openalex-snapshot

Efficient and accurate P-value computation for Position Weight Matrices

inferredcites →https://doi.org/10.1186/gb-2008-9-9-r137openalex-snapshot

Model-based Analysis of ChIP-Seq (MACS)

inferredcites →https://doi.org/10.1186/s12859-017-1537-8openalex-snapshot

GATK hard filtering: tunable parameters to improve variant calling for next generation sequencing targeted gene panel data

inferredcites →https://doi.org/10.1186/s12864-018-4718-6openalex-snapshot

A genome-wide survey of mutations in the Jurkat cell line

inferredcites →https://doi.org/10.1186/s13148-018-0533-9openalex-snapshot

Histone demethylase JARID1B/KDM5B promotes aggressiveness of non-small cell lung cancer and serves as a good prognostic predictor

inferredcites →https://doi.org/10.1371/journal.pbio.0060108openalex-snapshot

Allele-Specific Up-Regulation of FGFR2 Increases Susceptibility to Breast Cancer

inferredcites →https://doi.org/10.1371/journal.pcbi.1003118openalex-snapshot

Software for Computing and Annotating Genomic Ranges

inferredcites →https://doi.org/10.1371/journal.pgen.1002165openalex-snapshot

A Functional Variant at a Prostate Cancer Predisposition Locus at 8q24 Is Associated with PVT1 Expression

inferredcites →https://doi.org/10.1371/journal.pone.0125343openalex-snapshot

JARID1B Expression Plays a Critical Role in Chemoresistance and Stem Cell-Like Phenotype of Neuroblastoma Cells

inferredcites →https://doi.org/10.18632/oncotarget.26144openalex-snapshot

Overexpression of KDM5B/JARID1B is associated with poor prognosis in hepatocellular carcinoma

inferredcites →https://doi.org/10.3892/ijmm.2016.2614openalex-snapshot

Jumonji AT-rich interactive domain 1B overexpression is associated with the development and progression of glioma

inferredcites →https://doi.org/10.4161/fly.19695openalex-snapshot

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

inferredcites →https://doi.org/10.6084/m9.figshare.963153.v1openalex-snapshot

Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEM

What points at this work

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

inferred← citeshttps://doi.org/10.70675/9c32f63bza75fz4561z8619zaa33713157b5openalex-snapshot

Rôle et détection des enhancers au cours de la différentiation normale et en contexte leucémique

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