novoBreak: local assembly for breakpoint detection in cancer genomes

Chong, Zechen; Ruan, Jue; Gao, Min; Zhou, Wanding; Chen, Tenghui; Fan, Xian; Li, Ding; Lee, Anna Y.; Boutros, Paul C.; Chen, Junjie; Chen, Ken

doi:10.1038/nmeth.4084

Cited by 97 publications

(80 citation statements)

References 23 publications

(35 reference statements)

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“…Structural variants were called with BreakDancer (Chen et al, 2009), Pindel (Ye et al, 2009) and novoBreak (Chong et al, 2016) with default parameters. novoBreak is a tool used for SV detection in cancer genomes, especially somatic ones.…”

Section: Star Methodsmentioning

confidence: 99%

An Organismal CNV Mutator Phenotype Restricted to Early Human Development

Liu

Yuan

Carvalho

et al. 2017

Cell

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Summary De novo copy number variants (dnCNVs) arising at multiple loci in a personal genome have usually been considered to reflect cancer somatic genomic instabilities. We describe a multiple dnCNV (MdnCNV) phenomenon in which individuals with genomic disorders carry five to ten constitutional dnCNVs. These CNVs originate from independent formation incidences, are predominantly tandem duplications or complex gains, exhibit breakpoint junction features reminiscent of replicative repair, and show increased de novo point mutations flanking the rearrangement junctions. The active CNV mutation shower appears to be restricted to a transient peri-zygotic period. We propose that a defect in the CNV formation process is responsible for the ‘CNV-mutator state’, and that this state is dampened after early embryogenesis. The constitutional MdnCNV phenomenon resembles chromosomal instability in various cancers. Investigations of this phenomenon may provide unique access to understanding genomic disorders, structural variant mutagenesis, human evolution and cancer biology.

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Section: Star Methodsmentioning

confidence: 99%

An Organismal CNV Mutator Phenotype Restricted to Early Human Development

Liu

Yuan

Carvalho

et al. 2017

Cell

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“…Data were analyzed using the novoBreak assembly algorithm to detect breakpoint junctions (Figure 1E) (Chong et al, 2017; Liu et al, 2017). In total, 6 junctions were identified through a combination of aCGH and WGS analyses; of those junctions, 5 were confirmed through traditional Sanger-sequencing (Supp.…”

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confidence: 99%

Marker chromosome genomic structure and temporal origin implicate a chromoanasynthesis event in a family with pleiotropic psychiatric phenotypes

Grochowski

Yuan

et al. 2018

Human Mutation

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Small supernumerary marker chromosomes (sSMC) are chromosomal fragments difficult to characterize genomically. Here, we detail a proband with schizoaffective disorder and a mother with bipolar disorder with psychotic features who present with a marker chromosome that segregates with disease. We explored the architecture of this marker and investigated its temporal origin. Array comparative genomic hybridization (aCGH) analysis revealed three duplications and three triplications that spanned the short arm of chromosome 9, suggestive of a chromoanasynthesis-like event. Segregation of marker genotypes, phased using sSMC mosaicism in the mother, provided evidence that it was generated during a germline-level event in the proband's maternal grandmother. Whole-genome sequencing (WGS) was performed to resolve the structure and junctions of the chromosomal fragments, revealing further complexities. While structural variations have been previously associated with neuropsychiatric disorders and marker chromosomes, here we detail the precise architecture, human life-cycle genesis, and propose a DNA replicative/repair mechanism underlying formation.

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“…However, it almost takes one day for MuTect 6 obtaining the INDEL and SNP results, and eight hours for novoBreak 7 getting the SV results.…”

Section: Resultsmentioning

confidence: 99%

GVC: An ultra-fast and all-round genome variant caller

Zhang

Liang

Lü

et al. 2017

Preprint

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Germline and somatic variant detection from human and cancer whole-genome sequencing data is a challenge task for genome-wide association study and cancer genomics in precision medicine.Many confounding factors contribute the difficulties including complexity of variant, sequencing and alignment error, tumor clonality and sample purity etc. Current genomic variant callers are too time-consuming to meet the requirement of clinical application in precision medicine. We developed superfast and universal Genomic Variant Caller (GVC), which can simultaneously detect various genomic variants including SNV, sINDEL and SV from personal and normal-cancer paired whole-genome/exome sequencing data within fifteen minutes. What's more, it achieved higher sensitivity and precision than popular variant callers including GATK4, Mutect, NovoBreak in germline and somatic variant detection from NA12878 and ICGC-TCGA Dream Challenge Datasets respectuvely. It is worth mentioning that GVC achieved comparable performance in variant detection from NA12878 sequenced by three different high-throughput sequencing platforms including Illumina HiSeq2000, NovaSeq and BGISEQ-500.

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novoBreak: local assembly for breakpoint detection in cancer genomes

Cited by 97 publications

References 23 publications

An Organismal CNV Mutator Phenotype Restricted to Early Human Development

An Organismal CNV Mutator Phenotype Restricted to Early Human Development

Marker chromosome genomic structure and temporal origin implicate a chromoanasynthesis event in a family with pleiotropic psychiatric phenotypes

GVC: An ultra-fast and all-round genome variant caller

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