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Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads

Ruping Sun, Michael I. Love, Tomasz Zemojtel, Anne-Katrin Emde, Ho-Ryun Chung, Martin Vingron, Stefan A. Haas
2012 Computer applications in the biosciences : CABIOS  
We developed Breakpointer, a fast algorithm to locate breakpoints of structural variants (SVs) from single-end reads produced by next-generation sequencing (NGS).  ...  By taking advantage of local non-uniform read distribution and misalignments created by SVs, Breakpointer scans the alignment of single-end reads to identify regions containing potential breakpoints.  ...  Alternatively, to characterize SVs from single-end reads (SE), split-read methods can be adopted to generate pseudo PE (Ye et al., 2009; Smith, 2011) .  ... 
doi:10.1093/bioinformatics/bts064 pmid:22302574 fatcat:q6w66jihczdzbg7wbxp6v7qlxe

Mutation spectrum revealed by breakpoint sequencing of human germline CNVs

Donald F Conrad, Christine Bird, Ben Blackburne, Sarah Lindsay, Lira Mamanova, Charles Lee, Daniel J Turner, Matthew E Hurles
2010 Nature Genetics  
However, fewer than 0% of known germline CNVs have been mapped to the single-nucleotide level.  ...  We used targeted hybridization-based DNA capture and 454 sequencing to sequence 324 CNV breakpoints, including 315 deletions.  ...  We thank the Wellcome Trust Sanger Institute for informatics and sequencing support, H. Lam for sharing sequenced CNV breakpoint locations and colleagues at NimbleGen for support and discussions.  ... 
doi:10.1038/ng.564 pmid:20364136 pmcid:PMC3428939 fatcat:mjy4ywqkzzbixibouwexlh5kqy

Enhanced structural variant and breakpoint detection using SVMerge by integration of multiple detection methods and local assembly

Kim Wong, Thomas M Keane, James Stalker, David J Adams
2010 Genome Biology  
We present a pipeline, SVMerge, to detect structural variants by integrating calls from several existing structural variant callers, which are then validated and the breakpoints refined using local de  ...  We applied SVMerge to the analysis of a HapMap trio, demonstrating enhanced structural variant detection, breakpoint refinement, and a lower false discovery rate.  ...  Acknowledgements This work was supported by the Medical Research Council, UK and the Wellcome Trust. DJA is supported by Cancer Research-UK.  ... 
doi:10.1186/gb-2010-11-12-r128 pmid:21194472 pmcid:PMC3046488 fatcat:yyexy5ow7nd2ngij5lzd23tyea

Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome

A. R. Quinlan, R. A. Clark, S. Sokolova, M. L. Leibowitz, Y. Zhang, M. E. Hurles, J. C. Mell, I. M. Hall
2010 Genome Research  
We have developed an algorithm (HYDRA) to localize SV breakpoints by paired-end mapping, and a general approach for the genome-wide assembly and interpretation of breakpoint sequences.  ...  To investigate the origins of SV, we characterized 3316 breakpoint sequences at single-nucleotide resolution.  ...  Prorock for assistance with DNA sequencing; W.R.  ... 
doi:10.1101/gr.102970.109 pmid:20308636 pmcid:PMC2860164 fatcat:wrpf7wci4fehzenbsg6yuz7gc4

Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms

A. Malhotra, M. Lindberg, G. G. Faust, M. L. Leibowitz, R. A. Clark, R. M. Layer, A. R. Quinlan, I. M. Hall
2013 Genome Research  
To assess the prevalence and origins of complex genomic rearrangements (CGRs), we mapped 6179 somatic structural variation breakpoints in 64 cancer genomes from seven tumor types and screened for clusters  ...  Finally, assembly and analysis of 4002 somatic and 6982 germline breakpoint sequences reveal that somatic breakpoints show significantly less microhomology and fewer templated insertions than germline  ...  Simpson for advice regarding modifications to the SGA assembler and the TCGA Network for producing the data used in this study.  ... 
doi:10.1101/gr.143677.112 pmid:23410887 pmcid:PMC3638133 fatcat:nwwkwtzldvcirpni6a5kacdryi

BreakSeek: a breakpoint-based algorithm for full spectral range INDEL detection

Hui Zhao, Fangqing Zhao
2015 Nucleic Acids Research  
Here we present BreakSeek, a novel breakpoint-based algorithm, which can unbiasedly and efficiently detect both homozygous and heterozygous INDELs, ranging from several base pairs to over thousands of  ...  Although recent developed algorithms have integrated multiple signals to improve sensitivity for insertion and deletion (INDEL) detection, they are far from being perfect and still have great limitations  ...  Real datasets Paired-end sequence data for individual NA12878 were downloaded from the Sequence Read Archive (accession number ERP001229) and aligned to the hg19 human genome reference sequence using BWA  ... 
doi:10.1093/nar/gkv605 pmid:26117537 pmcid:PMC4538813 fatcat:r6kvwgd2pvfn5fgubwvtfw3zpa

Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data

Lynnette Fernandez-Cuesta, Ruping Sun, Roopika Menon, Julie George, Susanne Lorenz, Leonardo A Meza-Zepeda, Martin Peifer, Dennis Plenker, Johannes M Heuckmann, Frauke Leenders, Thomas Zander, Ilona Dahmen (+28 others)
2015 Genome Biology  
Identification of such fusion transcripts by transcriptome sequencing might help to discover new potential therapeutic targets.  ...  We developed TRUP (Tumor-specimen suited RNA-seq Unified Pipeline) (https://github.com/ruping/TRUP), a computational approach that combines split-read and read-pair analysis with de novo assembly for the  ...  This work was supported by the Deutsche Krebshilfe as part of the small-cell lung cancer genome-sequencing consortium (grant ID: 109679 to RKT, MP, RB, PN, MV, and SAH).  ... 
doi:10.1186/s13059-014-0558-0 pmid:25650807 pmcid:PMC4300615 fatcat:3rzmbyv26net7k54bn2hs34sza

Breakpoint Analysis of Transcriptional and Genomic Profiles Uncovers Novel Gene Fusions Spanning Multiple Human Cancer Types

Craig P. Giacomini, Steven Sun, Sushama Varma, A. Hunter Shain, Marilyn M. Giacomini, Jay Balagtas, Robert T. Sweeney, Everett Lai, Catherine A. Del Vecchio, Andrew D. Forster, Nicole Clarke, Kelli D. Montgomery (+6 others)
2013 PLoS Genetics  
Here, we developed a "breakpoint analysis" pipeline to discover candidate gene fusions by tell-tale transcript level or genomic DNA copy number transitions occurring within genes.  ...  Taken together, we provide a robust approach for gene fusion discovery, and our results highlight a more widespread role of fusion genes in cancer pathogenesis.  ...  Acknowledgments The authors would like to thank the members of the Pollack lab for helpful discussion. Author Contributions  ... 
doi:10.1371/journal.pgen.1003464 pmid:23637631 pmcid:PMC3636093 fatcat:yi3eyariwfh5xgdsm7ts6mdby4

Detection of fusion transcripts and their genomic breakpoints from RNA sequencing data [article]

Youri Hoogstrate, Malgorzata A. Komor, René Böttcher, Job van Riet, Harmen J.G. van de Werken, Stef van Lieshout, Ralf Hoffmann, Evert van den Broek, Anne S. Bolijn, Natasja Dits, Daoud Sie, David van der Meer (+16 others)
2021 bioRxiv   pre-print
Disco algorithm that makes use of both intronic and exonic RNA-seq reads to identify not only fusion transcripts but also genomic breakpoints in gene but also in intergenic regions. Dr.  ...  Disco identified TMPRSS2-ERG fusions with genomic breakpoints and other transcribed rearrangements from multiple RNA-sequencing cohorts. In breast cancer and glioma samples Dr.  ...  . ; https://doi.org/10.1101/2021.05.17.441778 doi: bioRxiv preprint To avoid artifacts from RNA post-processing such as circRNAs and read-throughs, only interchromosomal entries were interrogated.  ... 
doi:10.1101/2021.05.17.441778 fatcat:fmeacglbvnbbhohcifvv6muw6y

Detection and Interpretation of Genomic Structural Variation in Mammals [chapter]

Ira M. Hall, Aaron R. Quinlan
2011 Msphere  
We then present methods to identify SV breakpoints from next-generation sequence (NGS) data by paired-end mapping, split-read mapping, and local assembly, and discuss challenges that arise when interpreting  ...  They come in a broad range of shapes and sizes, from single-nucleotide polymorphisms (SNPs) to chromosomal rearrangements involving many megabases of DNA. As a rule, our appreciation for the different  ...  A more powerful approach to SV discovery is the use of longer (e.g., >200 bp) DNA sequences to characterize SV breakpoints at single base-pair resolution.  ... 
doi:10.1007/978-1-61779-507-7_11 pmid:22228015 fatcat:algdabtl4zhbxpei7klg7qsg54

Assessing structural variation in a personal genome—towards a human reference diploid genome

Adam C English, William J Salerno, Oliver A Hampton, Claudia Gonzaga-Jauregui, Shruthi Ambreth, Deborah I Ritter, Christine R Beck, Caleb F Davis, Mahmoud Dahdouli, Singer Ma, Andrew Carroll, Narayanan Veeraraghavan (+19 others)
2015 BMC Genomics  
Of these loci, 9,777 are supported as putative SVs by hybrid local assembly, long-read PacBio data, or multi-source heuristics.  ...  Conclusions: HS1011 SV analysis reveals the limits and advantages of multiple sequencing technologies, specifically the impact of long-read SV discovery.  ...  Acknowledgements This work was supported in part by grants from the National Human Genome Research Institute (NHGRI) (U54HG003273) to RAG, the US National Institute of Neurological Disorders and Stroke  ... 
doi:10.1186/s12864-015-1479-3 pmid:25886820 pmcid:PMC4490614 fatcat:2jy2bprzw5bcja6ah23bkirooy

LUMPY: a probabilistic framework for structural variant discovery

Ryan M Layer, Colby Chiang, Aaron R Quinlan, Ira M Hall
2014 Genome Biology  
Comprehensive discovery of structural variation (SV) from whole genome sequencing data requires multiple detection signals including read-pair, split-read, read-depth and prior knowledge.  ...  Owing to technical challenges, extant SV discovery algorithms either use one signal in isolation, or at best use two sequentially.  ...  This work was supported by an NIH/NHGRI award to AQ (1R01HG006693-01) and an NIH New Innovator Award (DP2OD006493-01) and a Burroughs Wellcome Fund Career Award to IH.  ... 
doi:10.1186/gb-2014-15-6-r84 pmid:24970577 pmcid:PMC4197822 fatcat:p3ejyvggbrbxlkteex4hshi4si

Discovery and genotyping of genome structural polymorphism by sequencing on a population scale

Robert E Handsaker, Joshua M Korn, James Nemesh, Steven A McCarroll
2011 Nature Genetics  
Our approach uses population-level relationships to re-interpret the technical features of sequence data that often reflect structural variation.  ...  "Discovery and genotyping of genome structural polymorphism by sequencing on a population scale." Nature genetics 43 (3): 269-276.  ...  specificity of SV discovery  ... 
doi:10.1038/ng.768 pmid:21317889 pmcid:PMC5094049 fatcat:nhwvmr3jlbejdaqaob5k4626ci

BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data

K. Chen, J. W. Wallis, C. Kandoth, J. M. Kalicki-Veizer, K. L. Mungall, A. J. Mungall, S. J. Jones, M. A. Marra, T. J. Ley, E. R. Mardis, R. K. Wilson, J. N. Weinstein (+1 others)
2012 Bioinformatics  
Despite recent progress, computational tools that identify gene fusions from next-generation whole transcriptome sequencing data are often limited in accuracy and scalability.  ...  Here, we present a software package, BreakFusion that combines the strength of reference alignment followed by read-pair analysis and de novo assembly to achieve a good balance in sensitivity, specificity  ...  Funding: The Cancer Center Support Grant from NCI (P30 CA016672 to UT MD Anderson); Center for Large-Scale Genome Sequencing and Analysis from NHGRI (U54 HG003079 to R.K.W); Structural Genomic Variation  ... 
doi:10.1093/bioinformatics/bts272 pmid:22563071 pmcid:PMC3389765 fatcat:lqcrkcifwzaslch7oltqtzkw74

Evaluation of Paired-End Sequencing Strategies for Detection of Genome Rearrangements in Cancer

Ali Bashir, Stanislav Volik, Colin Collins, Vineet Bafna, Benjamin J. Raphael, Christos A. Ouzounis
2008 PLoS Computational Biology  
We address the question of how much sequencing is required to detect rearrangement breakpoints and to localize them precisely using both theoretical models and simulation.  ...  We derive a formula for the probability that a fusion gene exists in a cancer genome given a collection of paired-end sequences from this genome.  ...  Acknowledgments We would like to thank the members of the Bafna and Pevzer labs at UCSD for helpful suggestions and discussions.  ... 
doi:10.1371/journal.pcbi.1000051 pmid:18404202 pmcid:PMC2278375 fatcat:nsxisowq6vf6nmwiqurslxewn4
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