BreakDancer: An algorithm for high resolution mapping of genomic structural variation

By Ken Chen, J. Wallis, M. McLellan, David E. Larson, Joelle Kalicki, C. Pohl, S. McGrath, Michael C. Wendl, Qunyuan Zhang, Devin P. Locke and 6 more. Nature Methods, 2009

1,513 citations recorded by the source corpus.

Detection and characterization of genomic structural variation are important for understanding the landscape of genetic variation in human populations and in complex diseases such as cancer. Recent studies demonstrate the feasibility of detecting structural variation using next-generation, short-insert, paired-end sequencing reads. However, the utility of these reads is not entirely clear, nor are the analysis methods with which accurate detection can be achieved. The algorithm BreakDancer predicts a wide variety of structural variants including insertion-deletions (indels), inversions and translocations. We examined BreakDancer's performance in simulation, in comparison with other methods and in analyses of a sample from an individual with acute myeloid leukemia and of samples from the 1,000 Genomes trio individuals. BreakDancer sensitively and accurately detected indels ranging from 10 base pairs to 1 megabase pair that are difficult to detect via a single conventional approach.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c06c1cfbcf132e4c2df681bd2171c380f907b552

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

In Molecular Biology

Citations in the corpus

Personalized Oncology Through Integrative High-Throughput Sequencing: A Pilot Study (2011, methodology): “12 7/4$PATIENT_1 !"#(1%&*2033'1+ &*0(22)(12 2 3.”
Assembly Algorithms for Next-Generation Sequencing Data (2010, neutral): “Mapping-based variant discovery algorithms include MoDIL [82], VariationHunter [83] and BreakDancer [84].”
Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma. (2018, methodology): “Genomic Data Commons https://portal.gdc.cancer.gov/legacy-archive Digital pathology images Genomic Data Commons Cancer Digital Slide Archive https://gdc-portal.nci.nih.gov/legacy-archive/ http://cancer.digitalslidearchive.net/ Software and Algorithms ABSOLUTE Carter et al., 2012 http://archive.broad”
Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes (2012, methodology): “SVs were called using: (1) paired-end mapping (Chen et al., 2009) (2) read depth (Abyzov et al., 2011), (3) split reads (Ye et al., 2009), and (4) junction mapping (Lam et al., 2010) to the breakpoint junction database from the 1000 G (Mills et al., 2011).”
Lessons from the cancer genome. (2013, neutral): “of foreign DNA (such as from viruses) (Beroukhim et al., 2007; Chen et al., 2009; Cibulskis et al., 2013; Dees et al., 2012; Kim and Salzberg, 2011; Kostic et al., 2011; Trapnell et al., 2009).”
An Integrated Pipeline for de Novo Assembly of Microbial Genomes (2012, methodology): “The algorithm is also related to structural variant detection algorithms [25,26].”
Sequence assembly demystified (2013, methodology): “A targeted, local assembly is done with relaxed criteria (that is, joining reads even if they overlap by only a small amount) to improve the ability to reconstruct sequences of uneven coverage; this approach is taken by BreakDancer 82 .”
Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement (2014, methodology): “0rc3 and BreakDancer 1 .”
The Sequence of 1504 Mutants in the Model Rice Variety Kitaake Facilitates Rapid Functional Genomic Studies (2017, methodology): “Genomic variants were called using a set of complementary tools, including SAMtools (Li and Durbin, 2009), BreakDancer (Chen et al., 2009), Pindel (Ye et al.”
LUMPY: a probabilistic framework for structural variant discovery (2012, methodology): “Both GASVPro and DELLY have also demonstrated substantial improvement over other popular SV tools such as Breakdancer [19] and HYDRA [20].”