BreakDancer：通过双末端读段比对识别基因组结构变异
BreakDancer: Identification of Genomic Structural Variation from Paired-End Read Mapping.
作者信息
Fan Xian, Abbott Travis E, Larson David, Chen Ken
机构信息
Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd Unit 1410, Houston, TX 77030.
The Genome Institute at Washington University in St. Louis, 4444 Forest Park Ave., St. Louis, MO 63108.
出版信息
Curr Protoc Bioinformatics. 2014;45:15.6.1-11. doi: 10.1002/0471250953.bi1506s45.
Abstract
The advent of the next-generation sequencing data has made it possible to cost-effectively detect and characterize genomic variation in human genomes. Structural variation, including deletion, duplication, insertion, inversion and translocation, is of great importance to human genetics due to its association with many genetic diseases. BreakDancer is a bioinformatics tool that relates paired-end read alignments from a test genome to the reference genome for the purpose of comprehensively and accurately detecting various types of structural variation.
摘要
下一代测序数据的出现使得经济高效地检测和表征人类基因组中的基因组变异成为可能。结构变异，包括缺失、重复、插入、倒位和易位，因其与许多遗传疾病相关，对人类遗传学具有重要意义。BreakDancer是一种生物信息学工具，它将测试基因组的双末端读段比对与参考基因组相关联，以便全面准确地检测各种类型的结构变异。
相似文献
1
BreakDancer: Identification of Genomic Structural Variation from Paired-End Read Mapping.
Curr Protoc Bioinformatics. 2014;45:15.6.1-11. doi: 10.1002/0471250953.bi1506s45.
2
BreakDancer: an algorithm for high-resolution mapping of genomic structural variation.
Nat Methods. 2009 Sep;6(9):677-81. doi: 10.1038/nmeth.1363. Epub 2009 Aug 9.
3
Detection of structural variants involving repetitive regions in the reference genome.
J Comput Biol. 2014 Mar;21(3):219-33. doi: 10.1089/cmb.2013.0129. Epub 2014 Feb 19.
4
Genome sequencing in cytogenetics: Comparison of short-read and linked-read approaches for germline structural variant detection and characterization.
Mol Genet Genomic Med. 2020 Mar;8(3):e1114. doi: 10.1002/mgg3.1114. Epub 2020 Jan 27.
5
Seeksv: an accurate tool for somatic structural variation and virus integration detection.
Bioinformatics. 2017 Jan 15;33(2):184-191. doi: 10.1093/bioinformatics/btw591. Epub 2016 Sep 14.
6
Robust and exact structural variation detection with paired-end and soft-clipped alignments: SoftSV compared with eight algorithms.
Brief Bioinform. 2016 Jan;17(1):51-62. doi: 10.1093/bib/bbv028. Epub 2015 May 20.
7
Complex structural variants in Mendelian disorders: identification and breakpoint resolution using short- and long-read genome sequencing.
Genome Med. 2018 Dec 7;10(1):95. doi: 10.1186/s13073-018-0606-6.
8
PRISM: pair-read informed split-read mapping for base-pair level detection of insertion, deletion and structural variants.
Bioinformatics. 2012 Oct 15;28(20):2576-83. doi: 10.1093/bioinformatics/bts484. Epub 2012 Jul 31.
9
An integrative probabilistic model for identification of structural variation in sequencing data.
Genome Biol. 2012;13(3):R22. doi: 10.1186/gb-2012-13-3-r22.
10
Precise detection of chromosomal translocation or inversion breakpoints by whole-genome sequencing.
J Hum Genet. 2014 Dec;59(12):649-54. doi: 10.1038/jhg.2014.88. Epub 2014 Oct 9.
引用本文的文献
1
Recql5-Deficient Mice as a Model for Studying Chromoanagenesis Phenomena.
Methods Mol Biol. 2025;2968:559-578. doi: 10.1007/978-1-0716-4750-9_34.
2
Identification of candidate cardiomyopathy modifier genes through genome sequencing and RNA profiling.
Front Cardiovasc Med. 2025 Jul 28;12:1546493. doi: 10.3389/fcvm.2025.1546493. eCollection 2025.
3
Uncovering minimal pathways in melanoma initiation.
Nat Commun. 2025 Jun 26;16(1):5369. doi: 10.1038/s41467-025-60742-0.
4
CYTO-SV-ML: A Machine Learning Tool for Cytogenetic Structural Variant Analysis in Somatic Cell Type Using Genome Sequences.
Life (Basel). 2025 Jun 9;15(6):929. doi: 10.3390/life15060929.
5
Chromosomal Inversions in Chromosome U of : A Story from Population Studies to Molecular Level.
Insects. 2025 Jun 1;16(6):586. doi: 10.3390/insects16060586.
6
Population genomics of sika deer reveals recent speciation and genetic selective signatures during evolution and domestication.
BMC Genomics. 2025 Apr 11;26(1):364. doi: 10.1186/s12864-025-11541-w.
7
Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing.
Nat Biotechnol. 2025 Apr 4. doi: 10.1038/s41587-025-02618-8.
8
Best practices for germline variant and DNA methylation analysis of second- and third-generation sequencing data.
Hum Genomics. 2024 Nov 5;18(1):120. doi: 10.1186/s40246-024-00684-8.
9
A stepwise guide for pangenome development in crop plants: an alfalfa (Medicago sativa) case study.
BMC Genomics. 2024 Oct 31;25(1):1022. doi: 10.1186/s12864-024-10931-w.
10
Sex chromosome turnover in hybridizing stickleback lineages.
Evol Lett. 2024 May 11;8(5):658-668. doi: 10.1093/evlett/qrae019. eCollection 2024 Sep.
本文引用的文献
1
The origin and evolution of mutations in acute myeloid leukemia.
Cell. 2012 Jul 20;150(2):264-78. doi: 10.1016/j.cell.2012.06.023.
2
Absolute quantification of somatic DNA alterations in human cancer.
Nat Biotechnol. 2012 May;30(5):413-21. doi: 10.1038/nbt.2203.
3
The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity.
Nature. 2012 Mar 28;483(7391):603-7. doi: 10.1038/nature11003.
4
Mapping copy number variation by population-scale genome sequencing.
Nature. 2011 Feb 3;470(7332):59-65. doi: 10.1038/nature09708.
5
Aligning short sequencing reads with Bowtie.
Curr Protoc Bioinformatics. 2010 Dec;Chapter 11:Unit 11.7. doi: 10.1002/0471250953.bi1107s32.
6
MapSplice: accurate mapping of RNA-seq reads for splice junction discovery.
Nucleic Acids Res. 2010 Oct;38(18):e178. doi: 10.1093/nar/gkq622. Epub 2010 Aug 27.
7
Genome remodelling in a basal-like breast cancer metastasis and xenograft.
Nature. 2010 Apr 15;464(7291):999-1005. doi: 10.1038/nature08989.
8
BreakDancer: an algorithm for high-resolution mapping of genomic structural variation.
Nat Methods. 2009 Sep;6(9):677-81. doi: 10.1038/nmeth.1363. Epub 2009 Aug 9.
9
Fast and accurate short read alignment with Burrows-Wheeler transform.
Bioinformatics. 2009 Jul 15;25(14):1754-60. doi: 10.1093/bioinformatics/btp324. Epub 2009 May 18.
10
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Genome Biol. 2009;10(3):R25. doi: 10.1186/gb-2009-10-3-r25. Epub 2009 Mar 4.
Zotero 插件