Summary: The locations in specific DNA sequences where CHROMOSOME BREAKS have occurred.
- Henssen A, Koche R, Zhuang J, Jiang E, Reed C, Eisenberg A, et al. PGBD5 promotes site-specific oncogenic mutations in human tumors. Nat Genet. 2017;49:1005-1014 pubmed publisher..These results define PGBD5 as an oncogenic mutator and provide a plausible mechanism for site-specific DNA rearrangements in childhood and adult solid tumors. ..
- Clark B, Shooter C, Smith F, Brawand D, Thein S. Next-generation sequencing as a tool for breakpoint analysis in rearrangements of the globin gene clusters. Int J Lab Hematol. 2017;39 Suppl 1:111-120 pubmed publisher..The combined NGS and bioinformatic strategy has proven to be highly successful and applicable to routine diagnostics. ..
- Bartenhagen C, Dugas M. Robust and exact structural variation detection with paired-end and soft-clipped alignments: SoftSV compared with eight algorithms. Brief Bioinform. 2016;17:51-62 pubmed publisher..Sensitivities above 85% and positive predictive values between 80 and 100% could be achieved consistently for all SV types on simulated data sets starting at relatively short 75 bp reads and low 10-15Ã— sequence coverage. ..
- Weinreb C, Oesper L, Raphael B. Open adjacencies and k-breaks: detecting simultaneous rearrangements in cancer genomes. BMC Genomics. 2014;15 Suppl 6:S4 pubmed publisher..These results lend support to the existence of simultaneous rearrangements, but also demonstrate the difficulty of characterizing such rearrangements using different criterion. ..
- Jamshidpey A, Jamshidpey A, Sankoff D. Sets of medians in the non-geodesic pseudometric space of unsigned genomes with breakpoints. BMC Genomics. 2014;15 Suppl 6:S3 pubmed publisher..We also prove the conjecture that the input permutations themselves are medians. ..
- Layer R, Chiang C, Quinlan A, Hall I. LUMPY: a probabilistic framework for structural variant discovery. Genome Biol. 2014;15:R84 pubmed publisher..We also report a set of 4,564 validated breakpoints from the NA12878 human genome. https://github.com/arq5x/lumpy-sv. ..
- Marotta M, Chen X, Inoshita A, Stephens R, Budd G, Crowe J, et al. A common copy-number breakpoint of ERBB2 amplification in breast cancer colocalizes with a complex block of segmental duplications. Breast Cancer Res. 2012;14:R150 pubmed publisher..The haplotypes we provide could be useful to identify the potential association between the complex region and ERBB2 amplification. ..
- Ni X, Xia Q, Zhang H, Cheng S, Li H, Fan G, et al. Updated foxtail millet genome assembly and gene mapping of nine key agronomic traits by resequencing a RIL population. Gigascience. 2017;6:1-8 pubmed publisher..The whole genome resequencing and QTL mapping provided important tools for foxtail millet research and breeding. Resequencing of the RILs could also provide an effective way for high-quality genome assembly and gene identification. ..
- Chen K, Navin N, Wang Y, Schmidt H, Wallis J, Niu B, et al. BreakTrans: uncovering the genomic architecture of gene fusions. Genome Biol. 2013;14:R87 pubmed publisher..Applying BreakTrans to 43 breast cancer samples in The Cancer Genome Atlas identifies 90 genomically validated gene fusions. BreakTrans is available at http://bioinformatics.mdanderson.org/main/BreakTrans. ..