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I'm reading the Manta User Guide → it is a method to discover structural variants and indels from next generation sequencing data.

The word 'breakend' is used in several contexts

I have searched for a definition in duckduckgo, qwant and google but have not found a concise definition.

Thanks for you help

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A structural variant is an inversion, deletion, duplication, or translocation. A "breakend" is one endpoint of a structural variant. This paper (Alkan et al. Nature Review Genetics 2011) may help you understand: https://www.nature.com/articles/nrg2958

The Manta paper and documentation seem sparse on diagrams. DELLY, another structural variant caller, has diagrams in their publication. Their paper may be more of use: https://academic.oup.com/bioinformatics/article/28/18/i333/245403

Specific example: Say you're sequencing a chronic myeloid leukemia (CML) tumor. You will likely find reads that half map to the ABL1 gene on chr9 and half map to the BCR gene on chr22 (https://en.wikipedia.org/wiki/Philadelphia_chromosome). The genomic position of the location where chr9 turns to chr22 is called the breakpoint. The positions on chr9 and chr22 are the breakends.

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  • $\begingroup$ Is it correct to say that the breakpoint is always on the sequence that I'm aligning to the reference, while the breakends always refer to the genomic positions in the reference genome? $\endgroup$
    – ilam engl
    Mar 30, 2021 at 14:28
  • $\begingroup$ I'd say breakpoint and breakends both refer to the genomic positions in the reference genome. A breakpoint typically contains two breakends, one for each genomic position. The sequences you're aligning to the reference would be called "supporting reads". They could be split (half aligns to one position, half to another), or paired-end reads (one read maps to one position, its mate pair to another). $\endgroup$
    – rk13
    Mar 31, 2021 at 15:58

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