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The HLA genes are highly polymorphic. They typically share an extremely high sequence similarity with one another (e.g. there is a 92% sequence identity between HLA–B and HLA-C). The identification of HLA-HLA fusion (or readthrough) candidates is most likely the result of errors during the alignment of the sequencing reads to the human genome. This is typically due to the presence of sequencing errors or polymorphisms, which leads to an erroneous mapping of the two paired reads to different HLA genes. Therefore, HLA-HLA events represent sequencing artefacts rather than real fusion events. Although the ex post identification of such HLA artefacts is trivial, their presence may steal computational power, thus increasing the time required by FusionAnalyser to complete a run. The HLA-HLA filter is active by default.
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