Comments (3)
Gene that CTX hits the intron must be broken in the midst of its coding frame (exon continuation is broken) therefore PREDICTED_LOF should be justified for that matter. If both breakpoints were in the intergenic region then PREDICTED_LOF assessment might have been problematic.
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Thanks for the response and clarifying that.
The breakpoints are not overlapping at any exon (one bp is intergenic, the other is in intronic site).
I still don't see how so many genes have been computed under PREDCITED_LOF.
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Hi @Nehir291, please refer to the SVAnnotate tool documentation for definitions of each annotation: https://gatk.broadinstitute.org/hc/en-us/articles/21905053774363-SVAnnotate. For translocations, PREDICTED_LOF is assigned if a breakpoint falls at any point in the transcript, so an intronic breakpoint would still be annotated as PREDICTED_LOF for any impacted genes. This is because only part of the gene exists on each chromosome after the translocation, which is likely to result in a truncated transcript subject to nonsense-mediated decay.
Perhaps in some cases this definition is overly permissive, such as if only the UTR or one shorter exon is removed by the translocation - those cases could be worth revisiting.
I hope this helps explain the behavior you are seeing. If this does not fully explain all the PREDICTED_LOF annotations you are observing, please share the CTX breakpoints, the annotations, the SVAnnotate version, and the GTF used so we can investigate further.
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