How to annotate translocation varaints?

[DayTimeMouse]

Hi,

Thanks for developing this nice tool.

How to annotate translocation variants via ANNOVAR?

The REF and ALT fields in the VCF file for SVs do not contain any bases. How can I annotate these translocation variants to genes? For example, I want to know which genes these translocations occur in, whether new genes are formed, etc.

Best wishes.

[kaichop]

you can treat it as two variants, to know where the translocation breakpoints are and how they impact the gene. The new gene needs to be predicted by hand, calculating whether a new ORF is formed by concatenating the two existing transcripts. This also replies on a few assumptions such as that the exon structure (splicing pattern) is in tact, which may not be the case. In general you need to look at transcriptome data to show whether there is really a new gene.

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On Wed, Jan 22, 2025 at 10:23 AM DayTimeMouse ***@***.***> wrote: Hi, Thanks for developing this nice tool. How to annotate translocation variants via ANNOVAR? The REF and ALT fields in the VCF file for SVs do not contain any bases. How can I annotate these translocation variants to genes? For example, I want to know which genes these translocations occur in, whether new genes are formed, etc. Best wishes. — Reply to this email directly, view it on GitHub <#272>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3OFDTV3HMMBZVE5VLVT2L6ZY3AVCNFSM6AAAAABVVGPYIKVHI2DSMVQWIX3LMV43ASLTON2WKOZSHAYDINRYGA4DANY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[DayTimeMouse]

I'm confused about the .variant_function in the output results. What does NONE(dist=NONE) mean? Also, does something like ENSG00000215912.13(dist=266273), ENSG00000285945.1(dist=81223) suggest that the breakpoint(chr1 4132525) might affect these two genes?

TRA1:
intergenic	NONE(dist=NONE),ENSG00000287870.1(dist=594200)	chr1	1	1	A	T
intergenic	NONE(dist=NONE),ENSG00000293062.1(dist=1951739)	chr21	254225	254225	A	T
TRA2:
intergenic	ENSG00000215912.13(dist=266273),ENSG00000285945.1(dist=81223)	chr1	4132525	4132525	A	T
intergenic	ENSG00000287396.1(dist=54543),ENSG00000284745.1(dist=89454)	chr1	4317962	4317962	A	T