About 'Splice Type'

[小林賢子]

Dear Dr. Haas

I am always grateful for your teachings.

Now I would like to ask three questions.

1.

You explain about the parameter 'SpliceType' as follows,

 'SpliceType' indicates whether the proposed breakpoint occurs at reference exon junctions as provided by the reference transcript structure annotations (ex. gencode).

And you assign the symbol INCL_NON_REF_SPLICE or ONLY_REF_SPLICE to the elements.

Please spell the abbreviations in full so that I will understand about 'Splice Type' better.

2.

I have a result of STAR-Fusion of a cell-line whose RNA-seq data are from total RNA.

The Splice Type of STX8::IDI2 (chr17:9545172:-, chr10:1022775:) is output as INCL_NON_REF_SPLICE.

The break point of IDI2 is on 5'UTR. So, is the assigning INCL_NON_REF_SPLICE because the break point is not exon junction?

3. 

 Generally, there are many kind of RNAs in total RNA, such  as mRNA, rRNA, lncRNA, cfRNA, and so on. Then what would you call such RNA as INCL_NON_REF_SPLICE type? For example, the above-mentioned STX8::IDI2.

Tetsuko Kobayashi 

Japan

[Brian Haas]

hi,

responses below

On Fri, Mar 29, 2024 at 10:11 PM 小林賢子 <tkobaya...@gmail.com> wrote:

Dear Dr. Haas

I am always grateful for your teachings.

Now I would like to ask three questions.

1.

You explain about the parameter 'SpliceType' as follows,

 'SpliceType' indicates whether the proposed breakpoint occurs at reference exon junctions as provided by the reference transcript structure annotations (ex. gencode).

And you assign the symbol INCL_NON_REF_SPLICE or ONLY_REF_SPLICE to the elements.

Please spell the abbreviations in full so that I will understand about 'Splice Type' better.

Can you elaborate and give examples?

 

2.

I have a result of STAR-Fusion of a cell-line whose RNA-seq data are from total RNA.

The Splice Type of STX8::IDI2 (chr17:9545172:-, chr10:1022775:) is output as INCL_NON_REF_SPLICE.

The break point of IDI2 is on 5'UTR. So, is the assigning INCL_NON_REF_SPLICE because the break point is not exon junction?

It means that there's no annotated splice breakpoint there.  You'll want to look at the breakpoint to see if it matches expected splice site dinucleotides (eg. GT-AG).  Try using FusionInspector to examine the fusion in more detail.

 

3. 

 Generally, there are many kind of RNAs in total RNA, such  as mRNA, rRNA, lncRNA, cfRNA, and so on. Then what would you call such RNA as INCL_NON_REF_SPLICE type? For example, the above-mentioned STX8::IDI2.

It only refers to whether the breakpoint is at reference annotation exon boundaries or not - there's no indication of what type of RNA molecule it is.

 

Tetsuko Kobayashi 

Japan

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Brian J. Haas
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[Brian Haas]

Thanks for the additional info.  FusionInspector should report any breakpoints it finds and doesn't require the GT-AG rule.   STAR-Fusion on the other hand will in most cases by default reject fusions that don't involve proper splicing as likely RT artifacts.

There are some other very interesting fusions in there too - PML--RARA and the PVT1 fusions in particular - both relevant to cancer.  Also, the KANSL1--ARL17A shows up in ~ 1/3 of those with European ancestry ( a normal fusion ).

On Mon, Apr 1, 2024 at 3:31 AM 小林賢子 <tkobaya...@gmail.com> wrote:

Dear Dr. Haas

Thank you very much for your responses. I am thinking.

This time I attached an output file by FusionInspector (Validate mode) that contains the STX8::IDI2 on 11th row. This was categorized as INCL_NON_REF_SPLICE.

I confirmed that adjacent nucleotides of this fusion break points were GT-AG (by Ensembl).

I noticed all output fusions were marked with GT and AG in the output list.

So I confuse whether the GT-AG rule satisfaction is an essential requirement of  the fusion detection algorithm?

T. Kobayashi

2024年3月30日(土) 23:39 Brian Haas <bh...@broadinstitute.org>:

[小林賢子]

Dear Dr. Haas

Thank you very much for your responses. I am thinking.

This time I attached an output file by FusionInspector (Validate mode) that contains the STX8::IDI2 on 11th row. This was categorized as INCL_NON_REF_SPLICE.

I confirmed that adjacent nucleotides of this fusion break points were GT-AG (by Ensembl).

I noticed all output fusions were marked with GT and AG in the output list.

So I confuse whether the GT-AG rule satisfaction is an essential requirement of  the fusion detection algorithm?

T. Kobayashi

2024年3月30日(土) 23:39 Brian Haas <bh...@broadinstitute.org>:

hi,

responses below