what does DNA sequence of one specific mutation site change to?

[Ye, Ruisong]

Hi,

 

I am trying to analyze a mutation to perform downstream experiment.

 

 

Here I show a gene of my interest LZTR1, and I am interested in X217 mutation site(splice mutation), I want to know what mutation happened to this site, Next I tried to track its detailed sequence by “Sample ID” located below, such as “TCGA-2Y-A9H3”  and locate the mutation region

 

 

And  Next I zoom in the mutation region

 

 

I only see the reference sequence here(I have double checked the sequence above orange bar, it is Not mutation sequence, similar situation with other mutation sites), how can I know what is the exact DNA sequence of this mutation change to??

 

Thank you so much, this question has been bothered me  long time! It would be greatly appreciated if you can help me out!  Thanks!

 

Best regards

 

Ruisong

 

 

 

Sent from Mail for Windows

 

[Nikolaus Schultz]

Hi Ruisong,

You can see the nucleotide change details for each mutation by enabling additional columns in the Mutations Table. See screenshot below.

Niki.

On Aug 9, 2023, at 4:09 PM, Ye, Ruisong <r...@luc.edu> wrote:

Hi,

 

I am trying to analyze a mutation to perform downstream experiment.

 

<FAE26061F56D46EAA302C70AAD44F3C5.png>

 

Here I show a gene of my interest LZTR1, and I am interested in X217 mutation site(splice mutation), I want to know what mutation happened to this site, Next I tried to track its detailed sequence by “Sample ID” located below, such as “TCGA-2Y-A9H3”  and locate the mutation region

 

<680B1F96574441DCAB2E5547B63AA304.png>

 

And  Next I zoom in the mutation region

<B56B14EF49634E96AA3235888953E665.png>

 

 

I only see the reference sequence here(I have double checked the sequence above orange bar, it is Not mutation sequence, similar situation with other mutation sites), how can I know what is the exact DNA sequence of this mutation change to??

 

Thank you so much, this question has been bothered me  long time! It would be greatly appreciated if you can help me out!  Thanks!

 

Best regards

 

Ruisong 

 

 

 

Sent from Mail for Windows

 

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[Ye, Ruisong]

Hi, Niki,

Thank you so much for your email.

Follow your suggestion,  it is easier to find what does the mutation change in "Ref" and "Var",  I have tested many mutation sites including single amnio acid mutations and some splice mutation. Here I just have a more specific mutation site like LZTR1 X217_Splice(splice mutation) , it only has the reference sequence but no Var sequence(see screenshot below), How can I have its DNA mutation sequence? I did see other splice mutation sites have mutation details, like X595_Splice.

Thanks again for your help!

Best,

Ruisong

---

From: Nikolaus Schultz <nsch...@gmail.com>
Sent: Thursday, August 17, 2023 12:00 PM
To: Ye, Ruisong <r...@luc.edu>
Cc: cbiop...@googlegroups.com <cbiop...@googlegroups.com>
Subject: Re: [cbioportal] what does DNA sequence of one specific mutation site change to?

 

[Nikolaus Schultz]

Hi,

A “-“ in the Var column indicates that the nucleotides in the Ref column are deleted. In this example, the deletion is predicted to affect splicing, probably because the deletion spans an intron-exon junction.

Niki.

On Aug 17, 2023, at 3:15 PM, Ye, Ruisong <r...@luc.edu> wrote:

Hi, Niki,

Thank you so much for your email.

Follow your suggestion,  it is easier to find what does the mutation change in "Ref" and "Var",  I have tested many mutation sites including single amnio acid mutations and some splice mutation. Here I just have a more specific mutation site like LZTR1 X217_Splice(splice mutation) , it only has the reference sequence but no Var sequence(see screenshot below), How can I have its DNA mutation sequence? I did see other splice mutation sites have mutation details, like X595_Splice.

<image.png>

<image.png>

Thanks again for your help!

Best,

Ruisong

---

From: Nikolaus Schultz <nsch...@gmail.com>
Sent: Thursday, August 17, 2023 12:00 PM
To: Ye, Ruisong <r...@luc.edu>
Cc: cbiop...@googlegroups.com <cbiop...@googlegroups.com>
Subject: Re: [cbioportal] what does DNA sequence of one specific mutation site change to?

 

Hi Ruisong,

You can see the nucleotide change details for each mutation by enabling additional columns in the Mutations Table. See screenshot below.

Niki.

<PastedGraphic-1.png>

[Ye, Ruisong]

Ok, Niki,

I got it, That's great,  Thank you so much for your help! Have a nice day!

Best regards,

Ruisong

---

From: Nikolaus Schultz <nsch...@gmail.com>
Sent: Thursday, August 17, 2023 4:04 PM