? regarding SV feature on cBioportal

[Alireza Samiei]

Hi cBioPortal team,

I have a question about the structural variant (SV) feature. 

I'm looking at PLAG1 translocations in uterine leiomyosarcoma and have been working with the "Soft Tissue and Bone Sarcoma (MSK, Nat Commun 2022)" dataset, which has 541 samples. When I searched for PLAG1 translocations using the SV feature, I found 2 cases (see attached screenshot).

I'm wondering whether all 7494 samples were computationally analyzed for structural variants, or if only some of them have been processed so far? I'm trying to get a sense of how common PLAG1 translocations actually are in uterine leiomyosarcoma (541 case are uterine LMS out of the 7494 total sarcoma samples).

Thank you for making this valuable resource available to the community and thanks so much for your help.

Warm regards, 

Ali

[Tali Mazor]

Hi Ali,

Thanks for the kind words.

It appears that all samples in this study have been profiled for structural variants. You can see this by looking in the study view at the 'Data Types' chart where it says 100% of samples have structural variant data:

However, that is only half the information you need. This study used targeted sequencing, so it is important to know if your gene of interest is included in the panel. One way to determine this is to look at the 'Structural Variant Genes' chart and search for your gene of interest:

You can see the Frequency is NA. If you hover your mouse over the 'NA', you'll see a tooltip that explains that no samples are profiled for this gene.

Another way you can determine this is to run a query for PLAG1, but look at the OncoPrint tab rather than the Structural Variants tab. Here you can see that PLAG1 is not profiled in any samples:

If you hover over any of the called structural variants, you'll find a link to the gene panel where you can see which genes have been profiled.

It does sometimes happen that structural variants are called in a gene which is not profiled. It might be that the partner gene is profiled, or these might be off target reads. Regardless, since PLAG1 is not profiled, you cannot calculate an accurate frequency. If you want to determine the frequency of PLAG1 structural variants, you'll need to find a study where PLAG1 is profiled.

-Tali

--
You received this message because you are subscribed to the Google Groups "cBioPortal for Cancer Genomics Discussion Group" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cbioportal+...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/cbioportal/DM6PR07MB8109680C43F0EC353F2102A6EBABA%40DM6PR07MB8109.namprd07.prod.outlook.com.

[corrie painter]

Hi Team,

I had asked Tony Wu about this before and received the following information, adding here in case helpful:

Our team looked at the combined bed files from 18.0 public and 19.3 consortium datasets, both show that 24 assays from 8 sites (UMIAMI, WAKE, JHU, CHOP, COLU, UCSF, UHN and MDA) have PLAG1 coverage. 

Of these sites, only 3 of them (WAKE, COLU and UMIAMI) have reported/submitted patients with uterine leiomyosarcoma (13 patients total) and only 1 has mutations in the PLAG1 gene.

[corrie painter]

Actually, let me verify with Tony. 

On Wed, Dec 17, 2025 at 6:03 PM William J. Gibson <willj...@gmail.com> wrote:

Oh awesome!

On Wed, Dec 17, 2025 at 6:01 PM corrie painter <corrie....@gmail.com> wrote:

SV

On Wed, Dec 17, 2025 at 6:00 PM William J. Gibson <willj...@gmail.com> wrote:

Thanks Corrie. Do we know if this is a mutation or a structural variant?

[William J. Gibson]

Thanks Corrie. Do we know if this is a mutation or a structural variant?

On Wed, Dec 17, 2025 at 5:24 PM corrie painter <corrie....@gmail.com> wrote:

[Popoola, Jumi]

Hello All,

Yes - the GENIE patient referenced below was a mutation, not structural variant (based on the latest 19.5 consortium dataset).

Thanks and best wishes

Jumi

Jumi Popoola, PhD ​​​​ SCIENTIFIC PROGRAM MANAGER Executive Office American Association for Cancer Research 1401 H Street, NW, Suite 740 | Washington, DC 20005 267‑765‑1027 Direct  jumi.p...@aacr.org  |  www.AACR.org Please note that this e-mail and any files transmitted with it may be privileged, confidential, and protected from disclosure under applicable law. This information is intended only for the person or entity to which it is addressed and may contain confidential or privileged material. Any review, retransmission, dissemination, or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and delete the material from any computer.

---

From: Wu, Tony <ton...@aacr.org>
Sent: Wednesday, December 17, 2025 10:23 PM
To: corrie painter <corrie....@gmail.com>; William J. Gibson <willj...@gmail.com>
Cc: Tali Mazor <tma...@ds.dfci.harvard.edu>; Alireza Samiei <alireza...@bfor.org>; cbiop...@googlegroups.com <cbiop...@googlegroups.com>; Alireza_samiei <Alireza...@icloud.com>; jeffrey....@gmail.com <jeffrey....@gmail.com>; Popoola, Jumi <jumi.p...@aacr.org>
Subject: Re: [cbioportal] ? regarding SV feature on cBioportal

 

Hi Everyone,

Looks like the single PLAG1 uLMS patient referenced below was a mutation, not structural variant. This patient was treated at Columbia.

Copying Jumi from our team who performed the original query and can provide additional details if helpful.

Thanks,

Tony

Tony Wu, PhD ​​​​ ASSISTANT DIRECTOR STRATEGIC PARTNERSHIPS AND BUSINESS DEVELOPMENT Executive Office American Association for Cancer Research® 615 Chestnut Street, 17th Floor | Philadelphia, PA, 19106-4404 215-446-9920 Direct ton...@aacr.org  |  www.AACR.org Please note that this e-mail and any files transmitted with it may be privileged, confidential, and protected from disclosure under applicable law. This information is intended only for the person or entity to which it is addressed and may contain confidential or privileged material. Any review, retransmission, dissemination, or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and delete the material from any computer.

From: corrie painter <corrie....@gmail.com>
Date: Wednesday, December 17, 2025 at 21:58
To: William J. Gibson <willj...@gmail.com>
Cc: Tali Mazor <tma...@ds.dfci.harvard.edu>, Alireza Samiei <alireza...@bfor.org>, cbiop...@googlegroups.com <cbiop...@googlegroups.com>, Alireza_samiei <Alireza...@icloud.com>, jeffrey....@gmail.com <jeffrey....@gmail.com>, Wu, Tony <ton...@aacr.org>
Subject: Re: [cbioportal] ? regarding SV feature on cBioportal

Hi Tony,

Are you able to verify whether the PLAG1 LMS patient referenced below was a mutation or structural variant?

Thank you?

Corrie

On Wed, Dec 17, 2025 at 6:00 PM William J. Gibson <willj...@gmail.com> wrote:

***CAUTION: EXTERNAL EMAIL. This email originated from outside the AACR. Do not open attachments or click on links from unknown or suspicious senders. Report suspicious emails using the Phish Alert Button***

[William J. Gibson]

Oh awesome!

On Wed, Dec 17, 2025 at 6:01 PM corrie painter <corrie....@gmail.com> wrote:

SV

On Wed, Dec 17, 2025 at 6:00 PM William J. Gibson <willj...@gmail.com> wrote:

[corrie painter]

Thank you Tony. 

On Wed, Dec 17, 2025 at 6:00 PM William J. Gibson <willj...@gmail.com> wrote:

***CAUTION: EXTERNAL EMAIL. This email originated from outside the AACR. Do not open attachments or click on links from unknown or suspicious senders. Report suspicious emails using the Phish Alert Button***

[corrie painter]

SV

On Wed, Dec 17, 2025 at 6:00 PM William J. Gibson <willj...@gmail.com> wrote:

[Wu, Tony]

On Wed, Dec 17, 2025 at 6:00 PM William J. Gibson <willj...@gmail.com> wrote:

***CAUTION: EXTERNAL EMAIL. This email originated from outside the AACR. Do not open attachments or click on links from unknown or suspicious senders. Report suspicious emails using the Phish Alert Button***

[corrie painter]

Hi Tony,

Are you able to verify whether the PLAG1 LMS patient referenced below was a mutation or structural variant?

Thank you?

Corrie

On Wed, Dec 17, 2025 at 6:00 PM William J. Gibson <willj...@gmail.com> wrote:

[Jeffrey Tsao]

Thanks all for confirming.

Jeff