Question about How to use cBioPortal: how to pull the variant frequency in a selected tumor type/dataset?

[Su,Fei]

Hi, dear ATCG, thanks for the webinar on How to use cBioPortal effectively! My question is:

 

Is there a selection from the column that shows the variant frequency in a selected tumor type/dataset? For instance, can I pull from below KRAS G12D frequency in NSCLC from below?

My understanding is that the Allele Freq (T) is for each patient/sample ID.

 

 

Thanks,

 

Fei Su, PhD

Research Scientist

Khalifa Institute for Personalized Cancer Therapy

UT MD Anderson Cancer Center

6565 MD Anderson Blvd | Z4.3014 | Houston, TX 77030

(713) 563-0431

F...@mdanderson.org

 

 

The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

[Paul van Dijk]

Dear Su,Fei,

Thank you for attending the webinar(s), I hope you enjoyed it so far.

Regarding your question: what I think you want to achieve, can be accomplished by using OQL (this topic will be covered in detail in the webinar of May 14). 

In short, at the cBioPortal landing page select the study of interest (NSCLC in your case). Then go to query by gene and enter the following in the "enter genes" box: KRAS: MUT = G12D

This will yield this result:

https://www.cbioportal.org/results/oncoprint?Action=Submit&RPPA_SCORE_THRESHOLD=2.0&Z_SCORE_THRESHOLD=2.0&cancer_study_list=nsclc_pd1_msk_2018&case_set_id=nsclc_pd1_msk_2018_cnaseq&data_priority=0&gene_list=KRAS%253A%2520MUT%2520%253D%2520G12D&geneset_list=%20&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=nsclc_pd1_msk_2018_mutations&profileFilter=0&tab_index=tab_visualize&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=nsclc_pd1_msk_2018_cna

See also the FAQ at https://www.cbioportal.org/oql

I hope this helps.

Best,

Paul

--
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 on the web visit https://groups.google.com/d/msgid/cbioportal/9a841cf838414f7d8fd3c1d3067c60f9%40mdanderson.org.

--

Paul van Dijk  |  Business Analyst

E.   paulv...@thehyve.nl
T.   +31(0)30 700 9713

W.  www.thehyve.nl

[Su,Fei]

Paul, good morning,

 

Thanks for the response! I guess I main question is where to the mutation frequency in this study? My understanding is that the Allele Freq (T) is for each patient/sample ID and is not what I need.

 

Thanks!

Fei

 

From: Paul van Dijk <paulv...@thehyve.nl>
Sent: Monday, May 11, 2020 1:53 AM
To: Su,Fei <F...@mdanderson.org>
Cc: cbiop...@googlegroups.com
Subject: [EXT] Re: [cbioportal] Question about How to use cBioPortal: how to pull the variant frequency in a selected tumor type/dataset?

 

WARNING: This email originated from outside of MD Anderson. Please validate the sender's email address before clicking on links or attachments as they may not be safe.

 

[Su,Fei]

Paul, I got it. I can get the data from the Cancer Types Summary, correct? Thanks!

 

From: Su,Fei
Sent: Monday, May 11, 2020 9:37 AM
To: 'Paul van Dijk' <paulv...@thehyve.nl>
Cc: cbiop...@googlegroups.com
Subject: RE: [EXT] Re: [cbioportal] Question about How to use cBioPortal: how to pull the variant frequency in a selected tumor type/dataset?

 

Paul, good morning,

 

Thanks for the response! I guess I main question is where to the mutation frequency in this study? My understanding is that the Allele Freq (T) is for each patient/sample ID and is not what I need.

 

Thanks!

Fei

 

From: Paul van Dijk <paulv...@thehyve.nl>
Sent: Monday, May 11, 2020 1:53 AM
To: Su,Fei <F...@mdanderson.org>
Cc: cbiop...@googlegroups.com
Subject: [EXT] Re: [cbioportal] Question about How to use cBioPortal: how to pull the variant frequency in a selected tumor type/dataset?

 

WARNING: This email originated from outside of MD Anderson. Please validate the sender's email address before clicking on links or attachments as they may not be safe.

 

Dear Su,Fei,

[Paul van Dijk]

Hi Fei,

As soon as you start querying with OQL (e.g. the earlier example: KRAS: MUT = G12D) you will see something like:

"The results below reflect the OQL specification from your query."

or

The results below do not reflect the OQL specification from your query.

for every tab (Cancer Types Summary, Plots, Mutations) you choose after querying this gene and specific mutation. So this warning is included and sometimes you have the option to reflect the specific mutation or all the mutations for the chosen gene (e.g. when clicking the mutations tab).

Hope this further clarifies your question.

Best

Paul

[Su,Fei]

Hi, Paul, I have a question about the Webinar “Expression Data Analysis”. I need to see the correlation about CDK4 copy number change and protein expression, So I did:

 

1.       Quick select TCGA PanCancer Atlas Studies, Query CDK4

2.       Identifies top Cancer types with high Amp frequency under Cancer Type Summary tab: Sarcoma, GBM, ACC, Melanoma,

3.       Under DataSets, confirmed data sets in above Cancer types that have RPPA data as below:

a.       Glioblastoma Multiforme (TCGA, Firehose Legacy)

b.       Glioblastoma (TCGA, Cell 2013)

c.       Skin Cutaneous Melanoma (TCGA, Firehose Legacy)

d.       Sarcoma (TCGA, Firehose Legacy)

4.       Select data set for three independent query listed below, check Genomic profile/Protein expression Z score; select patient/Samples with protein data (RPPA) (244); query CDK4.

a.       Glioblastoma Multiforme (TCGA, Firehose Legacy)

b.       Skin Cutaneous Melanoma (TCGA, Firehose Legacy)

c.       Sarcoma (TCGA, Firehose Legacy)

5.       Result: for all three queries, I can not find RPPA or protein tab or under Vertical Axis/data type under Plot tab.

 

Would you please trouble shoot?

 

Thanks,

Fei

[Su,Fei]

Second question: For the plot below (Fig 1.), what is the reason that the amp (red circle) samples are distributed in all five X-categories (from deep deletion to gain to amplification)? Why the amp (red circle) samples don’t line up under the amplification like ERBB2 (Fig 2.)? Thanks for the help! Fei

 

Fig 1.            Fig 2.

 

From: Su,Fei
Sent: Wednesday, June 24, 2020 9:42 AM
To: 'Paul van Dijk' <paulv...@thehyve.nl>
Cc: 'cbiop...@googlegroups.com' <cbiop...@googlegroups.com>
Subject: RE: [EXT] Re: [cbioportal] Question about How to use cBioPortal: how to pull the variant frequency in a selected tumor type/dataset?

 

Hi, Paul, I have a question about the Webinar “Expression Data Analysis”. I need to see the correlation about CDK4 copy number change and protein expression, So I did:

 

1.       Quick select TCGA PanCancer Atlas Studies, Query CDK4

2.       Identifies top Cancer types with high Amp frequency under Cancer Type Summary tab: Sarcoma, GBM, ACC, Melanoma,

3.       Under DataSets, confirmed data sets in above Cancer types that have RPPA data as below:

a.       Glioblastoma Multiforme (TCGA, Firehose Legacy)

b.       Glioblastoma (TCGA, Cell 2013)

c.       Skin Cutaneous Melanoma (TCGA, Firehose Legacy)

d.       Sarcoma (TCGA, Firehose Legacy)

4.       Select data set for three independent query listed below, check Genomic profile/Protein expression Z score; select patient/Samples with protein data (RPPA) (244); query CDK4.

a.       Glioblastoma Multiforme (TCGA, Firehose Legacy)

b.       Skin Cutaneous Melanoma (TCGA, Firehose Legacy)

c.       Sarcoma (TCGA, Firehose Legacy)

5.       Result: for all three queries, I can not find RPPA or protein tab or under Vertical Axis/data type under Plot tab.

 

Would you please trouble shoot?

 

Thanks,

Fei