Question: Clinical Data for CCLE Cell Lines
0
gravatar for dog.seal6363
5.1 years ago by
United States
dog.seal63630 wrote:

Hello,

I was wondering if anyone knows how and where I could obtain the clinical data for the cell lines from the Cancer Cell Line Encyclopedia. Also, does anyone know if they label the race of the patients?

Thank you for answering my questions. 

 

snp ccle • 1.9k views
ADD COMMENTlink modified 20 months ago by Amos Bairoch40 • written 5.1 years ago by dog.seal63630

Yes table S2 only contains the cell line names, description and Xref to the Cellosaurus. The genome ancestry values are not in these files. I got the file I am using to plug the info in the Cellosaurus from Julie Dutil directly. You should contact her. Alternatively you will be able to programatically get them from the Cellosaurus XML at the next release.

ADD REPLYlink written 20 months ago by Amos Bairoch40

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized. SUBMIT ANSWER is for new answers to original question.

This comment should have gone under @Charles' answer.

ADD REPLYlink written 20 months ago by genomax92k

genomax - Thank you for noting this (and being able to respond before I could): I will create a link to this as a comment under my answer.

Amos - I would also say creating another comment under my answer (and deleting this comment) is an acceptable solution :)

ADD REPLYlink modified 19 months ago • written 19 months ago by Charles Warden7.9k
1
gravatar for Amos Bairoch
20 months ago by
Amos Bairoch40
Switzerland, Geneva, Swiss Institute of Bioinformatics
Amos Bairoch40 wrote:

If for the clinical information, you mean the cancer type than you can do this using the Cellosaurus. You can parse the XML version available at ftp://ftp.expasy.org/databases/cellosaurus and look for cell lines in CCLE which you can do be either taking all cell lines with:

<comment category="Part of"> Cancer Cell Line Encyclopedia (CCLE) project </comment>

or with an Xref to the CCLE as shown in this example:

</xref>
<xref database="CCLE" category="Cell line databases/resources" accession="1321N1_CENTRAL_NERVOUS_SYSTEM">
  <url>https://portals.broadinstitute.org/ccle/page?cell_line=1321N1_CENTRAL_NERVOUS_SYSTEM]]></url>
</xref>

and then you can get the cancer type using the disease list which is linked to the NCI Thesaurus disease ontology as in the example below:

 <disease-list>
    <cv-term terminology="NCIt" accession="C60781">Astrocytoma</cv-term> 
   </disease-list>

In term of "race", the next release of the Cellosaurus (release 30 in May 2019) will contain a new "section" called "Genome ancestry" which will contain the computed genome ancestry information from the ECLA resource which just became available:

http://ecla.moffitt.org/

See: https://www.ncbi.nlm.nih.gov/pubmed/30894373

ADD COMMENTlink written 20 months ago by Amos Bairoch40
0
gravatar for Charles Warden
20 months ago by
Charles Warden7.9k
Duarte, CA
Charles Warden7.9k wrote:

Figure 2 of this paper shows some ancestry predictions (for cell lines, which includes CCLE):

http://cancerres.aacrjournals.org/content/79/7/1263.figures-only

It doesn't look like they had any individuals with ambiguous ancestry (which seems odd to me), but I don't doubt the over-representation of European ancestry individuals.

However, I was also a little confused because it seems like the predicted ancestries are missing from Table S2 and/or I couldn't find an "Interactive" web-interface for the results. Perhaps somebody else could find what I may have over-looked?

ADD COMMENTlink written 20 months ago by Charles Warden7.9k

Amos Bairoch has some relevant information in this comment

ADD REPLYlink written 19 months ago by Charles Warden7.9k

Also, based upon a tweet response, I believe this is the web-interface: http://ecla.moffitt.org/#/home

ADD REPLYlink written 19 months ago by Charles Warden7.9k

We did assign ancestry categories for discussing distributions of the cell line collections. However, we chose not to include that information in the supplementary data and present only ancestry proportions. At an individual level, these categories may may contradict self perception so we prefered to avoid presenting this information. However, if you have questions specific to a particular cell line (s), please do not hesitate to contact me.

ADD REPLYlink written 19 months ago by Julie Dutil0
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