Question: High School Researcher: Is it possible to gain access to publicly available whole cancer genome data sets with supplemented clinical data?
0
gravatar for dani.cmh.lee
4.0 years ago by
United States
dani.cmh.lee0 wrote:

Hello, 

I am a young aspiring high school researcher, trying to work in the field of Bioinformatics. For my research it seems I would need access to whole cancer genomes with supplemented clinical data. Would this be at all accessible or even possible for someone of my age to obtain such data? If so from, where can I access such data?

 

Thanks,

DL

ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by dani.cmh.lee0

Can you elaborate on what you are looking for specifically? "Cancer" is a broad topic. Some cell lines like K562 are essentially cancer and I think they have genomes out there.

Are you testing a specific hypothesis? There might be other resources like Oncomine that can help you.

You may want to partner with an academic advisor in your area if you haven't already. Email a researcher at a university that is near you and studies what you want to look at and tell them to take you on.

Generally the connection between data and metadata (data about the data) is bad. (Bad for everyone, not just high school researchers.) 

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by Michele Busby2.1k
1
gravatar for Shamim Sarhadi
4.0 years ago by
IRAN
Shamim Sarhadi210 wrote:

Maybe you would find it useful to look at GEO

http://www.ncbi.nlm.nih.gov/geo/

ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by Shamim Sarhadi210
0
gravatar for pld
4.0 years ago by
pld4.8k
United States
pld4.8k wrote:

http://cancergenome.nih.gov/

https://cghub.ucsc.edu/

There are tougher rules around accessing that data, I'm not sure if they'll let you. I believe the genomes themselves aren't available to just anyone since they are PII.

ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by pld4.8k

I've looked into the TCGA Data portal, however I was wondering how severely limited the data access is to such data. Are there any other potential sources of such data?

ADD REPLYlink written 4.0 years ago by dani.cmh.lee0

Probably not, genomes are considered personally identifiable information and the NIH (and therefore anyone who has their grants) is probably going to control access to this data fairly strictly.

Do you need the genomes specifically, or could you make use of other types of data?

You could always email them or see if there's a local laboratory you could work with on your project.

 

Have you looked here?

http://www.1000genomes.org/

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by pld4.8k

Do the genomes provided at 1000genomes have any supplementary data in relation to them. My project is a bit of a clinically-based study so availability of the clinical data would also be quite important.

ADD REPLYlink written 4.0 years ago by dani.cmh.lee0

Did you even look at the website?

The samples for the 1000 Genomes Project mostly are anonymous and have no associated medical or phenotype data; for some of the populations the collectors have phenotype data but these data are not at Coriell and are not distributed. Although the 1000 Genomes samples have no phenotype data, the genetic variation data produced by the Project will be used by researchers to study many diseases, in sets of disease and control samples that have been carefully phenotyped. More information about using the 1000 Genomes project data is available on the data tab of this website.

http://www.1000genomes.org/about

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by pld4.8k

Did you even read her initial question before suggesting something that was clearly not relevant? Perhaps she asked because she read it, and wondered why you were suggesting 1000G.

ADD REPLYlink written 4.0 years ago by Emily_Ensembl19k

I misread that section that I posted.

I took it as the 1000G project didn't track that data but it might be available from other sources, which is not the case.

 

ADD REPLYlink written 4.0 years ago by pld4.8k
0
gravatar for William
4.0 years ago by
William4.5k
Europe
William4.5k wrote:

You can have a look at the Personal Genome project from George Church. It's all open data from willing participants. I don't think they have cancer genomes but I think you should be able to download germline genome data and phenotypes / traits.  

[quote]

Sharing Personal Genomes

The Personal Genome Project was founded in 2005 and is dedicated to creating public genome, health, and trait data. Sharing data is critical to scientific progress, but has been hampered by traditional research practices—our approach is to invite willing participants to publicly share their personal data for the greater good.

[/quote]

http://www.personalgenomes.org/

ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by William4.5k

Are there similar resources to this done elsewhere with similar level of availability?

While the data is nicely available, it is to a degree limited in the scope of doing a clinical study upon cancer.

ADD REPLYlink written 4.0 years ago by dani.cmh.lee0
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