Question: what is difference between preliminary somatic mutations, somatic mutations and validated somatic mutations
1
gravatar for Nitin Sharma
22 months ago by
Nitin Sharma30
Institute for Cancer Research, Dept. of Tumor Biology, Oslo University Hospital, Oslo, Norway
Nitin Sharma30 wrote:

Dear All,

I recently started working in Cancer Genomics and started to work on cBioPortal. As I was scrolling through the FAQs of cBioPortal I came across this information

"Why do some cancer studies have mutation data and others do not? We store mutation data for published cancer studies. We do not, however store mutation data for provisional cancer data sets generated by TCGA. This is because provisional studies contain preliminary somatic mutations, which per NCI guidelines cannot be redistributed until they have been validated. As each cancer study is published and finalized by the TCGA, we will import the corresponding mutation data."

which got me confused, as down the line I will be looking to work on TCGA data as well

Thus can someone explain to me what is the difference between preliminary somatic mutations, somatic mutations and validated somatic mutations.

Also are all somatic mutations in TCGA are preliminary somatic mutations? If yes, what is the reason behind it and as TCGA is very well used database how to handle this situation.

Can you also tell me other examples in terms of databases where such scenario can happen?

Thanks in advance

ADD COMMENTlink written 22 months ago by Nitin Sharma30

i can imagine the difference between preliminary somatic mutations and somatic mutations and validated somatic mutations , is other assays associated to the studies. You can find a mutation in NGS for example but even it's not confirmed by RNA-seq and protein impact it is not validated for example ?

They said there http://www.cbioportal.org/faq.jsp : Studies from literature were curated manually .

ADD REPLYlink written 22 months ago by Titus910
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