RNA-seq Data on Prostate Cancer Publicly Available from BGI

A comment from reader dogfacemacgee is informative enough so that we made it a main post.

The Chicoms are actually releasing real sequence for patients BGI has put RNA- seq for Prostate cancer into SRA here.

The study is RNA-seq analysis of prostate cancer in the Chinese population identifies recurrent gene fusions, cancer-associated long noncoding RNAs and aberrant alternative splicings [ PMID : 22349460 ]

The reads coverage actually viewable at NCIs Cancer Genome Workbench (CGWB) : here.

or TP53.

The aligned sequence reads are viewable by zooming in and using the bambino tool available with a right mouse click (bambino view details) if you have java example : here.

With the patient protections in the capitalist countries, perhaps its the communists who can open source disease data.

We hear about similar issues, when we talk to cancer researchers at Fred Hutch and University of Washington. Each hospital around USA got some amount of cancer data from their respective patients, but their real value comes from aggregating all data and looking for rare marker. However, they cannot search in the entire collection of data for disease markers, because a huge bureaucracy is created to protect ‘patient privacy’, and doing anything to keep them happy is extremely expensive. Going by the argument of Titus Brown, privacy is impossible to achieve for internet users, because that distorts ‘internet reality’ for ad distributors. However, when it comes to real research, privacy is utterly important.

Cui bono?