bbgm - the discussion - Latest Comments in Trendspotting: Molecular profiling data resources

Re: Trendspotting: Molecular profiling data resources

mndoci — Mon, 21 Jul 2008 18:16:33 -0000

Walter, very real concerns, and the kinds my previous company spent a lot of its time thinking about.

Like most data types, microarray results will become more commoditized, i.e. the reliability and alignment issues will get resolved. The reference, annotation, etc information will become metadata that accompanies your data sources. It's a question of making sure all the experimental details are included with the results being provided. They key is that there will be a body of work available that should make it less necessary to do your own microarray experiments except when absolutely necessary.

Re: Trendspotting: Molecular profiling data resources

mndoci — Mon, 21 Jul 2008 16:12:51 -0000

Indeed and growing, but most companies still run their own arrays, and integrate public information as required. The future will be the opposite. You run your own arrays as required, but primarily use public (or private) resources. Additionally these won't just be databases, but web services, where the combination or resources and how they are mashed up will be the key value.

Re: Trendspotting: Molecular profiling data resources

Sanjiv — Mon, 21 Jul 2008 13:46:09 -0000

I fully agree with you. However, such databases, listed below, are already available for the scientific community -

GEO - http://www.ncbi.nlm.nih.gov...

ArrayExpress - http://www.ebi.ac.uk/microa...

Phenogen Informatics - http://phenogen.uchsc.edu/

Stanford Microarray Database - http://genome-www5.stanford...

Users can select any number of experiments/samples to carry out the meta-analysis using the available tools.

Re: Trendspotting: Molecular profiling data resources

gitch — Mon, 21 Jul 2008 12:57:28 -0000

Just a thought:
One of GINA's directives is that genomic data will be protected under HIPAA such that it will be treated like a SSN, address, and other classic identifiers. An interpretation of the definition provided within GINA of genomic data certainly includes sequence data, but also is likely to include genotyping microarray results, and perhaps expression microarray results.

What is to become of these large public repositories of microarray data on human subjects when genomic data, with the very broad definition provided within GINA, becomes protected health information?