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By Gary Stiehr, June 12, 2009 11:03 pm

A depiction of the structure of DNA

Illumina will offer a service to sequence a person’s genome for $48,000 (a doctor’s prescription is required).  Note that this is only the sequencing and not the actual analysis of that sequence data.  The consumer must choose from a few different providers to do the actual analysis of the genome sequence data.  Currently, the representation of a human genome as Illumina is proposing (30-fold coverage of your DNA sequence) would require the transfer of terabytes of data to the company doing the analysis.  Of course, there are various parts to “analysis” so depending on where Illumina stops and the other companies take over, this actually could be a lot less data (e.g., gigabytes).

So this raises at least a couple of possible challenges for Illumina:

• How will the data be transferred?
• How will the data be secured?

Transferring the Data

One could see that data transfer of on the order terabytes of data would not be a problem if the turnaround time is long enough.  Although if the service becomes more and more popular, scaling may be a problem (or at least synchronizing network abilities with analysis providers).  Nevertheless, will Illumina establish encrypted network connections with the consumer’s/doctor’s chosen analysis provider?  Will they transfer the data encrypted on external hard drives?  If on external hard drives, how will tracking of the multiple pieces be tracked?

Securing the Data

I’m assuming the security/encryption questions may have answers based off of current electronic health records implementations although I’m not sure if electronic patient information systems are typically interconnected between different health care organizations.  That is, aren’t these systems usually secured/confined within the network of a particular health care organization?  If it is placed on external hard drives and shipped, would the encryption of terabytes of data per patient be challenging?

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By Gary Stiehr, July 3, 2008 1:20 am

HPCwire’s article Gravity Attracts a GigE HPC Cluster describes some of the features of the new ATLAS cluster at the Max Planck Institute for Gravitational Physics. The 144 10-GigE port non-blocking switch from Woven was a technical feature that stood out. Additionally, it would be interesting to find out what file system is being used on the 42 storage nodes.

Also, the article mentions “An additional 500 GB of direct-connected storage is provided on each compute node. The CPU on any server can access the local disk storage on any other server as well as the central storage nodes.” I wonder in what way that local disk space is made available to the other servers.