04 October 2012

Hard and software for personalized medicine

Genome analysis in a box
Modern genomics facilitates the diagnosis of diseases
and gives the key to individual treatmentDmitry Krylov, Voice of America

The company Knome, working in the field of analysis of individual genomes, has released a new product.

This company is known as the creator of software used by doctors to interpret genomic data. The current innovation marks the company's transition to a different business model.

If earlier the company sold software, today it begins to supply customers with computer hardware with a pre-installed set of programs. With the total transition to cloud servers observed in IT, this is a rather unexpected step. What made the company switch to an outdated business model? This question is just the tip of the genomic iceberg, the contours of which we will try to outline.

First, a few words about what this and similar software does and who its main customers are. The price of an individual genome today confidently breaks the mark of one thousand dollars. Some companies offer sequencing devices for five hundred dollars or less, although their data is not as complete and accurate.

The speed of DNA reading has also radically increased: today it is a matter of several hours or even twenty to thirty minutes. Genome-reading machines no longer require specially trained lab technicians and can be run on a regular desktop next to a computer. Via USB, all data flows to the hard drive ... and then the fun begins. By themselves, these data do not say anything about diseases, treatment methods and predispositions of the host genome. To analyze them, you need complex, or rather, very, very complex software. This is what Knome and other similar startups offer.

The new knoSYS100 product is a computer cluster of four Intel Xeon E5-2665 2.4GHz processors with 8 cores and 16 threads. Hard drives store from 18 to 54 TB of useful information. The kGAP software package of the same company runs on this hardware. It supports several functions that begin with reading genomic information. It is created and stored in several dissimilar formats. kGAP uses DNA sequences from Illumina sequencers, Life Technologies and Complete Genomics. These are the three largest manufacturers of equipment that reads genomes.

Further, the software package allows you to visualize data and analyze individual genes. This gives doctors the key to solving clinical problems about the diagnosis of a particular disease, to the selection of individual treatment and allows them to give advice on the prevention of possible diseases. So far, these functions are quite limited, but the more such technologies are used, the larger amounts of data will be available for analysis and more accurate predictions.

The transition from the sale of software to computer systems is primarily due to the fact that medical institutions are not able to maintain the level of data protection required by regulatory documents.

In addition, they do not always have enough qualified IT specialists to service the software. Installing and maintaining this software is far from trivial, because it requires the use of many libraries and quite powerful processors capable of calculating data in real time. But this is just the tip of the iceberg. Its full contours touch upon the key question of modern genomics: who will have access to the collected genomic data?

Their formal owners are genome owners who pay for sequencing, but those who develop programs for analyzing this data are no less interested in them. This explains the competition and incompatibility of the data standards that are currently present on the market, as well as the attempts of companies to establish control over possibly large flows of this data. These processes have direct parallels in the recent history of the competition of video and audio formats of different companies and the struggle for the rights to distribute licensed digital products.

Portal "Eternal youth" http://vechnayamolodost.ru04.10.2012

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