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June 23, 2024

New software reduces cost of genome analysis

By SAMHITA ILANGO | February 14, 2013

We all have different hair, different skin colors, and other very different features. Surprisingly, despite all the disparities that make us a unique individual, the order of 99.9 percent of our nucleotide bases are exactly the same. We’ve come to know this through a burgeoning field of research called genomic analysis. Recently, in fact, an advanced software was recently designed by Knome Inc. that can analyze data locally without the use of the Internet, while reducing the price of analysis to an even lower price than other contemporary methods.

While genetic sequencing has become a vital component to many fields of research, it also came at an exorbitant cost in the past. Only a few years ago, the cost of mapping a single person’s genome was about $250,000, which included the cost of labor, administration, sequencing instruments, equipment, data processing, submission of data to public database and library time. Steve Jobs, for example, was one of only 20 people in the world to have his gene sequenced. It cost him around $100,000 to examine the genetic factors behind his diagnosed cancer.

However, in the past few years, the cost of sequencing or mapping one person’s genome has rapidly plummeted to a more affordable cost of $6,000. It is predicted to continue declining.

A new factor contributing to the decline of the price is a new software designed by Knome Inc. It was designed to interpret sequences in a more accessible manner from within lab. Without the need for online sources for information, the software is able to find significant genetic markers locally, and at a fast pace.

Knome is a human-genome interpretation company. It launched in 2007 and focuses mainly on helping clients interpret whole human genomes. Their new hardware is roughly the size of a file cabinet and will be shipped out in upcoming months to researchers studying the genetic basis for rare diseases and drug response. Knome has also produced a state-of-the-art software program for the machine called knoSYSTM100. It provides technical support and standard updates for the machine.

The machine runs on an informatics engine that converts whole genome sequence data into standardized, richly annotated databases that can quickly be compared to other sequences. The knoSYSÔ software has a widespread application for managing mapping data through pipelines that compares samples, filters variants, runs gene panels, and, eventually, reports results. One of the main features allows users to run gene panels through gene tests that can be executed at the ease of a button.

This compact machine may not seem to have improved dramatically from it’s predecessors, but there is a catch. The user-friendly machine is not only soundproof and lockable, but starts up with just a plug-in. In general, people can be identified by genetic data posted on the Internet. However, Knome’s machine can offer extreme privacy as it has the ability to discretely analyze data directly in an office space.

In fact, Lee Watkins, Jr. from the Center for Inherited Disease Research at Hopkins is considering to purchase the machine. The privacy and control someone has over the machinery is appealing. For this reason, more researchers like Watkins are considering investing their funds for this new technology. Some are planning on using the Knome for its use in a clinical setting. As progressively more efficient and cheaper genomic studies go unplugged, the study of genetic diseases and other genome studies are expected to flourish.

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