Putting the Proton to Work
The Proton can tackle all sorts of sequencing whether it's DNA- or RNA- (ribonucleic acid) based. Life Technologies says the machine is a good fit for sequencing the following:
- Entire transcriptomes, or the transcript of the expressed genes in the genome
- Human genomes, or the complete set of genetic instructions located in a cell
- Human exomes, the areas in DNA that code for proteins
Earlier, low-resolution sequencing techniques only allowed researchers to examine small stretches of genetic data. Researchers also had to already have an idea of what they were trying to find. With this newer generation of sequencers, they're able to capture much longer stretches of data. Ready to untangle some? The two most important ingredients in this process will be the DNA strands and the sequencer's sensor-filled chip.
Before you can collect data, you have to prepare your sample, right? There are systems for that. Automated ones. For example, at the time we wrote this article, you could buy the Ion OneTouch System for $14,490 to handle sample preparation in roughly four hours for the Proton's predecessor, the Personal Genome Machine.
Now we're moving on to the chip. The Proton I semiconductor chip is filled with 165 million sensors that work a little like the ones inside a digital camera. Above the sensors are tiny wells where the sample DNA sits. The samples are blasted with nucleotides (the building blocks of nucleic acids like DNA). If a nucleotide joins up with the sample, a hydrogen ion is released, so these sensors monitor the acidity of the solution for changes. Technically speaking, this pH-based method is called Ion Semiconductor Sequencing.
The chip is where the power of the Proton machine really resides. The Proton II chip is slated to have 660 million sensors. All those sensors are kind of handy when you remember that 3.1 billion bases make up the human genome. As with digital cameras, stronger chips mean more finely detailed results and, for sequencers, longer views of the DNA strand. With every advancement in semiconductors comes another step up in resolution.
Once loaded into the Proton, the chip, with all its sensors, reads the strand of DNA while software analyzes the data for completion and accuracy, delivering the data to researchers.
According to Life Technologies, the sensor and sample prep kit come out to about $1,000 total, and the Proton is a small unit, so it's not exactly an energy hog.
In a way, the actual sequencing is the easy part. The next big area of development in software is helping researchers and doctors see and understand patterns in the genome more easily. After all, the human genome contains more than 20,000 genes [source: NOVA]. A veritable warehouse of genetic information that must be sorted in order to make any findings.
Now that we have a rough understanding of the process, let's explore the possible uses for sequencing.