Scientists at Ion Torrent Systems Inc. have created a DNA sequencing technique using semiconductors instead of the costly and complex optical technology. They say their device has a much lower cost, it is portable and can be upgraded (scalable). Their aim is to achieve the target price of $1,000 for a genome sequencing.
Company founder, Dr. Jonathan Rothberg, the machine’s inventor, and team wrote in the journal Nature this week:
“The seminal importance of DNA sequencing to the life sciences, biotechnology and medicine has driven the search for more scalable and lower-cost solutions.”
The company claims their device has a wide DNA sequencing range, from microbes to humans.
The device, referred to by the company as a PGM (Personal Genome Machine), uses a massively parallel array of semiconductor sensors which measure the hydrogen ions produced during DNA replication. This is done in real time. Put more simply, the machine has a silicon chip which has 1.2 million sensors consisting of tiny wells – these are filled with beads containing DNA strands to be sequenced. The well has detectors which measure the hydrogen ions that are produced during DNA replication. The DNA sequencing can be completed within approximately two hours, instead of weeks.
Ion Torrent Systems’ vice president of marketing and business development, Maneesh Jain, said sequencing of E. coli in Germany and China during recent outbreaks were identified during the first three days using PGMs, rather than several weeks. This gave health authorities valuable time to do something about it.
Jain added that the company’s PGM is used in labs all over the world, in over 40 countries.
Dr. Jonathan Rothberg says their machine was used to decode the genome of co-founder of Intel, Gordon Moore.
Dr. Rothberg said:
“Gordon Moore worked out all the tricks that gave us modern semiconductors, so he should be the first person to be sequenced on a semiconductor.”
The DNA coding device sells for $49,000 dollars, considerably less that its current rivals.
Several companies are competing to reach the $1,000 price tag for a human genome sequencing, the price experts say could pave the way for routine sequencing in medical practice. Ion Torrent Systems believe they will achieve the $1,000 target by 2013.
The scientists wrote in Nature that:
“(Dr. Moore’s genome’s genetic variant indicates a) 56% chance of brown eyes . . . . typical amount of freckling . . . . moderately higher odds of smelling asparagus in one’s urine.”
The authors added that, surprisingly, Dr. Moore’s genome denotes a higher risk of mental retardation. Obviously the man turned out to be highly intelligent, making one wonder how useful this genomic data is.
Dr. Rothberg stressed that we are at least a decade away from understanding the human genome properly; in a way which could be really useful. However, the new device is useful when focusing on a selection of genes, as might be the case when researching cancer.
DNA sequence is the exact ordering of the bases – A (adenine), T (thymine), G (guanine), C (cytosine) – in a molecule of DNA. DNA sequencing refers to identifying the exact order of the base pairs in a segment of DNA.
Jonathan M. Rothberg, Wolfgang Hinz, Todd M. Rearick, Jonathan Schultz, William Mileski, Mel Davey, John H. Leamon, Kim Johnson, Mark J. Milgrew, Matthew Edwards, Jeremy Hoon, Jan F. Simons, David Marran, Jason W. Myers, John F. Davidson, Annika Branting, John R. Nobile, Bernard P. Puc, David Light, Travis A. Clark, Martin Huber, Jeffrey T. Branciforte, Isaac B. Stoner, Simon E. Cawley, Michael Lyons et al.
Nature 475, 348-352 (21 July 2011) doi:10.1038/nature10242
Written by Christian Nordqvist