IBM presenta il sequenziatore di DNA di "ridotte dimensioni"

[F1R3BL4D3]

IBM Research Aims to Build Nanoscale DNA Sequencer to Help Drive Down Cost of Personalized Genetic Analysis

Yorktown Heights, NY - 06 Oct 2009: In an effort to build a nanoscale DNA sequencer, IBM (NYSE: IBM) scientists are drilling nano-sized holes in computer-like chips and passing DNA strands through them in order to read the information contained within their genetic code.

This advanced research effort to demonstrate a silicon-based “DNA Transistor” could help pave the way to read human DNA easily and quickly, generating advancements in health condition diagnosis and treatment. The challenge in the effort is to slow and control the motion of the DNA through the hole so the reader can accurately decode what is in the DNA. If successful, the project could improve throughput and reduce cost to achieve the vision of personalized genome analysis at a cost of $100 to $1,000. In comparison, the first sequencing ever done by the Human Genome Project (HGP) cost $3 billion.

Having access to an individual’s personal genetic code could advance personalized medicine by using genomic and molecular data to facilitate the discovery and clinical testing of new products, and help determine a person's predisposition to a particular disease or condition.

A team of IBM scientists from four fields – nanofabrication, microelectronics, physics and biology -- are converging to master the technique that threads a long DNA molecule through a three nanometer wide hole, known as a nanopore, in a silicon chip. A nanometer is one one-billionth of a meter or about 100,000 times smaller than the width of a human hair. As the molecule is passed through the nanopore, it is ratcheted one unit of DNA at a time, as an electrical sensor “reads” the DNA. This sensor that identifies the genetic information is the subject of intense ongoing research. The information gathered from the reader could be used to gain a better understanding of an individual’s medical makeup to help further the pursuit of personalized healthcare.

“The technologies that make reading DNA fast, cheap and widely available have the potential to revolutionize bio-medical research and herald an era of personalized medicine,” said IBM Research Scientist Gustavo Stolovitzky. “Ultimately, it could improve the quality of medical care by identifying patients who will gain the greatest benefit from a particular medicine and those who are most at risk of adverse reaction.”

IBM Research is working to optimize a process for controlling the rate at which a DNA strand moves through a nano-scale aperture on a thin membrane during analysis for DNA sequencing. While scientists around the world have been working on using nanopore technology to read DNA, nobody has been able to figure out how to have complete control of a DNA strand as it travels through the nanopore. Slowing the speed is critical to being able to read the DNA strand. IBM scientists believe they have a unique approach that could tackle this challenge.

To control the speed at which the DNA flows through the microprocessor nanopore, IBM researchers have developed a device consisting of a multilayer metal/dielectric nano-structure that contains the nanopore. Voltage biases between the electrically addressable metal layers will modulate the electric field inside the nanopore. This device utilizes the interaction of discrete charges along the backbone of a DNA molecule with the modulated electric field to trap DNA in the nanopore. By cyclically turning on and off these gate voltages, scientists showed theoretically and computationally, and expect to be able prove experimentally, the plausibility of moving DNA through the nanopore at a rate of one nucleotide per cycle – a rate that IBM scientists believe would make DNA readable.

A human genome sequencing capability affordable for individuals is the ultimate goal of the DNA sequencing and is commonly referred to as “$1,000 genome.”

In the Fall of 2005, IBM revised its corporate privacy and equal opportunity policies to reflect the corporation's intention to handle information about an employee's genetics with a high regard for its privacy, and also to refrain from using genetic test information to discriminate against a person in the employment context. At that time, IBM was arguably the first company in the world to restrict genetic data from being used to make employment-related decisions.

On May 21, 2008, the United States signed into law the Genetic Information Nondiscrimination Act (GINA) that protects Americans against discrimination based on their genetic information when it comes to health insurance and employment. The bill passed the Senate unanimously and the House by a vote of 414 to 1. The long-awaited measure, which has been debated in Congress for 13 years, is helping to pave the way for people to take full advantage of the promise of personalized medicine without fear of discrimination.

http://www-03.ibm.com/press/us/en/pr...ease/28558.wss

Video:
http://www.youtube.com/watch?v=wvclP3GySUY

http://www.youtube.com/watch?v=pKi30ai35mU

sembra carina come cosa ed è anche interessante il funzionamento (primo video).

[Jarni]

Bello... così posso costruirmi i virus!!!

[F1R3BL4D3]

Più lo leggo e più mi piace.

If successful, the project could improve throughput and reduce cost to achieve the vision of personalized genome analysis at a cost of $100 to $1,000. In comparison, the first sequencing ever done by the Human Genome Project (HGP) cost $3 billion.

Per chi guarda ai riscontri pratici sembra interessante la riduzione sensibile dei costi e si avvicinano le cure personalizzate.

[Lorekon]

interessante

è già stato testato da qualcuno esterno a IBM?
ci sono indicazioni sulle performance in termini di tempo e di fedeltà?
com'è il pre-processing? si butta denta il DNA così com'è (nel senso, va fatta la libreria)?
ci son indicazioni circa la lunghezza delle letture?
questo influenza pesantemente la capacità di calcolo necessaria ad assemblare le sequenze (infatti con i sistemi massivi paralleli che sono lo stato dell'arte attualmente, tipo Illumina, Solexa, 454 etc ma anche il SOLiD, che leggono solo un centinaio di basi a botta, ci vogliono poi dei computeroni per assemblare tutto e anche tecnici che lo facciano, il che costa e non poco).

ultimamente (ultimi 2-3 anni) stanno uscendo parecchi di queti apparecchi (giocodi parole ) che promettono molto ma IMHO è difficile che tutta questa potenza possa trovare un'applicazione che la sfrutti... sempre IMHO per il 90 % delle applicazioni il buon vecchio Sanger è ancora la scelta migliore (se non hai molte sequenze, ovviamente, e con "molte" intendo sopra le 1000 sequenze )
Ormai in outsourcing con 4 € ti fanno una lettura di 800-1000 basi di qualità sufficiente, compresa la spedizione!!

per chi fosse interessato http://en.wikipedia.org/wiki/Next-ge...encing_methods

[Lorekon]

Originariamente inviato da F1R3BL4D3

Più lo leggo e più mi piace.



Per chi guarda ai riscontri pratici sembra interessante la riduzione sensibile dei costi e si avvicinano le cure personalizzate.

riguardo la genotipizzazione per alcuni tipi di malattie molto legate alla genetica, tipo appunto le malattie genetiche in senso stretto o quelle la familiarità come fattore di rischio importante, penso che sarebbe utilissimo (basta pensare alla HapMap http://hapmap.ncbi.nlm.nih.gov/ http://www.molecularlab.it/news/view.asp?n=3303)

per tutto il resto mi sembra prematuro. non mi fido ancora molto della farmacogenomica diciamo

[F1R3BL4D3]

Per il momento dovrebbe essere solo un'annuncio di una realizzazione interna ad IBM e mi sa che siamo anche agli inizi e non ci siano molte altre informazioni.
Si potrebbe provare a scrivere ai contatti che ci sono sul sito

[Tommy81]

bisognerebbe vedere anche la precisione nel sequenziare il DNA... cioè il tasso di errore per tot basi nucleotidiche