Boffins at Japanese IT giant Panasonic have been showing off a “lab-on-a-chip” capable of rapidly analysing patient DNA so that doctors can quickly and easily identify disease and prescribe effective medication. The testing chip, developed with Belgium-based research firm IMEC, is less than half the size of a business card and …
Prior Art perhaps
Boy 17 builds DNA testing machine in his bedroom to find out why his brother had ginger hair.
Fred Turner 17 analysed his bothers hair to prove the theory red hair appears in people with a mutated gene in the MC1R protein. He built a polymerase chain reaction machine using an old video player ( possibly Panasonic ) after a similar one was built in the US. It amplifies DNA strands so they can be analysed in a lab.
After the DNA was heated to 95C in a solution then added to an enzyme primer for a two hour cycle.
Ok so it was in Saturdays Daily Mail page 29 but hey he is one clever kid.
Note what's impressive.
It's hours, not days or weeks.
It (can) make detailed DNA analysis routine
Which can include identifying what pharmaceuticals cannot be metabolized by someone (making their prescription completely pointless, of which there are at least 200 known) as well as what chemo drugs could work for cancer treatment.
In fact it could cover any condition for which a large number of drugs exist but but whose performance varies widely on an individual basis.
Thumbs up for (potentially) bringing it out of a rare lab technique and into a routine diagnostic.
Re: Note what's impressive.
and I'll agree. Its a very useful advance in the art of DNA analysis.
Regretfully this may well become...
...analysing patient DNA so that insurance companies can screw you.
Kudos to the inventor, though.
Re: Regretfully this may well become...
"...analysing patient DNA so that insurance companies can screw you."
Then it would be the duty of %Government% to ban such practices from insurance companies, and make sure that results taken using this technology are not used for discriminating their patients.
And it would be %Citizens% duty (our duty) to put pressure on our governments to carry out their duties.
I understand that won't be an easy task, though. :-(
Could also be useful for forensics - PC Plod does a test on the spot rather than arrest someone, bail them and then wait 2 or 3 weeks (or longer) for the results to come back negative.
Now if they can make it affordable enough for home use they really will have something interesting.
How PCR works
Changing temperatures IS important, but it's a bit more than that. Polymerase Chain Reaction, a key to most modern biotechnology, was invented in the 1980s, and won its somewhat eccentric California surfer-dude inventor (google Mullis) a speedy Nobel Prize as a result.
Most cells duplicate their DNA as they prepare to divide into two, so each resulting daughter cell gets its own full copy of the parental cell's DNA. PCR takes the DNA-copying enzyme from that process, and directs it to work on a specific stretch of DNA to duplicate that same stretch of DNA over and over again. Two short pieces of DNA (20 or so bases long), whose sequences match the DNA sequences at each end of the specific stretch, are included in the reaction to direct amplification solely to that stretch. Exponential growth is the bio-savant's friend in this case, as after the first duplication cycle, twice as many DNA copies of the given stretch are present; after the 2nd cycle 4 times as many copies are present, and so forth.
In theory, after 30 cycles, about 1 thousand million (2^30) times as many copies of the desired stretch of DNA are present, so that DNA from a small sample of hundreds or dozens of cells can be easily amplified, and even DNA from a tiny sample of just a few cells can often be amplified.
But what about changing temperatures? The brilliance of the process is that each step is performed without having to mechanically manipulate the DNA; rather just a temperature change is sufficient:
1) Initially, the temperature is raised to 95C or so to "melt" the DNA duplexes -- to separate the double strands one from the other so that the short DNA fragments and enzyme can access the now single-stranded DNA.
2) Next, the temperature is lowered to "anneal" the short added pieces of DNA to the main strand. These "oligos" will anneal or bind only to the sequence on the main strand that exactly matches their own, typically at temperatures in the range of 50C to 72C.
3) Finally, the temperature is raised a bit, usually to 72C, to allow the DNA-copying enzyme, starting from the end of the annealed oligo, to create a matching second strand for the stretch of interest.
This 3-temperature cycle is then repeated as many times as desired. The Panasonic system seems to take only 18 seconds per cycle, which is quite good; typical large-scale benchtop machines often take a few minutes per cycle. The more important advance represented by this system, though, is the all-in-one nature, able to take an unprocessed biological sample (e.g. the drop of blood) as input and to report SNPs present in that sample within an hour. As there are millions of SNPs throughout the genome, the practical efficiency of this system will depend greatly on how many *different* SNPs can be checked in parallel in a single run of the machine. If only a few or few tens can be checked, that is still useful, but if thousands or more can be checked in a single run, that would be quite impressive.
Re: How PCR works
Pardon my ignorance here (which is why I ask), isn't there a risk of damage to DNA from all this forced replication?
Re: How PCR works
Not so much damage to the DNA (it's tough!) as introducing errors during the replication. When cells replicate their DNA, the error rate is on the order of 1 in 10^9 per replication cycle, so only a few errors per mammal-sized genome. In the simplified PCR process, the error rate is typically on the order of 1 in 10^6 per cycle. As long as you use the *population* of amplified DNA fragments for your downstream analysis, this shouldn't be a problem, as the vast majority of fragments will have the correct, non-mutated base at each position. If instead you pick out a single molecule for analysis (say, by cloning it), there's a real chance you may get unlucky and choose a molecule with a new error in the sequence. Much depends on the total length of the DNA segments amplified, the specific conditions of the reaction, the specific enzyme used, and so forth.
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