Dawn of the age of genomics?

At a conference in Florida the UK company Oxford Nanopore Technologies presented a USB-stick that can read DNA sequences. “This will bring genetic information into medical practice.”

The article in New Scientist (25 February 2012) shows the MinION device, which has already sequenced a 5,000 base pair (genetic letters ATC and G) viral genome successfully. And although the device is not designed for sequencing an entire human genome (3 billion base pairs), it could be practical for genotyping cancer cells in a biopsy or determining if bone fragments on an archeological site belong to the same individual, explains New Scientist. Moreover, the device’s market price – about 700 euros – won’t be a serious impediment for professional research.

The device works by reading the letter sequence of one half of a long DNA molecule, which is pulled through a biological nanopore (10 nanometres across). The functional unit is formed by a polymerase enzyme that unzips the DNA’s double helix and feeds one half into a hollow protein that is stuck, like a valve, in a lipid membrane. The DNA bases slipping through the pore one by one disturb an ionic current that flows through it. Since each of the four bases influences the current slightly differently, the base types (‘genetic letters’) can be inferred from the variations in the ionic current.

A larger device, called the GridION, working according to the same principle, can handle larger genomes: it sequences an entire human genome in around 15 minutes, the manufacturer says.

Professor Cees Dekker, of the bionanoscience department at Applied Sciences, is currently drafting a comment on the device for Nature Biotechnology. He knows Dr Hagan Bayley, who co-founded the Oxford-based company, well, and Prof. Dekker had anticipated the device’s launch. “The big advantage of this technology,” Prof. Dekker explains, “is the large read length.” Other sequencing technologies cut up the DNA molecule randomly into very small pieces, sequence it, and then have to puzzle out how to reconstruct the entire sequence. However, this reconstruction easily misses repetitions, insertions and deletions in the genome. In principle the nanopore sequencing could do this better, but it’s not very precise (with 1 of each 25 base pairs misread). Multiple takes can compensate for this, however, as it does for every other sequencing technique.

The other key point is that this device promises to make DNA sequencing dirt cheap. One-thousand dollars used to be the magical limit, but now it looks like the price for a whole genome will go down to a few hundred dollars. “That will bring it right into the medical practice,” says Prof. Dekker. Preventive behavioral healthcare, based on your genetic susceptibilities and personalized medicine (only getting drugs that work for you), are among the first benefits. Prof. Dekker expects genetic information to be applied in medical practice in just a couple years time.

Bio-informatics expert, Dr Jeroen de Ridder (EEMCS), does not agree, however. He believes the datasets are much too large to be handled through ordinary data infrastructure (“downloading a set may cost a week”). Secondly, correlating genetics to cancers and other complex diseases is still heavily researched and often difficult. Recent studies comparing different methods for finding mutations in sequenced data from the same tumor showed little inter-similarity. “No good news for the use of genetics in choosing the right therapy,” De Ridder says. Much the same applies to the search for ‘disease genes’. Only the easiest have been identified thus far, and most diseases seem to be related to a combination of genes (and nurture).

So it seems that doctors may soon gain access to their patients’ genetic information, but it may be a while until they know what to do with it.

Zijlstra vindt zo’n onderzoek overbodig, zei hij maandag in de Tweede Kamer. Volgens universiteitenvereniging VSNU en hogescholenvereniging HBO-raad liggen de ‘zuivere overhead’-kosten – door hen gedefinieerd als het aantal aanstellingen van ondersteunend personeel aan een hogeschool of universiteit – namelijk rond de 25 procent van het instellingsbudget.
Dat aandeel vindt de staatssecretaris te hoog. Daarom wil hij afspraken maken om dit te verminderen, zodat het vrijgespeelde geld weer in het “primaire proces” kan worden geïnvesteerd.

Dinsdag stemming
Het is niet de eerste keer dat er in de Tweede Kamer wordt gediscussieerd over het ondersteunend personeel op hogescholen en universiteiten. Beleidsmedewerkers, bestuurders, en secretariaten worden daaronder gerekend. Maar hoe zit het bijvoorbeeld met studievoorlichters en de studentenpsychologen? Minister Plasterk boog zich hier al eerder over, omdat ook de kosten van het ondersteunend personeel onduidelijk zouden zijn.
PvdA-kamerlid Jadnanansing wil weten waarop de staatssecretaris denkt te kunnen besparen. Ze diende daarom een motie in om de Algemene Rekenkamer de kosten van de overhead precies in kaart te laten brengen. Alleen dan is duidelijk waar het geld precies aan wordt uitgegeven. Ze kreeg bijval van de SP en de PVV. Dinsdag wordt er over de motie gestemd.

Redacteur Redactie

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