{"id":1825,"date":"2012-03-08T09:27:05","date_gmt":"2012-03-08T09:27:05","guid":{"rendered":"http:\/\/www.joswassink.nl\/insight\/?p=1825"},"modified":"2012-03-08T09:27:05","modified_gmt":"2012-03-08T09:27:05","slug":"dawn-of-the-age-of-genomics","status":"publish","type":"post","link":"https:\/\/www.joswassink.nl\/insight\/?p=1825","title":{"rendered":"Dawn of the age of genomics?"},"content":{"rendered":"

\"\"<\/a>At a conference in Florida the UK company Oxford Nanopore Technologies presented a USB-stick that can read DNA sequences. \u201cThis will bring genetic information into medical practice.\u201d<\/strong><\/p>\n

The article in New Scientist<\/em> (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\u2019s market price – about 700 euros – won\u2019t be a serious impediment for professional research.
\nThe 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\u2019s 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 (\u2018genetic letters\u2019) can be inferred from the variations in the ionic current.<\/p>\n

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.<\/p>\n

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\u2019s launch. \u201cThe big advantage of this technology,\u201d Prof. Dekker explains, \u201cis the large read length.\u201d 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\u2019s 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.<\/p>\n

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. \u201cThat will bring it right into the medical practice,\u201d 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.
\nBio-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 (\u201cdownloading a set may cost a week\u201d). 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. \u201cNo good news for the use of genetics in choosing the right therapy,\u201d De Ridder says. Much the same applies to the search for \u2018disease genes\u2019. Only the easiest have been identified thus far, and most diseases seem to be related to a combination of genes (and nurture).<\/p>\n

So it seems that doctors may soon gain access to their patients\u2019 genetic information, but it may be a while until they know what to do with it.<\/p>\n

 <\/p>\n","protected":false},"excerpt":{"rendered":"

At a conference in Florida the UK company Oxford Nanopore Technologies presented a USB-stick that can read DNA sequences. \u201cThis will bring genetic information into medical practice.\u201d 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. […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[3,6],"tags":[63,81,132,247,292,304,383],"class_list":["post-1825","post","type-post","status-publish","format-standard","hentry","category-articles","category-delta","tag-bio-informatics","tag-cees-dekker","tag-dna","tag-jeroen-de-ridder","tag-minion","tag-nanopores","tag-sequencers"],"_links":{"self":[{"href":"https:\/\/www.joswassink.nl\/insight\/index.php?rest_route=\/wp\/v2\/posts\/1825","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.joswassink.nl\/insight\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.joswassink.nl\/insight\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.joswassink.nl\/insight\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.joswassink.nl\/insight\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=1825"}],"version-history":[{"count":0,"href":"https:\/\/www.joswassink.nl\/insight\/index.php?rest_route=\/wp\/v2\/posts\/1825\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.joswassink.nl\/insight\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1825"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.joswassink.nl\/insight\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=1825"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.joswassink.nl\/insight\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=1825"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}