{"id":1718,"date":"2011-12-01T13:39:31","date_gmt":"2011-12-01T13:39:31","guid":{"rendered":"http:\/\/www.joswassink.nl\/insight\/?p=1718"},"modified":"2011-12-01T13:39:31","modified_gmt":"2011-12-01T13:39:31","slug":"tu-algorithm-identifies-cancer-gene-networks","status":"publish","type":"post","link":"https:\/\/www.joswassink.nl\/insight\/?p=1718","title":{"rendered":"TU algorithm identifies cancer gene networks"},"content":{"rendered":"<p><strong><a rel=\"attachment wp-att-1719\" href=\"http:\/\/www.joswassink.nl\/insight\/?attachment_id=1719\"><img loading=\"lazy\" decoding=\"async\" class=\"alignright size-thumbnail wp-image-1719\" title=\"scderidder_548x329\" src=\"http:\/\/www.joswassink.nl\/insight\/wp-content\/uploads\/2011\/12\/scderidder_548x329-300x180.jpg\" alt=\"\" width=\"300\" height=\"180\" \/><\/a>A recent article on colon cancer, published in \u2018Nature Genetics\u2019,  identifies many more cancer genes than expected. The biologists used a  data analysis tool developed at TU Delft, in collaboration with the  Netherlands Cancer Institute.<\/strong><\/p>\n<p>To identify genes involved in colon cancer, the researchers used mice  as a model for human cancer formation. The mice carry a piece of DNA  that can jump to another location, causing a mutation there. Fittingly  named the \u2018Sleeping Beauty\u2019 transposon, the gene only jumps once it has  been \u2018kissed awake\u2019 by a certain chemical.<!--more--><\/p>\n<p>The result is widespread mutations throughout the mouse genome. Some of the mutations may be harmless, others can prove fatal.<\/p>\n<p>Molecular  biologists from the Sanger Institute (UK) collected and read DNA from  more than 400 mouse colon tumours. These tumours carry the genetic  mutations that cause cancer, but also harmless mutations. How to tell  these apart?<\/p>\n<p>That\u2019s where the bio-informatics researchers from TU  Delft come in. Dr Jeroen de Ridder (EEMCS), co-author of the article,  explains that large numbers of tumours are essential for the analysis.  The method that he and his colleagues developed calculates the  likelihood of the presence of a certain mutated gene in multiple tumours  on the basis of coincidence. The lower the probability, the more likely  it is that the gene plays an active part in cancerous growth. In all  modesty, De Ridder says their method, which is called Gaussian Kernel  Convolution (GKC) and was developed in 2006 in collaboration with the  Netherlands Cancer Institute (NKI), has become a world standard in  bio-informatics analysis of \u2018insertional mutagenesis screens\u2019.<\/p>\n<p>\u201cWe  found many more cancer genes than expected,\u201d says De Ridder, referring  to the colon cancer study. More than 800 genes with mutations were  identified, of which more than 200 have been suggested to be deregulated  in human colorectal cancer. \u201cMany genes can contribute to tumour  growths in combination with other genes.\u201d Analysis of the data yielded  no less than 38 genetic networks involved in cancer formation.<\/p>\n<p>\u201cOur  analysis has shown that large numbers of genes are involved in tumours,  but not all players may be equally important,\u201d says De Ridder. It is  now suggested that some mutations are actively driving towards cancer  growth and other mutations are more like passengers picked up along the  way as the disease develops. Researchers are now trying to tease out  those key drivers.<\/p>\n<p><em>\u2019Nature Genetics\u2019, 6 November 2011, doi:10.1038\/ng.990<\/em><\/p>\n","protected":false},"excerpt":{"rendered":"<p>A recent article on colon cancer, published in \u2018Nature Genetics\u2019, identifies many more cancer genes than expected. The biologists used a data analysis tool developed at TU Delft, in collaboration with the Netherlands Cancer Institute.<\/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":[63,73,132,194],"class_list":["post-1718","post","type-post","status-publish","format-standard","hentry","category-articles","category-delta","tag-bio-informatics","tag-cancer","tag-dna","tag-genes"],"_links":{"self":[{"href":"https:\/\/www.joswassink.nl\/insight\/index.php?rest_route=\/wp\/v2\/posts\/1718","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=1718"}],"version-history":[{"count":0,"href":"https:\/\/www.joswassink.nl\/insight\/index.php?rest_route=\/wp\/v2\/posts\/1718\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.joswassink.nl\/insight\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1718"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.joswassink.nl\/insight\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=1718"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.joswassink.nl\/insight\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=1718"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}