{"id":1342,"date":"2016-06-01T11:22:56","date_gmt":"2016-06-01T10:22:56","guid":{"rendered":"http:\/\/blogs.kent.ac.uk\/biosciences\/?p=1342"},"modified":"2016-06-01T12:09:51","modified_gmt":"2016-06-01T11:09:51","slug":"research-seminar-species-independent-identification-of-known-and-novel-recurrent-genomic-entities-in-multiple-cancer-patients","status":"publish","type":"post","link":"https:\/\/blogs.kent.ac.uk\/biosciences\/2016\/06\/01\/research-seminar-species-independent-identification-of-known-and-novel-recurrent-genomic-entities-in-multiple-cancer-patients\/","title":{"rendered":"Research Seminar: Species-independent identification of known and novel recurrent genomic entities in multiple cancer patients."},"content":{"rendered":"<p><strong>Dr. Jose Izarzugaza, Centre for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark <\/strong><\/p>\n<p><b>Tuesday 7th June, 1.00 p.m., Stacey Lecture Theatre 1<\/b><\/p>\n<p>&nbsp;<\/p>\n<p>The discovery\u00a0of viruses and other disease-causing pathogens from high throughput sequencing\u00a0data often requires that taxonomic annotation occurs prior to\u00a0association to\u00a0disease. Although this bottom-up approach is effective in some cases, it fails\u00a0to detect novel pathogens and remote variants not present in reference\u00a0databases. We propose an alternate approach that utilizes sequence clustering\u00a0for the identification of nucleotide sequences that co-occur across multiple\u00a0sequencing\u00a0data instances. Thus, not limited to reported species. We applied the\u00a0workflow to 686 sequencing libraries from 252 different cancers and 56\u00a0controls. We used our pipeline to associate recurrent sequences to the onset of\u00a0the disease but also to the use of common laboratory kits to identify common\u00a0methodological or technical artifacts sourcing erroneous conclusions, as we\u00a0have\u00a0observed in the recent literature. We provide examples of identified\u00a0inhabitants of the healthy tissue flora as well as experimental contaminants.<\/p>\n<p>&nbsp;<\/p>\n<ul class=\"kent-social-links\"><li><a href='http:\/\/www.facebook.com\/sharer.php?u=https:\/\/blogs.kent.ac.uk\/biosciences\/2016\/06\/01\/research-seminar-species-independent-identification-of-known-and-novel-recurrent-genomic-entities-in-multiple-cancer-patients\/&amp;t=Research Seminar: Species-independent identification of known and novel recurrent genomic entities in multiple cancer patients.' target='_blank'><i class='ksocial-facebook' title='Share via Facebook'><\/i><\/a><\/li><li><a href='http:\/\/twitter.com\/home?status=Research Seminar: Species-independent identification of known and novel recurrent genomic entities in multiple cancer patients.%20https:\/\/blogs.kent.ac.uk\/biosciences\/2016\/06\/01\/research-seminar-species-independent-identification-of-known-and-novel-recurrent-genomic-entities-in-multiple-cancer-patients\/' target='_blank'><i class='ksocial-twitter' title='Share via Twitter'><\/i><\/a><\/li><li><a href='https:\/\/plus.google.com\/share?url=https:\/\/blogs.kent.ac.uk\/biosciences\/2016\/06\/01\/research-seminar-species-independent-identification-of-known-and-novel-recurrent-genomic-entities-in-multiple-cancer-patients\/' target='_blank'><i class='ksocial-google-plus' title='Share via Google Plus'><\/i><\/a><\/li><li><a href='http:\/\/linkedin.com\/shareArticle?mini=true&amp;url=https:\/\/blogs.kent.ac.uk\/biosciences\/2016\/06\/01\/research-seminar-species-independent-identification-of-known-and-novel-recurrent-genomic-entities-in-multiple-cancer-patients\/&amp;title=Research Seminar: Species-independent identification of known and novel recurrent genomic entities in multiple cancer patients.' target='_blank'><i class='ksocial-linkedin' title='Share via Linked In'><\/i><\/a><\/li><li><a href='mailto:content=https:\/\/blogs.kent.ac.uk\/biosciences\/2016\/06\/01\/research-seminar-species-independent-identification-of-known-and-novel-recurrent-genomic-entities-in-multiple-cancer-patients\/&amp;title=Research Seminar: Species-independent identification of known and novel recurrent genomic entities in multiple cancer patients.' target='_blank'><i class='ksocial-email' title='Share via Email'><\/i><\/a><\/li><\/ul>","protected":false},"excerpt":{"rendered":"<p>Dr. Jose Izarzugaza, Centre for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark Tuesday 7th June, 1.00 p.m., Stacey Lecture Theatre 1 &hellip; <a href=\"https:\/\/blogs.kent.ac.uk\/biosciences\/2016\/06\/01\/research-seminar-species-independent-identification-of-known-and-novel-recurrent-genomic-entities-in-multiple-cancer-patients\/\">Read&nbsp;more<\/a><\/p>\n","protected":false},"author":32117,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":[],"categories":[50580],"tags":[],"_links":{"self":[{"href":"https:\/\/blogs.kent.ac.uk\/biosciences\/wp-json\/wp\/v2\/posts\/1342"}],"collection":[{"href":"https:\/\/blogs.kent.ac.uk\/biosciences\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/blogs.kent.ac.uk\/biosciences\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/blogs.kent.ac.uk\/biosciences\/wp-json\/wp\/v2\/users\/32117"}],"replies":[{"embeddable":true,"href":"https:\/\/blogs.kent.ac.uk\/biosciences\/wp-json\/wp\/v2\/comments?post=1342"}],"version-history":[{"count":1,"href":"https:\/\/blogs.kent.ac.uk\/biosciences\/wp-json\/wp\/v2\/posts\/1342\/revisions"}],"predecessor-version":[{"id":1343,"href":"https:\/\/blogs.kent.ac.uk\/biosciences\/wp-json\/wp\/v2\/posts\/1342\/revisions\/1343"}],"wp:attachment":[{"href":"https:\/\/blogs.kent.ac.uk\/biosciences\/wp-json\/wp\/v2\/media?parent=1342"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.kent.ac.uk\/biosciences\/wp-json\/wp\/v2\/categories?post=1342"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.kent.ac.uk\/biosciences\/wp-json\/wp\/v2\/tags?post=1342"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}