{"id":3123,"date":"2021-03-26T10:10:54","date_gmt":"2021-03-26T10:10:54","guid":{"rendered":"https:\/\/www.value-dx.eu\/?p=3123"},"modified":"2021-03-26T10:10:54","modified_gmt":"2021-03-26T10:10:54","slug":"value-dx-developed-sample-collection-and-management-manuals-for-trials","status":"publish","type":"post","link":"https:\/\/www.value-dx.eu\/index.php\/2021\/03\/26\/value-dx-developed-sample-collection-and-management-manuals-for-trials\/","title":{"rendered":"VALUE-Dx developed sample collection and management manuals for trials"},"content":{"rendered":"\n<style type=\"text\/css\" data-created_by=\"avia_inline_auto\" id=\"style-css-av-jzkylawd-ba86e75d702405f62001a756eb35483d\">\n.avia-section.av-jzkylawd-ba86e75d702405f62001a756eb35483d{\nbackground-color:#08b4a0;\nbackground-image:unset;\n}\n<\/style>\n<div id='av_section_1'  class='avia-section av-jzkylawd-ba86e75d702405f62001a756eb35483d main_color avia-section-default avia-no-border-styling  avia-builder-el-0  el_before_av_section  avia-builder-el-first  avia-bg-style-parallax container_wrap fullsize'  ><div class='container av-section-cont-open' ><main  role=\"main\" itemprop=\"mainContentOfPage\"  class='template-page content  av-content-full alpha units'><div class='post-entry post-entry-type-page post-entry-3123'><div class='entry-content-wrapper clearfix'>\n\n<style type=\"text\/css\" data-created_by=\"avia_inline_auto\" id=\"style-css-av-kmq561dk-9c926af9e4c03cd464fb788bf6079752\">\n#top .av-special-heading.av-kmq561dk-9c926af9e4c03cd464fb788bf6079752{\npadding-bottom:10px;\n}\nbody .av-special-heading.av-kmq561dk-9c926af9e4c03cd464fb788bf6079752 .av-special-heading-tag .heading-char{\nfont-size:25px;\n}\n.av-special-heading.av-kmq561dk-9c926af9e4c03cd464fb788bf6079752 .av-subheading{\nfont-size:15px;\n}\n<\/style>\n<div  class='av-special-heading av-kmq561dk-9c926af9e4c03cd464fb788bf6079752 av-special-heading-h3 blockquote modern-quote modern-centered  avia-builder-el-1  el_before_av_codeblock  avia-builder-el-first '><h3 class='av-special-heading-tag '  itemprop=\"headline\"  >VALUE-Dx developed sample collection and management manuals for trials<\/h3><div class=\"special-heading-border\"><div class=\"special-heading-inner-border\"><\/div><\/div><\/div>\n\n<\/div><\/div><\/main><!-- close content main element --><\/div><\/div>\n<style type=\"text\/css\" data-created_by=\"avia_inline_auto\" id=\"style-css-av-1cjng-9db903d36b325f87b66fb9ba7e96614e\">\n.avia-section.av-1cjng-9db903d36b325f87b66fb9ba7e96614e{\nbackground-color:#1b7ca4;\nbackground-image:unset;\n}\n<\/style>\n<div id='av_section_2'  class='avia-section av-1cjng-9db903d36b325f87b66fb9ba7e96614e main_color avia-section-default avia-no-border-styling  avia-builder-el-3  el_after_av_section  el_before_av_section  avia-bg-style-scroll container_wrap fullsize'  ><div class='container av-section-cont-open' ><div class='template-page content  av-content-full alpha units'><div class='post-entry post-entry-type-page post-entry-3123'><div class='entry-content-wrapper clearfix'>\n\n<style type=\"text\/css\" data-created_by=\"avia_inline_auto\" id=\"style-css-av-k0i4yzrj-318dd765ad6f41d2fe86b741f8548ed0\">\n.flex_column.av-k0i4yzrj-318dd765ad6f41d2fe86b741f8548ed0{\nborder-radius:0px 0px 0px 0px;\npadding:50px 5% 50px 5%;\n}\n<\/style>\n<div  class='flex_column av-k0i4yzrj-318dd765ad6f41d2fe86b741f8548ed0 av_one_full  avia-builder-el-4  el_before_av_one_fifth  avia-builder-el-first  first flex_column_div  '     ><section  class='av_textblock_section av-yfjs-a24130328363a5d48e40d9c86a7bb2c6 '   itemscope=\"itemscope\" itemtype=\"https:\/\/schema.org\/BlogPosting\" itemprop=\"blogPost\" ><div class='avia_textblock'  itemprop=\"text\" ><p><img fetchpriority=\"high\" decoding=\"async\" class=\" wp-image-41 alignleft\" src=\"https:\/\/www.value-dx.eu\/wp-content\/uploads\/2019\/07\/shutterstock_138963686-300x201.jpg\" alt=\"\" width=\"360\" height=\"241\" srcset=\"https:\/\/www.value-dx.eu\/wp-content\/uploads\/2019\/07\/shutterstock_138963686-300x201.jpg 300w, https:\/\/www.value-dx.eu\/wp-content\/uploads\/2019\/07\/shutterstock_138963686-768x514.jpg 768w, https:\/\/www.value-dx.eu\/wp-content\/uploads\/2019\/07\/shutterstock_138963686-1030x689.jpg 1030w, https:\/\/www.value-dx.eu\/wp-content\/uploads\/2019\/07\/shutterstock_138963686-1500x1004.jpg 1500w, https:\/\/www.value-dx.eu\/wp-content\/uploads\/2019\/07\/shutterstock_138963686-705x472.jpg 705w, https:\/\/www.value-dx.eu\/wp-content\/uploads\/2019\/07\/shutterstock_138963686-450x301.jpg 450w\" sizes=\"(max-width: 360px) 100vw, 360px\" \/>WP2 has been working on the set-up of the VALUE-Dx biobank and continuing the optimisation of the protocols in preparation for the imminent start of WP4 clinical trials.<\/p>\n<p>Thanks to the expertise of <a href=\"https:\/\/www.combacte.com\/about\/lab-net\/\" target=\"_blank\" rel=\"noopener\">LAB-Net<\/a> members, the sample collection and management manuals for both trials have been developed. These manuals describe in depth how to collect samples for the microbiology sub-studies and how to process and store them until shipment to the VALUE-Dx UA\/UZA biobank in Antwerp. Additionally, the preparation of kits to be sent to the sites for the sample collection has begun, starting with kits to store the leftover samples from the diagnostic intervention implemented in the paediatric arm of the ADEQUATE trial.<\/p>\n<p>Regarding the optimisation of metagenomics protocols, the focus has been on the bioinformatics protocols that will be used to analyse the generated shotgun metagenomics data, as the wet lab protocols for sequencing are optimised for Illumina and PacBio. The pipeline will include tools for quality control and host reads removal, after which taxonomical classification, functional characterisation and assemblies will be performed. Furthermore, antimicrobial resistance genes and mutations will be studied with different tools, and <em>S. pneumoniae<\/em> serotypes will be identified if present in the sample. Validation of this pipeline is being done in shotgun metagenomics data from other studies, and will be further extended with a metagenome reconstruction step implemented by Bioaster.<\/p>\n<p>Concerning the biomarker sub-studies, specific manuals for sample collection and processing have been developed. These manuals describe how to collect, process and store plasma (EDTA and heparin) and RNA samples prior to their shipment to the UA\/UZA biobank in Antwerp. The kits required for blood collection and processing are being assembled for their subsequent use in the PRUDENCE trial. Additionally, the cytokine and chemokine analysis is being optimised, starting with the selection of the most relevant and promising biomarkers. Cytokine and chemokine panels are currently being designed. Also, we tested and recommended a double-spin plasma separation protocol to be utilised within the PRUDENCE trial, which will improve the quality of collected samples.<\/p>\n<\/div><\/section><\/div>\n<style type=\"text\/css\" data-created_by=\"avia_inline_auto\" id=\"style-css-av-3b8mw-b506a38e8d00a7f4906eea669cebc6be\">\n.flex_column.av-3b8mw-b506a38e8d00a7f4906eea669cebc6be{\nborder-radius:0px 0px 0px 0px;\npadding:0px 0px 0px 0px;\n}\n<\/style>\n<div  class='flex_column av-3b8mw-b506a38e8d00a7f4906eea669cebc6be av_one_fifth  avia-builder-el-6  el_after_av_one_full  el_before_av_one_fifth  first flex_column_div av-zero-column-padding  column-top-margin'     ><\/div>\n<style type=\"text\/css\" data-created_by=\"avia_inline_auto\" id=\"style-css-av-2lzlw-3d25ff9ce16d4f57844d3b5b4e0627c5\">\n.flex_column.av-2lzlw-3d25ff9ce16d4f57844d3b5b4e0627c5{\nborder-radius:0px 0px 0px 0px;\npadding:0px 0px 0px 0px;\n}\n<\/style>\n<div  class='flex_column av-2lzlw-3d25ff9ce16d4f57844d3b5b4e0627c5 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