{"id":4974,"date":"2018-08-21T09:52:23","date_gmt":"2018-08-21T08:52:23","guid":{"rendered":"http:\/\/www.library.sath.nhs.uk\/research\/?p=4974"},"modified":"2020-05-29T09:05:35","modified_gmt":"2020-05-29T08:05:35","slug":"design-and-implementation-of-a-custom-next-generation-sequencing-panel-for-selected-vitamin-d-associated-genes-2017","status":"publish","type":"post","link":"https:\/\/www.library.sath.nhs.uk\/research\/2018\/08\/21\/design-and-implementation-of-a-custom-next-generation-sequencing-panel-for-selected-vitamin-d-associated-genes-2017\/","title":{"rendered":"Design and implementation of a custom next generation sequencing panel for selected vitamin D associated genes (2017)"},"content":{"rendered":"<p><strong>Type of publication:<\/strong><br \/>\nJournal article<\/p>\n<p><strong>Author(s):<\/strong><br \/>\nBenson K.A.; Maxwell A.P.; Smyth L.J.; Kilner J.; McKnight A.J.; *<a href=\"http:\/\/orcid.org\/0000-0002-6126-3678\" target=\"_blank\" rel=\"noopener noreferrer\">Chand S.<\/a> <a href=\"http:\/\/orcid.org\/0000-0002-6126-3678\" target=\"_blank\" rel=\"noopener noreferrer\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone wp-image-5757 size-full\" src=\"http:\/\/www.library.sath.nhs.uk\/wp-content\/uploads\/2020\/05\/orcid_16x16.gif\" alt=\"\" width=\"16\" height=\"16\" \/><\/a>; Borrows R.<\/p>\n<p><strong>Citation:<\/strong><br \/>\nBMC Research Notes; Jul 2017; vol. 10 (no. 1); p. 348<\/p>\n<p><strong>Abstract:<br \/>\n<\/strong> BACKGROUND: Biologically active vitamin D has an important regulatory role within the genome. It binds the vitamin D receptor (VDR) in order to control the expression of a wide range of genes as well as interacting with the epigenome to modify chromatin and methylation status. Vitamin D deficiency is associated with several human diseases including end-stage renal disease.METHODS: This article describes the design and testing of a custom, targeted next generation sequencing (NGS) panel for selected vitamin D associated genes. Sequencing runs were used to determine the effectiveness of the panel for variant calling, to compare efficiency and data across different sequencers, and to perform representative, proof of principle association analyses. These analyses were underpowered for significance testing. Amplicons were designed in two pools (163 and 166 fragments respectively) and used to sequence two cohorts of renal transplant recipients on the Ion Personal Genome Machine (PGM)TM and Ion S5TM XL desktop sequencers.RESULTS: Coverage was provided for 43.8 kilobases across seven vitamin D associated genes (CYP24A1, CUBN, VDR, GC, NADSYN1, CYP27B1, CYP2R1) as well as 38 prioritised SNPs. Sequencing runs provided sufficient sequencing quality, data output and validated the effective library preparation and panel design.CONCLUSIONS: This novel, custom-designed, validated panel provides a fast, cost effective, and specific approach for the analysis of vitamin D associated genes in a wide range of patient cohorts. This article does not report results from a controlled health-care intervention.<\/p>\n<p><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC5534126\/\">Link to full-text<\/a>\u00a0[no password required]<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Type of publication: Journal article Author(s): Benson K.A.; Maxwell A.P.; Smyth L.J.; Kilner J.; McKnight A.J.; *Chand S. ; Borrows R. Citation: BMC Research Notes; Jul 2017; vol. 10 (no. 1); p. 348 Abstract: BACKGROUND: Biologically active vitamin D has<span class=\"ellipsis\">&hellip;<\/span><\/p>\n<div class=\"read-more\"><a href=\"https:\/\/www.library.sath.nhs.uk\/research\/2018\/08\/21\/design-and-implementation-of-a-custom-next-generation-sequencing-panel-for-selected-vitamin-d-associated-genes-2017\/\">Read more <span class=\"screen-reader-text\">Design and implementation of a custom next generation sequencing panel for selected vitamin D associated genes (2017)<\/span><span class=\"meta-nav\"> &#8250;<\/span><\/a><\/div>\n<p><!-- end of .read-more --><\/p>\n","protected":false},"author":12,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"content-type":"","footnotes":""},"categories":[200],"tags":[677,787,786],"class_list":["post-4974","post","type-post","status-publish","format-standard","hentry","category-staff-publication","tag-677","tag-genomics","tag-vitamin-d"],"_links":{"self":[{"href":"https:\/\/www.library.sath.nhs.uk\/research\/wp-json\/wp\/v2\/posts\/4974","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.library.sath.nhs.uk\/research\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.library.sath.nhs.uk\/research\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.library.sath.nhs.uk\/research\/wp-json\/wp\/v2\/users\/12"}],"replies":[{"embeddable":true,"href":"https:\/\/www.library.sath.nhs.uk\/research\/wp-json\/wp\/v2\/comments?post=4974"}],"version-history":[{"count":5,"href":"https:\/\/www.library.sath.nhs.uk\/research\/wp-json\/wp\/v2\/posts\/4974\/revisions"}],"predecessor-version":[{"id":5997,"href":"https:\/\/www.library.sath.nhs.uk\/research\/wp-json\/wp\/v2\/posts\/4974\/revisions\/5997"}],"wp:attachment":[{"href":"https:\/\/www.library.sath.nhs.uk\/research\/wp-json\/wp\/v2\/media?parent=4974"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.library.sath.nhs.uk\/research\/wp-json\/wp\/v2\/categories?post=4974"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.library.sath.nhs.uk\/research\/wp-json\/wp\/v2\/tags?post=4974"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}