{"id":34,"date":"2020-01-22T09:57:37","date_gmt":"2020-01-22T09:57:37","guid":{"rendered":"https:\/\/www.almacgroup.com\/diagnostics\/?page_id=34"},"modified":"2025-06-11T09:37:15","modified_gmt":"2025-06-11T08:37:15","slug":"bioinformatics","status":"publish","type":"page","link":"https:\/\/www.almacgroup.com\/diagnostics\/supporting-services\/data-sciences\/bioinformatics\/","title":{"rendered":"Bioinformatics"},"content":{"rendered":"\n<h3 class=\"wp-block-heading\" id=\"h-bioinformatics\">Bioinformatics <\/h3>\n\n\n\n<p>Almac Diagnostic Services Bioinformatics Team offer a high quality service for analysis of genomics data across a <a href=\"\/diagnostics\/supporting-services\/platforms-technologies\/\">range of platforms<\/a> (including Next Generation Sequencing (NGS), Nanostring and qPCR) and biomaterials, underpinned by our extensive experience analysing data from both in-house development projects and commercial clinical projects. We have access to the latest Illumina DRAGEN Secondary Analysis pipelines hosted on the Illumina Connected Analytics (ICA) cloud platform allowing robust, flexible end-to-end data solutions at scale from quality control (QC), processing and interpretation to data transfer directly to the client. <\/p>\n\n\n\n<p>The team offers the following capabilities across the core platforms listed below, however much of our work is tailored to specific data challenges for clients, which typically require bespoke solutions.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\" id=\"h-technology-analysis-pipelines\">Technology analysis pipelines <\/h3>\n\n\n\n<p><strong>RNA<\/strong><\/p>\n\n\n\n<p><strong>NGS (Next Generation Sequencing)<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Almac established QC &amp; pre-processing steps for bulk (Illumina TruSeq\u2122 RNA Exome, Total RNA-Seq and mRNA Stranded), small and single-cell <a href=\"https:\/\/www.almacgroup.com\/diagnostics\/rna-sequencing-solutions\/\">RNA-Seq<\/a>.<\/li>\n\n\n\n<li>Bulk RNASeq analysis includes access to the <a href=\"\/diagnostics\/claratreport\/\">Clara<sup>T<\/sup> Total mRNA Report<\/a>.<\/li>\n\n\n\n<li>Custom workflow development tailored to answer specific customer questions<\/li>\n<\/ul>\n\n\n\n<p><strong>Nanostring<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>nSolver QC and data normalisation<\/li>\n\n\n\n<li>Includes access to IO360\/BC360 Data Analysis Reporting if applicable.<\/li>\n<\/ul>\n\n\n\n<p><strong>qPCR<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>In-house software for reproducible data QC &amp; pre-processing<\/li>\n<\/ul>\n\n\n\n<p><strong>DNA<\/strong><\/p>\n\n\n\n<p><strong>Whole Exome Sequencing (WES) \/ Whole Genome Sequencing (WGS)<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Illumina DRAGEN QC and secondary analysis for<a href=\"https:\/\/www.almacgroup.com\/diagnostics\/portfolio-overview\/whole-exome-sequencing\/\">&nbsp;WES (Whole Exome Sequencing)<\/a> or <a href=\"https:\/\/www.almacgroup.com\/diagnostics\/whole-genome-sequencing-wgs-service\/\">WGS (Whole Genome Sequencing)<\/a><\/li>\n\n\n\n<li>Custom annotation, filtering and interpretation options available<\/li>\n<\/ul>\n\n\n\n<p><strong>Whole Genome Methylation Sequencing (WGMS)<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Almac established QC and processing steps for EM-seq \u2013 <a href=\"https:\/\/www.almacgroup.com\/diagnostics\/global-laboratories\/platforms-technologies\/dna-sequencing-solutions\/portfolio-overview-whole-genome-methylation-sequencing\/\">WGMS (Whole Genome Methylation Sequencing)<\/a><\/li>\n\n\n\n<li>DRAGEN pipelines for bisulphite-seq and custom workflow development tailored to answer specific customer questions<\/li>\n<\/ul>\n\n\n\n<p><strong>Medium \/&nbsp;Small Variant Panels<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Illumina DRAGEN Analysis Software for small variant, CNV and fusion detection from Illumina TruSight\u2122 Oncology 500 (TSO500) tissue and ctDNA panels.<\/li>\n\n\n\n<li>Archer Analysis pipelines applied to Archer\u00ae FusionPlex, VariantPlex and LiquidPlex panels<\/li>\n\n\n\n<li>Personal Genome Diagnostics (PGDx) analysis pipelines applied to PGDx elio tissue and plasma panels.<\/li>\n\n\n\n<li>Almac can also develop custom pipelines for other targeted panels<\/li>\n<\/ul>\n\n\n\n<p>To see our range or panel solutions visit <a href=\"https:\/\/www.almacgroup.com\/diagnostics\/global-laboratories\/platforms-technologies\/dna-sequencing-solutions\/portfolio-overview-whole-genome-methylation-sequencing\/\">Platforms &amp; Technologies<\/a><\/p>\n\n\n\n<h3 class=\"wp-block-heading\" id=\"h-bioinformatics-for-the-biomarker-discovery-process\">Bioinformatics for the biomarker discovery process <\/h3>\n\n\n\n<p>Almac Diagnostic Services has a well-developed gene expression biomarker discovery process incorporating in-house software that has been established over many years. Our pipelines are applicable to expression platforms, such as RNA-Seq, and Nanostring.<\/p>\n\n\n\n<p>Our expertise in biomarker development has been demonstrated through our own research in the <strong>oncology<\/strong> field, where we have discovered and validated a number of <a href=\"https:\/\/www.almacgroup.com\/diagnostics\/almac-rd-assays\/\">Almac proprietary biomarkers<\/a> from FFPE studies including <a href=\"\/diagnostics\/portfolio-overview\/ddir\/\">DDIR<\/a>, <a href=\"\/diagnostics\/portfolio-overview\/angio\/\">Angio<\/a>, <a href=\"\/diagnostics\/portfolio-overview\/emt\/\">EMT<\/a>, <a href=\"\/diagnostics\/portfolio-overview\/prostate-dx\/\">ProstateDx<\/a> and <a href=\"\/diagnostics\/portfolio-overview\/coldx\/\">ColDx<\/a> signature.<\/p>\n\n\n\n<p>We also have extensive expertise in the <strong>non-oncology field<\/strong> supporting client biomarker development projects in <a href=\"https:\/\/www.almacgroup.com\/diagnostics\/chronicdisease\/\">Chronic Disease<\/a>. These studies typically use fresh samples rather than archival samples, meaning degradation is less of an issue; however clinical endpoints are often poorly defined. In these cases we can perform analysis to guide selection of the most appropriate endpoint for your study.<\/p>\n\n\n\n<p>Our Bioinformatics team can perform post-hoc analyses to tailor developed models to specific patient subgroups, incorporation of other data types such as pharmacokinetic (PK Biomarkers), and building multi factorial models including predictive clinical factors in addition to off the shelf best practice solutions for differential expression and pathway \/ functional enrichment analyses.<\/p>\n\n\n\n<p>Almac Diagnostic Services can offer clients the following proprietary Bioinformatics analysis solutions to facilitate their Biomarker Discovery process:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><strong>Quality Control (QC) &amp; Exploratory Analysis (EA)<\/strong><\/li>\n\n\n\n<li><strong>Subtyping Workflow<\/strong><\/li>\n\n\n\n<li><strong>Signature Generation Workflow<\/strong><\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Quality Control (QC) &amp; Exploratory Analysis (EA)<\/h3>\n\n\n\n<p>For optimal biomarker discovery<strong>, Almac\u2019s QC and EA process ensures the best starting point for signature generation<\/strong>. We have&nbsp;<strong>defined QC processes and thresholds for most expression data generating platforms such as RNA-Seq and microarray<\/strong>. Our EA tool works with any expression data type and provides insight into all relationships within, and between, technical and clinical variables and the data structure based on principal components. The EA process aims to identify key factors driving sample groups within the dataset and reduce or remove the impact of technical effects that may hinder the biomarker discovery process.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Subtyping workflow<\/h3>\n\n\n\n<p>Almac\u2019s&nbsp;<strong>unsupervised analysis process<\/strong>&nbsp;is&nbsp;<strong>designed to find the underlying biological structure<\/strong>&nbsp;driving sample separation within a dataset, to identify stable sample and gene clusters driven by these transcripts. This process is of particular benefit when the response endpoint is poorly defined.&nbsp;<strong>Transcripts are identified by an iterative process of removing noise<\/strong> and&nbsp;<strong>testing the stability of resulting clusters<\/strong>. Once&nbsp;<strong>robust sample and gene clusters are identified<\/strong>, the&nbsp;<strong>association of sample characteristics to these clusters is tested<\/strong>, and&nbsp;<strong>functional enrichment of the gene clusters is performed<\/strong>&nbsp;to characterise the biology of the subgroups.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Signature Generation Workflow (SGW)<\/h3>\n\n\n\n<p>Almac\u2019s&nbsp;<strong>SGW<\/strong>&nbsp;has been developed according to&nbsp;<strong>MAQC best practice.&nbsp;<\/strong>All feature selection and performance metric generation are performed under a robust cross-validation process. The&nbsp;<strong>machine learning method<\/strong>&nbsp;depends on the nature of the endpoint of interest and dichotomous classifiers or continuous predictors can be developed to binary or continuous measures of response. Almac has&nbsp;<strong>custom-built functions to visualise the biological relevance of resulting signatures<\/strong> to guide final model selection, along with appropriate measures of performance.<\/p>\n\n\n\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Bioinformatics Almac Diagnostic Services Bioinformatics Team offer a high quality service for analysis of genomics data across a range of platforms (including Next Generation Sequencing (NGS), Nanostring and qPCR) and biomaterials, underpinned by our extensive experience analysing data from both in-house development projects and commercial clinical projects. We have access to the latest Illumina DRAGEN [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":30,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":""},"class_list":["post-34","page","type-page","status-publish","hentry"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO Premium plugin v25.3.1 (Yoast SEO v26.3) - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Bioinformatics - Diagnostic Services<\/title>\n<meta name=\"description\" content=\"High quality analysis of genomics data across a range of platforms (including Next Generation Sequencing (NGS), microarray and qPCR) and biomaterials.\" \/>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.almacgroup.com\/diagnostics\/supporting-services\/data-sciences\/bioinformatics\/\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Bioinformatics\" \/>\n<meta property=\"og:description\" content=\"High quality analysis of genomics data across a range of platforms (including Next Generation Sequencing (NGS), microarray and qPCR) and biomaterials.\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.almacgroup.com\/diagnostics\/supporting-services\/data-sciences\/bioinformatics\/\" \/>\n<meta property=\"og:site_name\" content=\"Diagnostic Services\" \/>\n<meta property=\"article:modified_time\" content=\"2025-06-11T08:37:15+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/www.almacgroup.com\/diagnostics\/wp-content\/uploads\/sites\/3\/2020\/11\/Almac_Logo-e1698941154737.jpeg\" \/>\n\t<meta property=\"og:image:width\" content=\"100\" \/>\n\t<meta property=\"og:image:height\" content=\"52\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/jpeg\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Estimated reading time\" \/>\n\t<meta name=\"twitter:data1\" content=\"4 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\/\/www.almacgroup.com\/diagnostics\/supporting-services\/data-sciences\/bioinformatics\/\",\"url\":\"https:\/\/www.almacgroup.com\/diagnostics\/supporting-services\/data-sciences\/bioinformatics\/\",\"name\":\"Bioinformatics - 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