{"id":7007,"date":"2015-04-27T15:39:53","date_gmt":"2015-04-27T19:39:53","guid":{"rendered":"http:\/\/admin.acceleratingscience.com\/?p=7007"},"modified":"2020-05-28T19:14:25","modified_gmt":"2020-05-28T19:14:25","slug":"using-ce-3-designing-a-27-plex-pcr-for-fragment-analysis","status":"publish","type":"post","link":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/using-ce-3-designing-a-27-plex-pcr-for-fragment-analysis\/","title":{"rendered":"Fragment Analysis using CE 3: Designing a 27-plex PCR for Fragment Analysis"},"content":{"rendered":"

Part 3 of our series on Sanger Sequencing by Capillary Electrophoresis is about primer design. Primer design for Sanger sequencing is a very straightforward process with online tools such as the Primer Designer\u2122 Tool<\/a> which offers >300,000 primer pairs targeting the human Exome as well as the OligoPerfect\u2122 Designer<\/a> But what about primer design for more specialized Sanger CE applications, such as for human identification?<\/p>\n

I interviewed Julio Mulero, a senior staff scientist with Thermo Fisher Scientific whose group develops highly-multiplexed products for human identification, such as the new GlobalFiler STR kits that amplifies 24 loci simultaneously.<\/p>\n

What can you tell me about the requirements for development of high-multiplex assays for this market?<\/strong><\/p>\n

We develop PCR-based kits that go as high as 27-plex, and have very specific performance requirements. Our amplicons are designed to be between 70 to 400bp in length, which is a \u2018sweet-spot\u2019 in terms of 1 bp capillary electrophoresis resolution. In order to maximize the numbers of loci, we use a six-dye format instrument like the 3500 Genetic Analyzer<\/a>. The individual loci targeted for the designs we make are determined by government organizations and the loci\u00a0 sometimes vary from one country to another. Some loci are very informative in some populations but not in others, and the GlobalFiler\u2122 STR kit was a result of integrating the most informative and widely used loci in one multiplex that could be used across the globe.<\/p>\n

The GlobalFiler<\/strong>\u2122 STR product goes to 24-plex, what goes to 27-plex?\u00a0 <\/strong><\/p>\n

We recently introduced the Yfiler\u2122 Plus PCR Amplification Kit<\/a>, a 27-plex assay. The Y-chromosome is unique in that it does not undergo significant recombination during meiosis, thus the variation in the Y-chromosome is created by mutations. This kit was designed for sexual assault cases, where discrimination is important between a very small amount of Y DNA (male) against a large amount of background (female) DNA. The ratio of Y DNA to background can be as low as one in a thousand.<\/p>\n

And on top of that you have to minimize the interaction of the primers with each other and off-target amplification events.\u00a0 The forensic market requires a master mix that is formulated to be robust to PCR inhibitors, which as you may know, can be a difficult problem to solve while balancing other important aspects of performance such as stability and stutter formation\u00a0 (artifacts of the PCR amplification which cause strand slippage due to the repetitive nature of STRs).<\/p>\n

That sounds complicated. Do you also need to optimize the PCR master mix?<\/strong><\/p>\n

Yes, we co-optimize them to each other. While we rely on bioinformatics to guide primer design, there is no substitute for the lab work needed to verify that our designs are meeting our performance parameters. Although we have over a decade of experience designing primers and formulating PCR master mixes, it does take several iterations to optimize the parameters that our customers value most (such as specificity mentioned earlier with Y-STRs or sensitivity with picograms amounts of input DNA) while minimizing the artifacts that impact sample genotype interpretation (such as stutter).<\/p>\n

Does your primer design work also involve real-time PCR?\u00a0\u00a0 <\/strong><\/p>\n

The QuantiFiler\u2122 Trio<\/a> and HP DNA Quantification Kits are the latest products our group developed for forensic applications.\u00a0 They were designed to accurately quantify low picogram amounts of DNA from forensic samples while providing additional information such as the quality of the DNA including qualitative measures of DNA degradation and PCR inhibition. This information is of great value to our customers because it helps guide how their samples will be processed downstream.<\/p>\n

(End of interview)<\/p>\n

You may not be necessarily working on fine-tuning a 27-plex PCR, but rest assured there are development scientists at Thermo Fisher Scientific that are continually refining products that are used everyday. To design your own primers use the\u00a0 Primer Designer\u2122 Tool<\/a> to select from >300,000 primer pairs targeting the human exome, and the OligoPerfect\u2122 Designer<\/a> is available for other sequencing applications.<\/p>\n

Check out the whole Series:<\/p>\n

Sanger Sequencing by CE 1: Foundations<\/a><\/p>\n

Sanger Sequencing using CE 2: Fragment Analysis<\/a><\/p>\n

Fragment Analysis using CE 3: Designing a 27-plex PCR<\/a><\/p>\n

Sanger Sequencing by CE 4: Bioinformatics<\/a><\/p>\n

Sanger Sequencing by CE 5: Sanger Sequencing Applications<\/a><\/p>\n

Sanger Sequencing by CE 6: Resources<\/a><\/p>\n

The QuantiFiler Kits are For Research, Forensic or Paternity Use Only.\u00a0 Not for use in diagnostic procedures. <\/strong><\/p>\n

Globalfiler Kits and Yfiler Kits: For Forensic or Paternity Use Only. <\/strong><\/p>\n

When used for purposes other than Human Identification, the instruments and software cited are for Research Use Only.\u00a0 Not for use in diagnostic procedures.<\/strong><\/p>\n","protected":false},"excerpt":{"rendered":"

Part 3 of our series on Sanger Sequencing by Capillary Electrophoresis is about primer design. Primer design for Sanger sequencing is a very straightforward process with online tools such as the Primer Designer\u2122 Tool which offers >300,000 primer pairs targeting the human Exome as well as the OligoPerfect\u2122 Designer But what about primer design for<\/p>\n","protected":false},"author":120,"featured_media":0,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"_kad_blocks_custom_css":"","_kad_blocks_head_custom_js":"","_kad_blocks_body_custom_js":"","_kad_blocks_footer_custom_js":"","_monsterinsights_skip_tracking":false,"_genesis_hide_title":false,"_genesis_hide_breadcrumbs":false,"_genesis_hide_singular_image":false,"_genesis_hide_footer_widgets":false,"_genesis_custom_body_class":"","_genesis_custom_post_class":"","_genesis_layout":"","_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[71,108],"tags":[17,99,43,25],"division":[],"class_list":{"0":"post-7007","1":"post","2":"type-post","3":"status-publish","4":"format-standard","6":"category-forensics","7":"category-lab-tips-and-tricks","8":"tag-applied-biosystems","9":"tag-fragment-analysis","10":"tag-pcr","11":"tag-sanger-sequencing","12":"entry"},"_selected_authors":"","_selected_reviewers":"","acf":[],"yoast_head":"\nFragment Analysis using CE 3: Designing a 27-plex PCR for Fragment Analysis - Behind the Bench<\/title>\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.thermofisher.com\/blog\/behindthebench\/using-ce-3-designing-a-27-plex-pcr-for-fragment-analysis\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Fragment Analysis using CE 3: Designing a 27-plex PCR for Fragment Analysis\" \/>\n<meta property=\"og:description\" content=\"Part 3 of our series on Sanger Sequencing by Capillary Electrophoresis is about primer design. Primer design for Sanger sequencing is a very straightforward process with online tools such as the Primer Designer\u2122 Tool which offers >300,000 primer pairs targeting the human Exome as well as the OligoPerfect\u2122 Designer But what about primer design for\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.thermofisher.com\/blog\/behindthebench\/using-ce-3-designing-a-27-plex-pcr-for-fragment-analysis\/\" \/>\n<meta property=\"og:site_name\" content=\"Behind the Bench\" \/>\n<meta property=\"article:publisher\" content=\"https:\/\/www.facebook.com\/thermofisher\" \/>\n<meta property=\"article:published_time\" content=\"2015-04-27T19:39:53+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2020-05-28T19:14:25+00:00\" \/>\n<meta name=\"author\" content=\"Behind The Bench Staff\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:creator\" content=\"@thermofisher\" \/>\n<meta name=\"twitter:site\" content=\"@thermofisher\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Behind The Bench Staff\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"4 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\\\/\\\/schema.org\",\"@graph\":[{\"@type\":\"Article\",\"@id\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/using-ce-3-designing-a-27-plex-pcr-for-fragment-analysis\\\/#article\",\"isPartOf\":{\"@id\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/using-ce-3-designing-a-27-plex-pcr-for-fragment-analysis\\\/\"},\"author\":{\"name\":\"Behind The Bench Staff\",\"@id\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/behindthebench\\\/#\\\/schema\\\/person\\\/9bbb2d67616274d3d4a21a584f7f4a0c\"},\"headline\":\"Fragment Analysis using CE 3: Designing a 27-plex PCR for Fragment Analysis\",\"datePublished\":\"2015-04-27T19:39:53+00:00\",\"dateModified\":\"2020-05-28T19:14:25+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/using-ce-3-designing-a-27-plex-pcr-for-fragment-analysis\\\/\"},\"wordCount\":753,\"commentCount\":0,\"keywords\":[\"Applied Biosystems\",\"Fragment Analysis\",\"PCR\",\"Sanger Sequencing\"],\"articleSection\":[\"Forensics\",\"Lab Tips and Tricks\"],\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"CommentAction\",\"name\":\"Comment\",\"target\":[\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/using-ce-3-designing-a-27-plex-pcr-for-fragment-analysis\\\/#respond\"]}]},{\"@type\":\"WebPage\",\"@id\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/using-ce-3-designing-a-27-plex-pcr-for-fragment-analysis\\\/\",\"url\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/using-ce-3-designing-a-27-plex-pcr-for-fragment-analysis\\\/\",\"name\":\"Fragment Analysis using CE 3: Designing a 27-plex PCR for Fragment Analysis - Behind the Bench\",\"isPartOf\":{\"@id\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/behindthebench\\\/#website\"},\"datePublished\":\"2015-04-27T19:39:53+00:00\",\"dateModified\":\"2020-05-28T19:14:25+00:00\",\"author\":{\"@id\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/behindthebench\\\/#\\\/schema\\\/person\\\/9bbb2d67616274d3d4a21a584f7f4a0c\"},\"breadcrumb\":{\"@id\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/using-ce-3-designing-a-27-plex-pcr-for-fragment-analysis\\\/#breadcrumb\"},\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/using-ce-3-designing-a-27-plex-pcr-for-fragment-analysis\\\/\"]}]},{\"@type\":\"BreadcrumbList\",\"@id\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/using-ce-3-designing-a-27-plex-pcr-for-fragment-analysis\\\/#breadcrumb\",\"itemListElement\":[{\"@type\":\"ListItem\",\"position\":1,\"name\":\"Home\",\"item\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/behindthebench\\\/\"},{\"@type\":\"ListItem\",\"position\":2,\"name\":\"Fragment Analysis using CE 3: Designing a 27-plex PCR for Fragment Analysis\"}]},{\"@type\":\"WebSite\",\"@id\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/behindthebench\\\/#website\",\"url\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/behindthebench\\\/\",\"name\":\"Behind the Bench\",\"description\":\"\",\"potentialAction\":[{\"@type\":\"SearchAction\",\"target\":{\"@type\":\"EntryPoint\",\"urlTemplate\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/behindthebench\\\/?s={search_term_string}\"},\"query-input\":{\"@type\":\"PropertyValueSpecification\",\"valueRequired\":true,\"valueName\":\"search_term_string\"}}],\"inLanguage\":\"en-US\"},{\"@type\":\"Person\",\"@id\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/behindthebench\\\/#\\\/schema\\\/person\\\/9bbb2d67616274d3d4a21a584f7f4a0c\",\"name\":\"Behind The Bench Staff\",\"image\":{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\\\/\\\/secure.gravatar.com\\\/avatar\\\/52d5c16ece4bd1c0a49a63521c2b6a25c54a3f0c33f7afed215ba7e0cdff69e3?s=96&d=mm&r=g\",\"url\":\"https:\\\/\\\/secure.gravatar.com\\\/avatar\\\/52d5c16ece4bd1c0a49a63521c2b6a25c54a3f0c33f7afed215ba7e0cdff69e3?s=96&d=mm&r=g\",\"contentUrl\":\"https:\\\/\\\/secure.gravatar.com\\\/avatar\\\/52d5c16ece4bd1c0a49a63521c2b6a25c54a3f0c33f7afed215ba7e0cdff69e3?s=96&d=mm&r=g\",\"caption\":\"Behind The Bench Staff\"},\"url\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/author\\\/behind-the-bench-staff\\\/\"}]}<\/script>\n<!-- \/ Yoast SEO Premium plugin. -->","yoast_head_json":{"title":"Fragment Analysis using CE 3: Designing a 27-plex PCR for Fragment Analysis - Behind the Bench","robots":{"index":"index","follow":"follow","max-snippet":"max-snippet:-1","max-image-preview":"max-image-preview:large","max-video-preview":"max-video-preview:-1"},"canonical":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/using-ce-3-designing-a-27-plex-pcr-for-fragment-analysis\/","og_locale":"en_US","og_type":"article","og_title":"Fragment Analysis using CE 3: Designing a 27-plex PCR for Fragment Analysis","og_description":"Part 3 of our series on Sanger Sequencing by Capillary Electrophoresis is about primer design. Primer design for Sanger sequencing is a very straightforward process with online tools such as the Primer Designer\u2122 Tool which offers >300,000 primer pairs targeting the human Exome as well as the OligoPerfect\u2122 Designer But what about primer design for","og_url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/using-ce-3-designing-a-27-plex-pcr-for-fragment-analysis\/","og_site_name":"Behind the Bench","article_publisher":"https:\/\/www.facebook.com\/thermofisher","article_published_time":"2015-04-27T19:39:53+00:00","article_modified_time":"2020-05-28T19:14:25+00:00","author":"Behind The Bench Staff","twitter_card":"summary_large_image","twitter_creator":"@thermofisher","twitter_site":"@thermofisher","twitter_misc":{"Written by":"Behind The Bench Staff","Est. reading time":"4 minutes"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"Article","@id":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/using-ce-3-designing-a-27-plex-pcr-for-fragment-analysis\/#article","isPartOf":{"@id":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/using-ce-3-designing-a-27-plex-pcr-for-fragment-analysis\/"},"author":{"name":"Behind The Bench Staff","@id":"https:\/\/admin.acceleratingscience.com\/behindthebench\/#\/schema\/person\/9bbb2d67616274d3d4a21a584f7f4a0c"},"headline":"Fragment Analysis using CE 3: Designing a 27-plex PCR for Fragment Analysis","datePublished":"2015-04-27T19:39:53+00:00","dateModified":"2020-05-28T19:14:25+00:00","mainEntityOfPage":{"@id":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/using-ce-3-designing-a-27-plex-pcr-for-fragment-analysis\/"},"wordCount":753,"commentCount":0,"keywords":["Applied Biosystems","Fragment Analysis","PCR","Sanger Sequencing"],"articleSection":["Forensics","Lab Tips and Tricks"],"inLanguage":"en-US","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/www.thermofisher.com\/blog\/behindthebench\/using-ce-3-designing-a-27-plex-pcr-for-fragment-analysis\/#respond"]}]},{"@type":"WebPage","@id":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/using-ce-3-designing-a-27-plex-pcr-for-fragment-analysis\/","url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/using-ce-3-designing-a-27-plex-pcr-for-fragment-analysis\/","name":"Fragment Analysis using CE 3: Designing a 27-plex PCR for Fragment Analysis - Behind the Bench","isPartOf":{"@id":"https:\/\/admin.acceleratingscience.com\/behindthebench\/#website"},"datePublished":"2015-04-27T19:39:53+00:00","dateModified":"2020-05-28T19:14:25+00:00","author":{"@id":"https:\/\/admin.acceleratingscience.com\/behindthebench\/#\/schema\/person\/9bbb2d67616274d3d4a21a584f7f4a0c"},"breadcrumb":{"@id":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/using-ce-3-designing-a-27-plex-pcr-for-fragment-analysis\/#breadcrumb"},"inLanguage":"en-US","potentialAction":[{"@type":"ReadAction","target":["https:\/\/www.thermofisher.com\/blog\/behindthebench\/using-ce-3-designing-a-27-plex-pcr-for-fragment-analysis\/"]}]},{"@type":"BreadcrumbList","@id":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/using-ce-3-designing-a-27-plex-pcr-for-fragment-analysis\/#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Home","item":"https:\/\/admin.acceleratingscience.com\/behindthebench\/"},{"@type":"ListItem","position":2,"name":"Fragment Analysis using CE 3: Designing a 27-plex PCR for Fragment Analysis"}]},{"@type":"WebSite","@id":"https:\/\/admin.acceleratingscience.com\/behindthebench\/#website","url":"https:\/\/admin.acceleratingscience.com\/behindthebench\/","name":"Behind the Bench","description":"","potentialAction":[{"@type":"SearchAction","target":{"@type":"EntryPoint","urlTemplate":"https:\/\/admin.acceleratingscience.com\/behindthebench\/?s={search_term_string}"},"query-input":{"@type":"PropertyValueSpecification","valueRequired":true,"valueName":"search_term_string"}}],"inLanguage":"en-US"},{"@type":"Person","@id":"https:\/\/admin.acceleratingscience.com\/behindthebench\/#\/schema\/person\/9bbb2d67616274d3d4a21a584f7f4a0c","name":"Behind The Bench Staff","image":{"@type":"ImageObject","inLanguage":"en-US","@id":"https:\/\/secure.gravatar.com\/avatar\/52d5c16ece4bd1c0a49a63521c2b6a25c54a3f0c33f7afed215ba7e0cdff69e3?s=96&d=mm&r=g","url":"https:\/\/secure.gravatar.com\/avatar\/52d5c16ece4bd1c0a49a63521c2b6a25c54a3f0c33f7afed215ba7e0cdff69e3?s=96&d=mm&r=g","contentUrl":"https:\/\/secure.gravatar.com\/avatar\/52d5c16ece4bd1c0a49a63521c2b6a25c54a3f0c33f7afed215ba7e0cdff69e3?s=96&d=mm&r=g","caption":"Behind The Bench Staff"},"url":"https:\/\/admin.acceleratingscience.com\/author\/behind-the-bench-staff\/"}]}},"taxonomy_info":{"category":[{"value":71,"label":"Forensics"},{"value":108,"label":"Lab Tips and Tricks"}],"post_tag":[{"value":17,"label":"Applied Biosystems"},{"value":99,"label":"Fragment Analysis"},{"value":43,"label":"PCR"},{"value":25,"label":"Sanger Sequencing"}]},"featured_image_src_large":false,"author_info":{"display_name":"Behind The Bench Staff","author_link":"https:\/\/admin.acceleratingscience.com\/author\/behind-the-bench-staff\/"},"comment_info":1,"category_info":[{"term_id":71,"name":"Forensics","slug":"forensics","term_group":0,"term_taxonomy_id":71,"taxonomy":"category","description":"","parent":0,"count":94,"filter":"raw","meta":[],"cat_ID":71,"category_count":94,"category_description":"","cat_name":"Forensics","category_nicename":"forensics","category_parent":0},{"term_id":108,"name":"Lab Tips and Tricks","slug":"lab-tips-and-tricks","term_group":0,"term_taxonomy_id":108,"taxonomy":"category","description":"","parent":0,"count":100,"filter":"raw","meta":[],"cat_ID":108,"category_count":100,"category_description":"","cat_name":"Lab Tips and Tricks","category_nicename":"lab-tips-and-tricks","category_parent":0}],"tag_info":[{"term_id":17,"name":"Applied Biosystems","slug":"applied-biosystems","term_group":0,"term_taxonomy_id":17,"taxonomy":"post_tag","description":"","parent":0,"count":193,"filter":"raw","meta":[]},{"term_id":99,"name":"Fragment Analysis","slug":"fragment-analysis","term_group":0,"term_taxonomy_id":99,"taxonomy":"post_tag","description":"","parent":0,"count":37,"filter":"raw","meta":[]},{"term_id":43,"name":"PCR","slug":"pcr","term_group":0,"term_taxonomy_id":43,"taxonomy":"post_tag","description":"","parent":0,"count":142,"filter":"raw","meta":[]},{"term_id":25,"name":"Sanger Sequencing","slug":"sanger-sequencing","term_group":0,"term_taxonomy_id":25,"taxonomy":"post_tag","description":"","parent":0,"count":87,"filter":"raw","meta":[]}],"jetpack-related-posts":[{"id":19885,"url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/sanger-sequencing-mix-dna-templates\/","url_meta":{"origin":7007,"position":0},"title":"Advancing the Gold Standard: Faster, Smarter, and Built for Challenging Templates","author":"Behind The Bench Staff","date":"August 5, 2026","format":false,"excerpt":"Sanger sequencing has long been the gold standard for accuracy, trusted by laboratories worldwide for applications ranging from plasmid verification to confirming next-generation sequencing results. Yet as research evolves, so do the demands placed on sequencing workflows. Today\u2019s labs are not only looking for accuracy\u2014they need speed, flexibility, and reliable\u2026","rel":"","context":"In "General"","block_context":{"text":"General","link":"https:\/\/admin.acceleratingscience.com\/behindthebench\/general\/"},"img":{"alt_text":"DNA sequencing sample tube with DNA helix and sequencing chromatogram representing Sanger sequencing workflow.","src":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/ChatGPT-Image-Aug-5-2026-09_44_12-AM.png?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/ChatGPT-Image-Aug-5-2026-09_44_12-AM.png?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/ChatGPT-Image-Aug-5-2026-09_44_12-AM.png?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/ChatGPT-Image-Aug-5-2026-09_44_12-AM.png?resize=700%2C400&ssl=1 2x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/ChatGPT-Image-Aug-5-2026-09_44_12-AM.png?resize=1050%2C600&ssl=1 3x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/ChatGPT-Image-Aug-5-2026-09_44_12-AM.png?resize=1400%2C800&ssl=1 4x"},"classes":[]},{"id":19509,"url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/cfdna-fragmentomics-analysis-qpcr-cancer-monitoring\/","url_meta":{"origin":7007,"position":1},"title":"qPCR-based fragmentomics for monitoring cancer disease progression","author":"Behind The Bench Staff","date":"March 5, 2026","format":false,"excerpt":"As fragmentomics gains momentum in cancer liquid biopsy research, attention is increasingly turning to how these structural cfDNA signals can be measured in a way that is both sensitive and practical. Established qPCR platforms offer an alternative to sequencing-based approaches for capturing fragment size information with high precision. Using a\u2026","rel":"","context":"In "Bioinformatics"","block_context":{"text":"Bioinformatics","link":"https:\/\/admin.acceleratingscience.com\/behindthebench\/bioinformatics\/"},"img":{"alt_text":"Scientist pipetting into a 96 well plate during qPCR workflow for cell free DNA fragmentomics analysis","src":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/03\/Picture1.png?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/03\/Picture1.png?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/03\/Picture1.png?resize=525%2C300&ssl=1 1.5x"},"classes":[]},{"id":19888,"url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/streptococcus-pneumoniae-serotype-identification-qpcr-nested-pcr\/","url_meta":{"origin":7007,"position":2},"title":"qPCR, Nested PCR, and the Search for Bacterial Serotypes","author":"Ashleigh Barlow","date":"August 5, 2026","format":false,"excerpt":"Article Summary In this episode of Absolute Gene-ius, Donna Paznar, former Head of Molecular Infection Diagnostics at the Medical University of Vienna, discusses her research on Streptococcus pneumoniae and its impact across the Austrian population. She explains why children can act as asymptomatic reservoirs, why tracking bacterial serotypes matters, and\u2026","rel":"","context":"In "Infectious Diseases"","block_context":{"text":"Infectious Diseases","link":"https:\/\/admin.acceleratingscience.com\/behindthebench\/infectious-diseases\/"},"img":{"alt_text":"Donna Paznar discussing molecular methods for identifying Streptococcus pneumoniae serotypes.","src":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/Paznar_Headshot_Jordan-Ruggieri-scaled.jpg?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/Paznar_Headshot_Jordan-Ruggieri-scaled.jpg?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/Paznar_Headshot_Jordan-Ruggieri-scaled.jpg?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/Paznar_Headshot_Jordan-Ruggieri-scaled.jpg?resize=700%2C400&ssl=1 2x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/Paznar_Headshot_Jordan-Ruggieri-scaled.jpg?resize=1050%2C600&ssl=1 3x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/Paznar_Headshot_Jordan-Ruggieri-scaled.jpg?resize=1400%2C800&ssl=1 4x"},"classes":[]},{"id":19810,"url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/integration-site-analysis-gene-therapy-safety\/","url_meta":{"origin":7007,"position":3},"title":"Genotoxicity, vectors, and the power of integration site analysis","author":"Ashleigh Barlow","date":"June 23, 2026","format":false,"excerpt":"Article Summary In this episode of Absolute Gene-ius, Michael Stump, PhD, President of ProtaGene, and Matteo Franco, Lead Scientist at ProtaGene, discuss how integration site analysis is helping researchers evaluate genotoxicity risks in cell and gene therapy workflows. Their conversation explores how viral vectors integrate into the genome, why integration\u2026","rel":"","context":"In "Gene Editing"","block_context":{"text":"Gene Editing","link":"https:\/\/admin.acceleratingscience.com\/behindthebench\/gene-editing\/"},"img":{"alt_text":"Matteo Franco, Lead Scientist at ProtaGene, discussing integration site analysis and genotoxicity assessment","src":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/06\/FRANCO-headshot_Jordan-Ruggieri.png?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/06\/FRANCO-headshot_Jordan-Ruggieri.png?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/06\/FRANCO-headshot_Jordan-Ruggieri.png?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/06\/FRANCO-headshot_Jordan-Ruggieri.png?resize=700%2C400&ssl=1 2x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/06\/FRANCO-headshot_Jordan-Ruggieri.png?resize=1050%2C600&ssl=1 3x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/06\/FRANCO-headshot_Jordan-Ruggieri.png?resize=1400%2C800&ssl=1 4x"},"classes":[]},{"id":19223,"url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/innovations-in-qpcr-technology\/","url_meta":{"origin":7007,"position":4},"title":"Innovations in qPCR Technology: What Researchers Need to Know","author":"Ashleigh Barlow","date":"October 29, 2025","format":false,"excerpt":"https:\/\/youtu.be\/z9Kb1xAnNcg?si=TVUIc8rUxZUOhCqA Real-time PCR, also known as quantitative polymerase chain reaction (qPCR) technology, has been a cornerstone of molecular biology research for decades. With continuous advancements, qPCR remains a critical tool for researchers worldwide. Damien Luk, Senior Director of Product Management at Thermo Fisher Scientific, shared his insights on the future\u2026","rel":"","context":"In "Developmental Biology"","block_context":{"text":"Developmental Biology","link":"https:\/\/admin.acceleratingscience.com\/behindthebench\/developmental-biology\/"},"img":{"alt_text":"A lineup of Thermo Fisher Scientific QuantStudio real-time PCR systems, including QuantStudio 3, 5, 6 Pro, 7 Pro, and 12K Flex instruments, displayed against a blue gradient background.","src":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2025\/10\/qPCR-Blog-Cover-Image.jpg?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2025\/10\/qPCR-Blog-Cover-Image.jpg?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2025\/10\/qPCR-Blog-Cover-Image.jpg?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2025\/10\/qPCR-Blog-Cover-Image.jpg?resize=700%2C400&ssl=1 2x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2025\/10\/qPCR-Blog-Cover-Image.jpg?resize=1050%2C600&ssl=1 3x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2025\/10\/qPCR-Blog-Cover-Image.jpg?resize=1400%2C800&ssl=1 4x"},"classes":[]},{"id":19345,"url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/precision-oncology-diagnostics\/","url_meta":{"origin":7007,"position":5},"title":"The Expanding Role of Molecular Diagnostics in Precision Oncology","author":"Behind The Bench Staff","date":"January 13, 2026","format":false,"excerpt":"https:\/\/www.youtube.com\/watch?v=F6FfHIizJBY For Dr. Harald Bartsch, a clinical pathologist in southern Bavaria, molecular diagnostic tools have become an indispensable part of his arsenal. \u201cI believe molecular diagnostics play a crucial role in modern oncology, and I see this as the direction everything is headed,\u201d says Dr. Bartsch. While immunohistochemistry remains central\u2026","rel":"","context":"In "Cancer Research"","block_context":{"text":"Cancer Research","link":"https:\/\/admin.acceleratingscience.com\/behindthebench\/cancer-research\/"},"img":{"alt_text":"Clinical Pathologist in a Molecular Diagnostics Laboratory","src":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/01\/Bartsch-1.jpg?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/01\/Bartsch-1.jpg?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/01\/Bartsch-1.jpg?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/01\/Bartsch-1.jpg?resize=700%2C400&ssl=1 2x"},"classes":[]}],"jetpack_sharing_enabled":true,"jetpack_featured_media_url":"","_links":{"self":[{"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/posts\/7007","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/users\/120"}],"replies":[{"embeddable":true,"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/comments?post=7007"}],"version-history":[{"count":0,"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/posts\/7007\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/media?parent=7007"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/categories?post=7007"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/tags?post=7007"},{"taxonomy":"division","embeddable":true,"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/division?post=7007"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}