{"id":8078,"date":"2014-10-21T13:43:15","date_gmt":"2014-10-21T17:43:15","guid":{"rendered":"http:\/\/admin.acceleratingscience.com\/?p=8078"},"modified":"2016-12-06T20:15:46","modified_gmt":"2016-12-06T20:15:46","slug":"comparing-benchtop-sequencers-as-technologies-mature-ashg-2014","status":"publish","type":"post","link":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/comparing-benchtop-sequencers-as-technologies-mature-ashg-2014\/","title":{"rendered":"Comparing Benchtop Sequencers As Technologies Mature | ASHG 2014"},"content":{"rendered":"

One of the most important attributes for a DNA sequencing system is accuracy.\u00a0 Scientists want the highest quality, reproducible data. Sequencing systems have strengths and weaknesses driven by the unique chemistry of each.\u00a0 One criticism of the Ion Torrent\u2122 sequencing chemistry has been that the fast and efficient lack of termination (which also gives it great speed) results in difficulty in long stretches of the same nucleotide (called a homopolymer tract).\u00a0 This results in a relatively high insertion and deletion (InDel) error rate. A sometimes less recognized feature of the Ion Torrent chemistry is that only a single nucleotide is presented at a given time to a polymerase.\u00a0 The absence of four competitive nucleotides results in a lower substitution error rate for the Ion Torrent system relative to systems with all four fluorescently tagged nucleotides presented simultaneously. The Ion PGM sequencer\u2019s high substitution accuracy has been observed by others in peer reviewed literature as well (Junemann et al., Nature Biotechnology 2013 31(14)294-296.).\u00a0 This leads to a question that many have asked before \u2013 which system is more accurate?\u00a0 Ion Torrent\u2019s Ion PGM\u2122 Sequencer<\/a> or Illumina\u2019s MiSeq Sequencer?<\/p>\n

 <\/p>\n

As sequencing technologies continue to gain acceptance in the clinical research world, new tools are becoming available online to help verify sequencing performance within an individual laboratory. The US National Institute of Standards and Technology (NIST) has invested a lot of effort in their Genome In A Bottle<\/a> (GIAB) initiative where a single reference sample is sequenced with many different technologies to derive a platform independent sequence. This is a great tool to verify both broad panels like whole exomes or whole genome sequencing.\u00a0 But when more tightly focused panels are involved, a single well-documented genome doesn\u2019t have enough genetic variation to get a good measure of accuracy.\u00a0 For example, in the GIAB sample, looking only at the targeted region on a cancer research panel like the Ion AmpliSeq\u2122 Cancer Hotspot Panel v2, one would expect to see only 14 variants \u2013 not enough variants to measure the accuracy of a panel with any robustness. To truly test if a gene panel is accurately sequenced, having a sample with broader truth would provide a better test. The AcroMetrix arm of Thermo Fisher Scientific has recently introduced a new AcroMetrix\u2122 Oncology Hotspot Control<\/a> to help address this problem. (We have recently written about the AcroMetrix panel<\/a> on Behind the Bench.)\u00a0 AcroMetrix synthesized over 500 COSMIC variants to be added at a few levels of concentration to the GIAB genomic sample.\u00a0 Because they spiked into this genomic background,\u00a0 users can determine for themselves the level of abundance to simulate somatic mutation detection conditions.<\/p>\n

 <\/p>\n

Having access to this wonderfully broad \u201ctruth\u201d control sample from AcroMetrix allows researchers to compare the accuracy of two sequencing platforms for a very focused set of top oncology targets using popular PCR amplification techniques.\u00a0 We at Ion Torrent ran a first trial at this question by comparing the whole systems from amplicon-generation to variant calling across both our Ion PGM\u2122 System and the MiSeq sequencer from Illumina.\u00a0 Our simple experiment involved running two runs with either a 1% or 3% somatic levels using Illumina\u2019s TruSeq Amplicon Caner Panel coupled with MiSeq sequencing and their recommended mapping and variant calling algorithms.\u00a0 We compared this to three runs of the Ion AmpliSeq\u2122 Cancer Hotspot Panel v2\u00a0 run on the Ion PGM\u2122 Sequencer with our new Ion PGM\u2122 Hi-Q\u2122 Sequencing Kit.\u00a0 Due to differences in targeted regions, we focused the comparison on the 13.6 kb of overlap between both panels.\u00a0 To compare accuracy, we measured both raw read accuracy across the length of the read and then consensus accuracy across read depth by measuring the sensitivity and positive predictive values between the two sequencing platforms.<\/p>\n

 <\/p>\n

\"lelivelt<\/a>Measuring the accuracy of single read at a time, the mean raw read error for the 3% mix was 0.55% for MiSeq and 0.42% for the Ion PGM\u2122 Sequencer.\u00a0 There was a lot of variability across the length of the read, so one could argue that the difference in these means is not statistically significant, but they are certainly comparable.\u00a0 Looking deeper into the accuracy comparison, we wanted to measure consensus accuracy when the redundancy of multiple reads is leveraged. The overall sensitivity (both SNPs and InDels) of MiSeq was 93.8% compared with 95.1% for the Ion PGM\u2122 Sequencer. The Positive Predictive Values of MiSeq was 98.1% compared to 100% for Ion PGM\u2122 Sequencer\u00a0 The results from the 1% mix were similar to the 3% mix.\u00a0 We also combined the 1% and 3% runs together for simplicity and sensitivity was 94.1% vs 91.3% and PPV was 99.8% vs 98% for PGM vs MiSeq respectively.\u00a0 Either separate or combined, the consensus accuracy results were statistically significant.<\/p>\n

 <\/p>\n

\"accuracy.png\"<\/a>We at Ion Torrent were pleased with these results because it\u2019s a reflection of an enormous amount of investment that we\u2019ve made in improving the accuracy of the Ion PGM\u2122 System. The new Ion PGM\u2122 Hi-Q\u2122 sequencing kit harnessed an exhaustive enzymatic screening process to find a sequencing chemistry with lower systematic error.\u00a0 Also, continued enhancements to our informatics pipeline improves our overall accuracy with significantly fewer false positive calls when compared with previous versions of Ion PGM\u2122 sequencing kits.\u00a0 The Ion PGM\u2122 sequencer coupled with the Ion AmpliSeq\u2122 chemistry to selectively amplify targets from as little as 10 ng of FFPE DNA brings enormous value to the oncology research market.<\/p>\n

 <\/p>\n

Having broad truth available from the Acrometrix Oncology Hotspot Control Kit and the result of this 2×5 run comparison allow us to ask the question \u2013 is the Ion PGM\u2122 System<\/a> with Ion AmpliSeq\u2122 Cancer Hotspot Panel v2<\/a>\u00a0 and Ion PGM Hi-Q\u2122 Sequencing Kit<\/a> the most accurate benchtop sequencer for targeted oncology panels?\u00a0 We\u2019ve released the data and methods on Ion Community http:\/\/ioncommunity.thermofisher.com\/docs\/DOC-9157<\/a> for anyone to inspect and the Acrometrix\u00ae <\/sup>Oncology Hotspot Control is commercially available for anyone to run the experience themselves.\u00a0 What we do know is that the Ion PGM\u2122 Sequencer continues to mature in its accuracy measurements.\u00a0 If you haven\u2019t run a PGM since 2011 or 2012, please fire it up with our latest HiQ chemistry and see how it\u2019s performing in your hands.<\/p>\n","protected":false},"excerpt":{"rendered":"

One of the most important attributes for a DNA sequencing system is accuracy.\u00a0 Scientists want the highest quality, reproducible data. Sequencing systems have strengths and weaknesses driven by the unique chemistry of each.\u00a0 One criticism of the Ion Torrent\u2122 sequencing chemistry has been that the fast and efficient lack of termination (which also gives it<\/p>\n","protected":false},"author":120,"featured_media":8083,"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":[54,113],"tags":[150,11,6],"division":[],"class_list":{"0":"post-8078","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","7":"category-cancer-research","8":"category-events-and-tradeshows","9":"tag-ashg-2014","10":"tag-ion-torrent","11":"tag-next-generation-sequencing","12":"entry"},"_selected_authors":"","_selected_reviewers":"","acf":[],"yoast_head":"\nComparing Benchtop Sequencers As Technologies Mature | ASHG 2014 - 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\/comparing-benchtop-sequencers-as-technologies-mature-ashg-2014\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Comparing Benchtop Sequencers As Technologies Mature | ASHG 2014\" \/>\n<meta property=\"og:description\" content=\"One of the most important attributes for a DNA sequencing system is accuracy.\u00a0 Scientists want the highest quality, reproducible data. Sequencing systems have strengths and weaknesses driven by the unique chemistry of each.\u00a0 One criticism of the Ion Torrent\u2122 sequencing chemistry has been that the fast and efficient lack of termination (which also gives it\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.thermofisher.com\/blog\/behindthebench\/comparing-benchtop-sequencers-as-technologies-mature-ashg-2014\/\" \/>\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=\"2014-10-21T17:43:15+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2016-12-06T20:15:46+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2016\/03\/lelivelt-1.png\" \/>\n\t<meta property=\"og:image:width\" content=\"790\" \/>\n\t<meta property=\"og:image:height\" content=\"565\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/png\" \/>\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=\"5 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\\\/comparing-benchtop-sequencers-as-technologies-mature-ashg-2014\\\/#article\",\"isPartOf\":{\"@id\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/comparing-benchtop-sequencers-as-technologies-mature-ashg-2014\\\/\"},\"author\":{\"name\":\"Behind The Bench Staff\",\"@id\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/behindthebench\\\/#\\\/schema\\\/person\\\/9bbb2d67616274d3d4a21a584f7f4a0c\"},\"headline\":\"Comparing Benchtop Sequencers As Technologies Mature | ASHG 2014\",\"datePublished\":\"2014-10-21T17:43:15+00:00\",\"dateModified\":\"2016-12-06T20:15:46+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/comparing-benchtop-sequencers-as-technologies-mature-ashg-2014\\\/\"},\"wordCount\":1024,\"commentCount\":0,\"image\":{\"@id\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/comparing-benchtop-sequencers-as-technologies-mature-ashg-2014\\\/#primaryimage\"},\"thumbnailUrl\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/behindthebench\\\/wp-content\\\/uploads\\\/sites\\\/9\\\/2016\\\/03\\\/lelivelt-1.png\",\"keywords\":[\"ASHG 2014\",\"Ion Torrent\",\"Next Generation Sequencing\"],\"articleSection\":[\"Cancer Research\",\"Events and Tradeshows\"],\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"CommentAction\",\"name\":\"Comment\",\"target\":[\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/comparing-benchtop-sequencers-as-technologies-mature-ashg-2014\\\/#respond\"]}]},{\"@type\":\"WebPage\",\"@id\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/comparing-benchtop-sequencers-as-technologies-mature-ashg-2014\\\/\",\"url\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/comparing-benchtop-sequencers-as-technologies-mature-ashg-2014\\\/\",\"name\":\"Comparing Benchtop Sequencers As Technologies Mature | ASHG 2014 - Behind the Bench\",\"isPartOf\":{\"@id\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/behindthebench\\\/#website\"},\"primaryImageOfPage\":{\"@id\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/comparing-benchtop-sequencers-as-technologies-mature-ashg-2014\\\/#primaryimage\"},\"image\":{\"@id\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/comparing-benchtop-sequencers-as-technologies-mature-ashg-2014\\\/#primaryimage\"},\"thumbnailUrl\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/behindthebench\\\/wp-content\\\/uploads\\\/sites\\\/9\\\/2016\\\/03\\\/lelivelt-1.png\",\"datePublished\":\"2014-10-21T17:43:15+00:00\",\"dateModified\":\"2016-12-06T20:15:46+00:00\",\"author\":{\"@id\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/behindthebench\\\/#\\\/schema\\\/person\\\/9bbb2d67616274d3d4a21a584f7f4a0c\"},\"breadcrumb\":{\"@id\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/comparing-benchtop-sequencers-as-technologies-mature-ashg-2014\\\/#breadcrumb\"},\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/comparing-benchtop-sequencers-as-technologies-mature-ashg-2014\\\/\"]}]},{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/comparing-benchtop-sequencers-as-technologies-mature-ashg-2014\\\/#primaryimage\",\"url\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/behindthebench\\\/wp-content\\\/uploads\\\/sites\\\/9\\\/2016\\\/03\\\/lelivelt-1.png\",\"contentUrl\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/behindthebench\\\/wp-content\\\/uploads\\\/sites\\\/9\\\/2016\\\/03\\\/lelivelt-1.png\",\"width\":790,\"height\":565},{\"@type\":\"BreadcrumbList\",\"@id\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/comparing-benchtop-sequencers-as-technologies-mature-ashg-2014\\\/#breadcrumb\",\"itemListElement\":[{\"@type\":\"ListItem\",\"position\":1,\"name\":\"Home\",\"item\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/behindthebench\\\/\"},{\"@type\":\"ListItem\",\"position\":2,\"name\":\"Comparing Benchtop Sequencers As Technologies Mature | ASHG 2014\"}]},{\"@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":"Comparing Benchtop Sequencers As Technologies Mature | ASHG 2014 - 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\/comparing-benchtop-sequencers-as-technologies-mature-ashg-2014\/","og_locale":"en_US","og_type":"article","og_title":"Comparing Benchtop Sequencers As Technologies Mature | ASHG 2014","og_description":"One of the most important attributes for a DNA sequencing system is accuracy.\u00a0 Scientists want the highest quality, reproducible data. Sequencing systems have strengths and weaknesses driven by the unique chemistry of each.\u00a0 One criticism of the Ion Torrent\u2122 sequencing chemistry has been that the fast and efficient lack of termination (which also gives it","og_url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/comparing-benchtop-sequencers-as-technologies-mature-ashg-2014\/","og_site_name":"Behind the Bench","article_publisher":"https:\/\/www.facebook.com\/thermofisher","article_published_time":"2014-10-21T17:43:15+00:00","article_modified_time":"2016-12-06T20:15:46+00:00","og_image":[{"width":790,"height":565,"url":"https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2016\/03\/lelivelt-1.png","type":"image\/png"}],"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":"5 minutes"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"Article","@id":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/comparing-benchtop-sequencers-as-technologies-mature-ashg-2014\/#article","isPartOf":{"@id":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/comparing-benchtop-sequencers-as-technologies-mature-ashg-2014\/"},"author":{"name":"Behind The Bench Staff","@id":"https:\/\/admin.acceleratingscience.com\/behindthebench\/#\/schema\/person\/9bbb2d67616274d3d4a21a584f7f4a0c"},"headline":"Comparing Benchtop Sequencers As Technologies Mature | ASHG 2014","datePublished":"2014-10-21T17:43:15+00:00","dateModified":"2016-12-06T20:15:46+00:00","mainEntityOfPage":{"@id":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/comparing-benchtop-sequencers-as-technologies-mature-ashg-2014\/"},"wordCount":1024,"commentCount":0,"image":{"@id":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/comparing-benchtop-sequencers-as-technologies-mature-ashg-2014\/#primaryimage"},"thumbnailUrl":"https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2016\/03\/lelivelt-1.png","keywords":["ASHG 2014","Ion Torrent","Next Generation Sequencing"],"articleSection":["Cancer Research","Events and Tradeshows"],"inLanguage":"en-US","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/www.thermofisher.com\/blog\/behindthebench\/comparing-benchtop-sequencers-as-technologies-mature-ashg-2014\/#respond"]}]},{"@type":"WebPage","@id":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/comparing-benchtop-sequencers-as-technologies-mature-ashg-2014\/","url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/comparing-benchtop-sequencers-as-technologies-mature-ashg-2014\/","name":"Comparing Benchtop Sequencers As Technologies Mature | ASHG 2014 - Behind the Bench","isPartOf":{"@id":"https:\/\/admin.acceleratingscience.com\/behindthebench\/#website"},"primaryImageOfPage":{"@id":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/comparing-benchtop-sequencers-as-technologies-mature-ashg-2014\/#primaryimage"},"image":{"@id":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/comparing-benchtop-sequencers-as-technologies-mature-ashg-2014\/#primaryimage"},"thumbnailUrl":"https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2016\/03\/lelivelt-1.png","datePublished":"2014-10-21T17:43:15+00:00","dateModified":"2016-12-06T20:15:46+00:00","author":{"@id":"https:\/\/admin.acceleratingscience.com\/behindthebench\/#\/schema\/person\/9bbb2d67616274d3d4a21a584f7f4a0c"},"breadcrumb":{"@id":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/comparing-benchtop-sequencers-as-technologies-mature-ashg-2014\/#breadcrumb"},"inLanguage":"en-US","potentialAction":[{"@type":"ReadAction","target":["https:\/\/www.thermofisher.com\/blog\/behindthebench\/comparing-benchtop-sequencers-as-technologies-mature-ashg-2014\/"]}]},{"@type":"ImageObject","inLanguage":"en-US","@id":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/comparing-benchtop-sequencers-as-technologies-mature-ashg-2014\/#primaryimage","url":"https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2016\/03\/lelivelt-1.png","contentUrl":"https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2016\/03\/lelivelt-1.png","width":790,"height":565},{"@type":"BreadcrumbList","@id":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/comparing-benchtop-sequencers-as-technologies-mature-ashg-2014\/#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Home","item":"https:\/\/admin.acceleratingscience.com\/behindthebench\/"},{"@type":"ListItem","position":2,"name":"Comparing Benchtop Sequencers As Technologies Mature | ASHG 2014"}]},{"@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":54,"label":"Cancer Research"},{"value":113,"label":"Events and Tradeshows"}],"post_tag":[{"value":150,"label":"ASHG 2014"},{"value":11,"label":"Ion Torrent"},{"value":6,"label":"Next Generation Sequencing"}]},"featured_image_src_large":["https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2016\/03\/lelivelt-1.png",760,544,false],"author_info":{"display_name":"Behind The Bench Staff","author_link":"https:\/\/admin.acceleratingscience.com\/author\/behind-the-bench-staff\/"},"comment_info":0,"category_info":[{"term_id":54,"name":"Cancer Research","slug":"cancer-research","term_group":0,"term_taxonomy_id":54,"taxonomy":"category","description":"","parent":0,"count":142,"filter":"raw","meta":[],"cat_ID":54,"category_count":142,"category_description":"","cat_name":"Cancer Research","category_nicename":"cancer-research","category_parent":0},{"term_id":113,"name":"Events and Tradeshows","slug":"events-and-tradeshows","term_group":0,"term_taxonomy_id":113,"taxonomy":"category","description":"","parent":0,"count":89,"filter":"raw","meta":[],"cat_ID":113,"category_count":89,"category_description":"","cat_name":"Events and Tradeshows","category_nicename":"events-and-tradeshows","category_parent":0}],"tag_info":[{"term_id":150,"name":"ASHG 2014","slug":"ashg-2014","term_group":0,"term_taxonomy_id":150,"taxonomy":"post_tag","description":"","parent":0,"count":10,"filter":"raw","meta":[]},{"term_id":11,"name":"Ion Torrent","slug":"ion-torrent","term_group":0,"term_taxonomy_id":11,"taxonomy":"post_tag","description":"","parent":0,"count":167,"filter":"raw","meta":[]},{"term_id":6,"name":"Next Generation Sequencing","slug":"next-generation-sequencing","term_group":0,"term_taxonomy_id":6,"taxonomy":"post_tag","description":"","parent":0,"count":171,"filter":"raw","meta":[]}],"jetpack-related-posts":[{"id":19885,"url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/sanger-sequencing-mix-dna-templates\/","url_meta":{"origin":8078,"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":19883,"url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/building-a-better-sample-qc-workflow-from-extraction-to-sequencing\/","url_meta":{"origin":8078,"position":1},"title":"Building a Better Sample QC Workflow: From Extraction to Sequencing","author":"Marlene Gasdia-Cochrane","date":"August 25, 2026","format":false,"excerpt":"Article Summary Successful genomics experiments don't begin with sequencing\u2014they begin with sample quality. Every downstream application, from PCR to next-generation sequencing (NGS), depends on starting with nucleic acids that are accurately quantified and free from contaminants that could compromise results. Establishing a consistent quality control workflow helps laboratories improve reproducibility\u2026","rel":"","context":"In "General"","block_context":{"text":"General","link":"https:\/\/admin.acceleratingscience.com\/behindthebench\/general\/"},"img":{"alt_text":"A pipette drops a liquid into a petri dish with a dna sequence background, science concept. It suggests medical or genetic research.","src":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/iStock-2216731026_petridish-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\/iStock-2216731026_petridish-scaled.jpg?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/iStock-2216731026_petridish-scaled.jpg?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/iStock-2216731026_petridish-scaled.jpg?resize=700%2C400&ssl=1 2x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/iStock-2216731026_petridish-scaled.jpg?resize=1050%2C600&ssl=1 3x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/08\/iStock-2216731026_petridish-scaled.jpg?resize=1400%2C800&ssl=1 4x"},"classes":[]},{"id":20004,"url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/a-guide-to-nucleic-acid-quality-control-dna-and-rna-purity\/","url_meta":{"origin":8078,"position":2},"title":"A Guide to Nucleic Acid Quality Control: DNA and RNA Purity","author":"Marlene Gasdia-Cochrane","date":"September 22, 2026","format":false,"excerpt":"Article Summary Nucleic acid quality control helps researchers evaluate DNA and RNA concentration and purity before downstream applications such as PCR, qPCR, and next-generation sequencing (NGS). A standardized workflow combining reliable extraction, concentration and purity assessment, application-appropriate quantification, and consistent laboratory practices can help identify sample issues early, improve reproducibility,\u2026","rel":"","context":"In "General"","block_context":{"text":"General","link":"https:\/\/admin.acceleratingscience.com\/behindthebench\/general\/"},"img":{"alt_text":"Close-up shot of a dna sequence on a screen, a digital representation of genetic code, used for analysis.","src":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/iStock-2212923489_dnasequence-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\/09\/iStock-2212923489_dnasequence-scaled.jpg?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/iStock-2212923489_dnasequence-scaled.jpg?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/iStock-2212923489_dnasequence-scaled.jpg?resize=700%2C400&ssl=1 2x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/iStock-2212923489_dnasequence-scaled.jpg?resize=1050%2C600&ssl=1 3x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2026\/09\/iStock-2212923489_dnasequence-scaled.jpg?resize=1400%2C800&ssl=1 4x"},"classes":[]},{"id":19447,"url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/philadelphia-chromosome-like-all-digital-pcr\/","url_meta":{"origin":8078,"position":3},"title":"Unlocking Cancer\u2019s Genetic Secrets with Digital PCR","author":"Behind The Bench Staff","date":"February 27, 2026","format":false,"excerpt":"In this episode of Absolute Gene-ius, we explore how digital PCR (dPCR) is transforming leukemia research with Valeria Rangel, a PhD candidate at the University of California, Irvine. Her work focuses on Philadelphia chromosome-like (Ph-like) B-cell acute lymphoblastic leukemia (ALL), a rare, aggressive subtype that disproportionately affects Hispanic populations. By\u2026","rel":"","context":"In "Cancer Research"","block_context":{"text":"Cancer Research","link":"https:\/\/admin.acceleratingscience.com\/behindthebench\/cancer-research\/"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2025\/11\/RANGEL-headshot-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\/2025\/11\/RANGEL-headshot-1.jpg?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2025\/11\/RANGEL-headshot-1.jpg?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2025\/11\/RANGEL-headshot-1.jpg?resize=700%2C400&ssl=1 2x"},"classes":[]},{"id":19223,"url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/innovations-in-qpcr-technology\/","url_meta":{"origin":8078,"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":19810,"url":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/integration-site-analysis-gene-therapy-safety\/","url_meta":{"origin":8078,"position":5},"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":[]}],"jetpack_sharing_enabled":true,"jetpack_featured_media_url":"https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2016\/03\/lelivelt-1.png","_links":{"self":[{"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/posts\/8078","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=8078"}],"version-history":[{"count":0,"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/posts\/8078\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/media\/8083"}],"wp:attachment":[{"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/media?parent=8078"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/categories?post=8078"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/tags?post=8078"},{"taxonomy":"division","embeddable":true,"href":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/wp-json\/wp\/v2\/division?post=8078"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}