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class="site-inner"><div class="content-sidebar-wrap"><main class="content"><article class="post-7727 post type-post status-publish format-standard has-post-thumbnail category-events-and-tradeshows tag-agbt-2016 tag-ion-torrent tag-next-generation-sequencing entry" aria-label="How are users applying Ion S5 systems in their research?"><header class="entry-header"><h1 class="entry-title">How are users applying Ion S5 systems in their research?</h1> <span class="post-info-author"> By <a href="https://www.thermofisher.com/blog/author/behind-the-bench-staff/" title="Posts by Behind The Bench Staff" rel="author">Behind The Bench Staff</a> </span> <span class="post-info-date"> 02.23.2016 </span> </header><div class="entry-content"><p><a href="https://www.thermofisher.com/blog/behindthebench/sharing-data-is-caring-agbt-2016/?socid=social_btb" target="_blank" rel="noopener noreferrer">AGBT</a> has been an amazing conference so far, with the plenary sessions of the day covering novel genomics applications and technology. As the sun set on the horizon, the focus shifted to workshops, in-suite presentations, and demos.</p> <p><a href="http://katalog.uu.se/profile/?id=N3-1440" target="_blank" rel="noopener noreferrer">Adam Ameur</a> of the National Genomics Infrastructure (NGI) from Uppsala, Sweden, and <a href="http://ehs.research.uiowa.edu/institutional-biosafety-committee" target="_blank" rel="noopener noreferrer">Lucy DesJardin</a> of the University of Iowa gave talks in the Ion Suite (Amarante 1).</p> <div class="page" title="Page 1"> <div class="layoutArea"> <div class="column"> <p><strong>A core lab’s perspective: experiences of human and microbial sequencing on the Ion S5 XL System</strong></p> <p style="padding-left: 30px"><img decoding="async" class="alignleft wp-image-7734" src="https://www.thermofisher.com/blog/behindthebench/wp-content/uploads/sites/9/2016/02/ion-300x241.jpg" alt="ion" width="249" height="200" srcset="https://www.thermofisher.com/blog/behindthebench/wp-content/uploads/sites/9/2016/02/ion-300x241.jpg 300w, https://www.thermofisher.com/blog/behindthebench/wp-content/uploads/sites/9/2016/02/ion-768x617.jpg 768w, https://www.thermofisher.com/blog/behindthebench/wp-content/uploads/sites/9/2016/02/ion-1024x823.jpg 1024w, https://www.thermofisher.com/blog/behindthebench/wp-content/uploads/sites/9/2016/02/ion-400x321.jpg 400w, https://www.thermofisher.com/blog/behindthebench/wp-content/uploads/sites/9/2016/02/ion.jpg 1068w" sizes="(max-width: 249px) 100vw, 249px" /></p> </div> </div> </div> <p style="padding-left: 30px">Adam discussed various applications that have been run successfully on the <a href="https://www.thermofisher.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-s5-ngs-targeted-sequencing.html?icid=fr-ions5seq-main?socid=social_btb" target="_blank" rel="noopener noreferrer">Ion S5™XL</a> platform. In his talk, he shared his experience with the Ion systems, emphasizing the ease of installation, set-up, and how the instruments didn’t take up too much room. His talk covered the simplicity of the Ion systems in every aspect, from installation, set up, to running experiments. Adam further explores all the projects his lab currently works on and the varied range of applications that are run on the Ion systems.</p> <ul> <li>Copy Number Variation in Cancer Cell Lines <ul> <li>CNV analysis are mostly done using microarrays and the team is exploring how the Ion S5 systems can help provide more.</li> <li>They tested a Leukemia cell line for which microarray data was available. The tested Ion S5 systems were successfully able to detect previously observed CNV gains and deletions on chromosomes 12 and 17</li> </ul> </li> <li>16S Metagenomics Studies. <ul> <li>Prior analysis of the bacterial composition of colon samples was performed on the <a href="https://www.thermofisher.com/order/catalog/product/4462921?ICID=search-product?socid=social_btb" target="_blank" rel="noopener noreferrer">Ion PGM™</a> using the <a href="https://www.thermofisher.com/order/catalog/product/A26216?socid=social_btb" target="_blank" rel="noopener noreferrer">Ion 16S™ Metagenomics kit</a>. The goal was to increase multiplexing with the Ion S5 XL and <a href="https://www.thermofisher.com/order/catalog/product/A27764?ICID=search-product?socid=social_btb" target="_blank" rel="noopener noreferrer">Ion 530™ chip</a></li> <li>They were able to run 32 samples on a single 530 chip with an average of ~525K reads per sample. With the Ion S5, they can do sequencing more efficiently.</li> </ul> </li> <li>Human Exome Sequencing <ul> <li>The core facility runs a lot of exomes on the <a href="https://www.thermofisher.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-proton-system-for-next-generation-sequencing.html?icid=fr-proton-main?socid=social_btb" target="_blank" rel="noopener noreferrer">Ion Proton™</a> and has generated a local database system that can perform rapid analysis.</li> <li>In a research test, using exome sequencing they were able to detect rare recessive diseases in two retrospective samples. With exome-seq producing over 17 Gbp of data.</li> </ul> </li> <li>Ion AmpliSeq Whole Transcriptome <ul> <li>AmpliSeq whole transcriptome is one of the core facilities’ main applications. This time, the goal was to evaluate the <a href="https://www.thermofisher.com/order/catalog/product/A27766?ICID=search-product?socid=social_btb" target="_blank" rel="noopener noreferrer">Ion 540™ chip</a> for AmpliSeq whole transcriptome samples and compare with previous results.</li> <li>They tested 24 tumor research samples and were able to reproduce the results observing high concordance with previous data.</li> </ul> </li> <li>Virus Integration Detection <ul> <li>HPV is a <a href="https://www.researchgate.net/profile/Bathula_Sreenivas_Reddy/publication/280005661_HPV_Caused_Cervical_Cancer/links/55a33aee08aea54aa8157bfc.pdf">causative agent</a> for cervical cancer and is a double-stranded DNA virus that integrates into the host genome. This integration of the HPV virus can lead to invasive <a href="https://www.researchgate.net/profile/Bathula_Sreenivas_Reddy/publication/280005661_HPV_Caused_Cervical_Cancer/links/55a33aee08aea54aa8157bfc.pdf">cervical cancer</a>.</li> <li>They tested the ability to multiplex on the Ion S5 system. They were able to detect the virus integration site and were able to multiplex >10 samples on the 530 chip.</li> </ul> </li> <li><a href="https://www.thermofisher.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-select-targets/ampliseq-target-selection.html?socid=social_btb" target="_blank" rel="noopener noreferrer">Ion AmpliSeq™ Panel</a> for Circular RNA Research <ul> <li>Circular RNA (circRNA) is a new class of noncoding RNA found in plants, archea, and animals. These are very stable molecules and is this is a growing field of research. The team wanted to develop an Ion AmpliSeq panel for circRNAs</li> <li>Since identification of circRNAs from RNA-seq is challenging, an AmpliSeq panel may potentially allow for increased specificity and sensitivity, precise RNA expression levels, and cost efficient, multiplexing, and high throughput capabilities.</li> <li>The team successfully developed the AmpliSeq research panel based on human brain RNA data. Their preliminary data shows high correlation in circRNA expression for replicate samples, they were able to cluster according to relative circRNA expression and could multiplex 11 human RNA samples – all in all, the Panel WORKED! (>5million reads)</li> </ul> </li> </ul> <p style="padding-left: 30px">Adam’s talk highlighted how the Ion S5 systems can be used for several applications with ease and simplicity. He mentioned, “Just using S5 is smooth and easy to operate.”</p> <p><b>Time Matters: The role of whole genome sequencing in high-resolution bacterial strain typing </b><b>for </b><b>foodborne </b><b>disease analysis</b></p> <p style="padding-left: 30px"><img decoding="async" class="alignleft size-medium wp-image-7735" src="https://www.thermofisher.com/blog/behindthebench/wp-content/uploads/sites/9/2016/02/IMG_0803-e1455898433251-200x300.jpg" alt="IMG_0803" width="200" height="300" srcset="https://www.thermofisher.com/blog/behindthebench/wp-content/uploads/sites/9/2016/02/IMG_0803-e1455898433251-200x300.jpg 200w, https://www.thermofisher.com/blog/behindthebench/wp-content/uploads/sites/9/2016/02/IMG_0803-e1455898433251-768x1152.jpg 768w, https://www.thermofisher.com/blog/behindthebench/wp-content/uploads/sites/9/2016/02/IMG_0803-e1455898433251-683x1024.jpg 683w, https://www.thermofisher.com/blog/behindthebench/wp-content/uploads/sites/9/2016/02/IMG_0803-e1455898433251-1250x1875.jpg 1250w, https://www.thermofisher.com/blog/behindthebench/wp-content/uploads/sites/9/2016/02/IMG_0803-e1455898433251-400x600.jpg 400w" sizes="(max-width: 200px) 100vw, 200px" />Lucy E DesJardin of the University of Iowa discussed the role of whole genome sequencing in high-resolution bacterial strain typing for foodborne disease research. Foodborne outbreak investigation takes time, and rapid responses and detection may allow for faster investigation and tracking.</p> <p style="padding-left: 30px">Salmonella is the most common foodborne disease in the United States accounting for 1 million illnesses, 19,000 hospitalizations, and 380 deaths annually. The bacteria can be transmitted via contact with animals, person-to-person, or by foods contaminated with small amounts of animal feces. There are over 40-50 cases per week reported to the CDC. Salmonella is genetically homogenous, and there is need for a more discriminatory method to strain-type so that cases in the cluster can be more accurately matched and investigated.</p> <p style="padding-left: 30px">The team studied Salmonella by performing whole genome analysis on the Ion S5XL system combined with the Ion Chef. The Ion Chef allowed for fast, easy, automated template preparation and the Ion S5 for sequencing. They also used web-based analysis using the <a href="https://www.thermofisher.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-data-analysis-workflow/ion-torrent-suite-software-plugins.html?socid=social_btb" target="_blank" rel="noopener noreferrer">AssemblerSPAdes Ion Torrent™ server plugin</a> for de novo assembly and phylogenetic analysis of the bacteria, allowing them to receive enhanced cluster resolution.</p> <p style="padding-left: 30px">In conclusion, the Ion S5 along with the Ion Chef can provide a fast rapid analysis of microbial DNA that may be helpful in future epidemics or outbreaks.</p> <p> </p> <p><strong>Missed AGBT 2016? We have you covered for everything – Check out our <a href="https://www.thermofisher.com/blog/behindthebench/what-you-missed-at-agbt-2016-a-complete-recap/?socid=social_btb" target="_blank" rel="noopener noreferrer">AGBT Recap</a></strong></p> <p> </p> <p>*For Research Use Only. 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