Ion AmpliSeq Designer
The AmpliSeq.com login page was redesigned to communicate more clearly to users what AmpliSeq technology is, how it can be used, and the benefits it provides. The new page implements direct links to application, educational pages, and videos.
The access to Ion AmpliSeq Designer functionalities for panel customization remains otherwise unchanged (same login credentials).
✓ Ion AmpliSeq™ Liverpool Lymphoid Network Panel
The Ion AmpliSeq™ Liverpool Lymphoid Network Panel for hemato-oncology research is a targeted NGS community panel designed by leading clinical researchers at Liverpool Clinical Labs for the classification of lymphoid malignancy samples. This targeted panel covers 60 genes, providing comprehensive coverage of key biomarkers (including NOTCH1 3’UTR) applicable for the study of a range of lymphoid neoplasms, including both B and T cell lymphomas. This panel provides high accuracy NGS results with rapid turnaround time has one of the lowest DNA input requirements. Its performance has been verified by the network on both the GeneStudio™ and Genexus™ Integrated Sequencer Systems in a multicenter study using >200 real-world clinical research samples.
✓ Ion AmpliSeq™ Liverpool MPN Panel
The Ion AmpliSeq™ Liverpool MPN Panel for hemato-oncology research is a targeted NGS community panel designed by leading clinical researchers at Liverpool Clinical Labs for the classification of myeloproliferative neoplasm (MPN) samples. This panel provides high accuracy NGS results with rapid turnaround time, is compatible with the simple and automated Genexus workflow, and has one of the lowest DNA input requirements. A single pool design allows sequencing a high volume of samples (32 per lane per run) for cost-effective analysis. This DNA panel contains targets from the 3 classical MPN genes (JAK2, MPL, and CALR) and other key targets from 22 additional genes (including FLT3, IDH1, and IDH2) to provide a comprehensive assessment and classification of MPN samples in a single test. The panel’s performance has been verified using real-world clinical research samples and demonstrated 100% sensitivity across variant types, including challenging targets like FLT3-ITDs.
The panel is intended for Research Use Only and not for use in diagnostic procedures.
Starting from this release, the 50X Spike-in format is available also for the Genexus ordering option for compatible custom Made-To-Order DNA designs with less than 123 amplicons per pool. After selecting the Genexus instrument in the order preview process, users can now select the 50X spike-in format from a new special instruction dropdown menu. Spike-in panels are meant to be physically combined with existing primary panels to expand their content. Spike-in amplicons shall not overlap with existing primary panel amplicons to avoid unwanted interactions. At this time, users are responsible for such amplicon compatibility check (e.g., by visual inspection of panel target bed files). Additional support is available at Regional support contact links (Americas, EMEA, Greater China, South Asia, Japan).
Kits for Ion PGM™, Ion OneTouch™ 2 (including GeneStudio™ S5 OneTouch™ 2 kits), and Ion Proton™ Systems have been discontinued on December 31st, 2023. Accordingly, in this release we have removed support for such kits and platforms from panel pages and documentations. Exceptions are all instances within the description text of Community Panel pages, where references were kept as integral part of the features of each panel at launch (actual instrument and chip compatibility information are available in the dedicated section of each page).
Starting from this release, when creating human (hg19/hg38) Made-To-Order gene panels, gene targets (CDS and CDS+UTR) can be flagged for enabling automatic gene-level CNV detection compatible designs according to general AmpliSeq CNV design guidelines provided in the informational link available in the panel creation page. When this option is selected for a gene target, the design pipeline will try to ensure that at least 12 amplicons are automatically assigned to that target (if needed, amplicons will be added into the gene introns, if available, and then into upstream and downstream regions of the gene). Amplicons automatically added for CNV compatibility purposes will be listed in a specific bed file in the design results.zip file.
Once the design is completed, single CNV gene targets for which the minimum number of amplicons is reached are flagged as “CNV compatible” (
), otherwise they are flagged as CNV incompatible (
).
The overall design CNV compatibility status will also be checked against the general AmpliSeq CNV design guidelines and reported in the solution summary table (using the same symbols above). A design is considered CNV compatible if, and only if all the following conditions are met: 1) at least one of the requested CNV gene targets is CNV-compatible; 2) more than 60 amplicons in total exist in the panel; 3) the number of amplicons assigned to each CNV-compatible gene target is less than 40% of the total amplicons in the panel (as a proxy for the theoretical ideal condition at 20% per CNV target).
The specific reason(s) for design-level CNV incompatibility will be reported in a banner on panel page with the intent to help users identifying, when possible, alternative design strategies. Additional support is available at Regional contact links (Americas, EMEA, Greater China, South Asia, Japan).
Whereas Copy Number Variants can in principle be detected following design guidelines and best practices using compatible custom Ion AmpliSeq panels and the Ion Reporter Software, experimental testing, optimization, and verification are recommended. CNV design compatibility per se does not guarantee CNV detection performance.
In newborn screening (NBS) research, next-generation sequencing can provide genetic insights that aid in the understanding of severe combined immunodeficiency (SCID) and other T cell lymphopenias. Designed with leading researchers from the Department of Newborn Screening at Oslo University Hospital (Norway), the Ion AmpliSeq™ Newborn Screening Research Spike-In Panel for Severe Combined Immunodeficiency is a spike-in panel that, when combined with an AmpliSeq On-Demand primary panel created on ampliseq.com using the CSV file available from a direct link on the panel page, enables the investigation of 188 genetic targets for SCID, inborn errors of metabolism (IEM), congenital hypothyroidism (CH), congenital adrenal hyperplasia (CAH), cystic fibrosis (CF), T-cell defects, and relevant US NBS genes using dried blood spot (DBS) DNA samples.
This panel is customizable to meet your unique research needs directly on AmpliSeq.com. Contact regional AmpliSeq Support (Americas, EMEA, Greater China, South Asia, Japan) for further assistance.
The panel is intended for Research Use Only and not for use in diagnostic procedures.
Starting from this release standard AmpliSeq Made-To-Order designs with less than 12 amplicons per pool can be ordered to be used as spike-in panels. Accordingly, the only available special instruction ordering options for these panels will be “50X – spike-in” (Tubes of primers pools only format) and “384-well plates only” (Tubes plus 384 well plates format). Panels falling in this category will have banners in their panel page to inform users of the same.
In this release we have updated AmpliSeq.com content to support new features introduced by Genexus Software 6.8 released on July 15th, 2023. These include:
Support for GX7 chip
Genexus Software 6.8 supports the new GX7 chip with custom AmpliSeq assays. GX7 chip enables 20-25M reads per lane (67% increase vs. GX5) expanding the sequencing capacity of the Genexus Integrated System.
Accordingly, we have updated Instrument(Chip) info in panel page, chip calculator, FAQ content and recommended consumables in Order Preview page with GX7 chip and supported consumables info.
Support for 48 Genexus AmpliSeq barcodes
The 48 Genexus AmpliSeq barcode plates introduced with Genexus Software 6.8 support automated AmpliSeq library preparation for custom panels for up to 48 libraries per run on both GX5 and GX7 chips, increasing the maximum library capacity per run by 50% and reducing sequencing costs per sample (in combination with the support for 6 reactions per strip 1-2 pair).
The new Genexus™ Barcodes 1-48 AS (Cat. A54129) and Genexus™ Barcodes 49-96 AS (Cat. A54130) are now listed for ordering among the recommended consumables in the Order Preview page.
Note: 48 Genexus AmpliSeq barcode plates do NOT support AmpliSeq HD library preparation.
Support for 24 samples per order for Ion AmpliSeq On-Demand panels for Genexus
When run on Genexus Software 6.8 (and above), all Ion AmpliSeq On-Demand panels for Genexus packages support library preparation for up to 24 samples per order (vs. previous 16 samples per order) when used in combination with 48 AmpliSeq Genexus barcode plates and when sequenced on a GX7 chip (regardless of the Genexus Barcode plate type used). The corresponding information has been updated for all Genexus AmpliSeq On-Demand formats in the Order Preview page.
Note: The price of AmpliSeq On-Demand panels for Genexus has remained unchanged, therefore reducing the panel price per sample by 33%.
Full support for Ion AmpliSeq HD 2-pool cfDNA assays on Genexus
Genexus Software 6.8 fully supports AmpliSeq HD 2-pool cfDNA panels both on GX5 and GX7 chips, allowing to investigate FFPE/liquid biopsy samples at full gene level with a single panel. Accordingly, we have now enabled the Genexus ordering option for AmpliSeq HD 2-pool cfDNA designs.
For more details on the use of custom AmpliSeq panels on Genexus 6.8, please refer to the new Ion AmpliSeq™ & Ion AmpliSeq™ HD Custom Assay User Guide (link to the same document is now available in the Order preview page for all Genexus order configurations).
While we have worked on fixing all known issues with the White Glove copy amplicon feature, unpredictable exceptions might still apply preventing users to obtain the desired subset design. In case of issues, please open a bioinformatics support ticket (Regional contact links: Americas, EMEA, Greater China, South Asia, Japan), providing the ID of the White Glove panel of origin and the list of amplicons that needs to be copied over. Resolutions requiring new White Glove design submissions will be considered for prioritization over existing projects based on available resources, but prioritization cannot be guaranteed.
The Ion AmpliSeq Designer Help documentation is currently under revision for the latest features and will be updated in future AmpliSeq Designer releases.
We have updated our support for dbSNP database to version 155 for both hg19 and hg38 human reference genomes.
Support for older dbSNP versions is not available, however users can always enter genomic coordinates if obsolete dbSNP annotations are needed.
Exceptions might apply to the copy amplicon feature for human White Glove designs preventing users to obtain the desired subset design. While we are working on fixing this. In case of issues with copying White Glove amplicons please open a bioinformatics support ticket (Americas, EMEA, Greater China, South Asia, Japan), providing the ID of the White Glove panel of origin and the list of amplicons that needs to be copied over. Resolutions requiring new White Glove design submissions will be considered for prioritization over existing projects based on available resources, but prioritization cannot be guaranteed.
The Ion AmpliSeq Designer Help documentation is currently under revision for the latest features and will be updated in future AmpliSeq Designer releases.
In this release we have introduced direct access to the Thermo Fisher Analytical Validation Consulting Services info page and to the form to request to be contacted by an AV Specialist for additional information. Links are available within banners in the login page and in the top bar of all pages once user is logged in, as well as a “Need help with panel validation process?” link within all panel pages.
Thermo Fisher Scientific AV Consulting Services are meant to accelerate and streamline your validation process, including all custom Ion AmpliSeq™ and Ion AmpliSeq™ HD panels, by providing technical project management of your research lab’s AV, potentially reducing your overall time to launch by 75%.
Note: AV Consulting availability and levels of service may vary by region. Please contact an AV Specialist at the provided link for more specific information.
We have renewed the look & feel of the Help section for a better navigation experience. Once navigating to the Help section, the Ion AmpliSeq Designer Help, Frequently Added Questions, User Guides, and Release Notes items and submenus are now always accessible in the side bar, while the content of the selected item is dynamically displayed on the rest of the page.
The newly released Ion AmpliSeq™ HD Library Kit with HD Enhancer (Cat. No. A57283), bringing improved performance to the manual library preparation of Ion AmpliSeq HD panels (Gene Studio workflow), is now available in the list of recommended consumables in the Order preview page for custom HD panels. It replaces the Ion AmpliSeq™ HD Library Kit (Cat. No. A37694) as the recommended library preparation kit.
The new look & feel for the Help section is currently available only when accessed after login. Access from the login page will be implemented in a future release.
The Ion AmpliSeq Designer Help documentation is currently under revision for the latest features and will be updated in future AmpliSeq Designer releases.
From this release, amplicons belonging to DNA human White Glove (WG) designs can be copied to new or existing draft designs to generate full/partial subset Made-To-Order panels with WG content*.
Both the source and the destination design must belong to the same AmpliSeq.com account, and both designs must have the same human reference (hg19 or hg38). WG amplicons can be copied directly from the WG panel page (only design-to-design through the “Copy Amplicons” button). Additional gene, region, amplicon targets can (optionally) be added to the design draft before submission to obtain the new subset panel. Made-To-Order subset panels with any WG content can NOT be shared with other users.
*Exceptions might apply, which will require a new full WG submission to obtain the desired subset design.
Users can now copy amplicons from Ion AmpliSeq HD to Ion AmpliSeq (human, hg19) Made-To-Order designs in addition to the already existing ability for the opposite process. For compatibility reasons, only amplicons within the overlapping size range of AmpliSeq HD and standard AmpliSeq chemistry (i.e., 125 to 175 bp) can be copied in this fashion.
Copying White Glove amplicons with amplicon ID length >30 characters is not available at this time. This limitation will be fixed in an upcoming release. In case of such an occurrence, please open a bioinformatics support ticket (Regional contact links: Americas , EMEA, Greater China, South Asia, Japan) indicating the White Glove panel of origin and providing a list of amplicons that need to be copied over.
The Help documentation is currently under revision for the latest features and will be updated in future AmpliSeq Designer releases.
Users can now optionally prioritize targets when creating custom Ion AmpliSeq™ and Ion AmpliSeq™ HD hotspot designs. When only overlapping amplicons are available for covering close-by targets in a 1-pool hotspot design, the design pipeline will eliminate one or more of them to resolve the conflict, resulting in the missed coverage of the input targets they would have covered. The new hotspot target prioritization functionality launched in this release (available for hotspot designs only, see FAQ for more details) allows users to define a priority which hotspot target(s) the design pipeline should attempt to retain when such overlapping amplicons conflicts occur. The corresponding amplicons - if available - will preferentially be kept in the final design. This feature aims at maximizing the coverage of the hotspot targets that are the most relevant for the user. Hotspot target prioritization is not meant for increasing the overall coverage of 1-pool hotspot designs; in case, lower specificity solutions (see FAQ) or 2-pool hotspot solutions (see below) are better suited for the scope.
Starting from this release, 2-pool solutions are also automatically generated for hotspot designs. These solutions allow maximizing coverage over the input targets in presence of overlapping amplicon conflicts and are made available whenever the 1-pool hotspot solutions do not cover all input targets.
The new hotspot target prioritization and 2-pool hotspot solutions features combined provide users with a wider choice of solutions to cover their hotspot targets of interest.
The feature to propose as Community panel is back again. A new "Propose as Community panel" button is now available in the design page of any human DNA or RNA custom Made-To-Order AmpliSeq™ and AmpliSeq™ HD panel. This functionality allows users to propose custom panels to be considered for sharing as AmpliSeq™ Community panels directly from the panel page by filling-in an online form with some basic information. Only custom panels previously ordered and verified for performance are eligible for being considered as Community panels. Evidence (e.g., publication, datasets, etc.) of the actual panel performance, along with indications on any protocol modifications and/or specific analysis setup applied, will be required.
Proposals are subject to review and approval by Thermo Fisher Scientific and submitters will be contacted with further details on the next steps once their proposals will have been evaluated.
The Help documentation is currently under revision for the latest features and will be updated in future AmpliSeq Designer releases.
The following improvements were introduced for the Search & Compare tool:
We introduced a new feature in the Start a new AmpliSeq design page for human DNA Made-to-Order panels (gene, hotspot and subset) to optionally include an oncology hotspot.bed file in the panel result files.
The hotspot.bed file will contain a curated list of oncology hotspots whose coordinates overlap with the designed amplicons. To learn more about hotspot.bed files and their use in variant analysis, visit the AmpliSeq FAQ.
Note: The underlying curated hotspot list might be subject to updates in future AmpliSeq release versions. In case, notification of any version change will be provided in the corresponding Release Notes.
Creating sub-panels by picking individual oligos from 384-well plates for AmpliSeq RNA fusion designs is not supported due to fusion assay design properties. Therefore, in alignment with Made-to-Order standard RNA fusion panels, the Tubes Only format is now the only option available when ordering AmpliSeq HD RNA fusion panels.
The Help documentation is currently under revision for the latest features and will be updated in future AmpliSeq Designer releases.
We have redesigned the Fixed Panels dashboard for enhanced user experience in searching, accessing, and managing Community and Ready-to-Use Panels.
Improvements include:
The Help documentation for the Redesigned My Design and Fixed Panel dashboard is currently under revision and will get updated in a future AmpliSeq Designer release.
We have revised the My Designs dashboard layout to make it clearer and improve user experience with accessing and managing custom designs. Enhancements include:
Starting from this version, AmpliSeq.com is not supported on Internet Explorer (any version). Users are encouraged to switch to an alternative supported browser to access AmpliSeq.com.
When a Made-To-Order design is submitted, the AmpliSeq pipeline computes several alternative solutions aimed at covering the required targets. Once the design is completed, only the High Specificity solution (recommended result) is presented to the user.
Increased coverage over this standard solution might have been achieved in one or more alternative solutions where amplicon design specificity constraints were iteratively relaxed. If such solutions exist, the user can add them to the available default solution clicking on the “Improve coverage” button in the panel page.
Since this approach has demonstrated to be useful to many customers, starting from this version we provide more detailed information on how the amplicon design specificity strategy works to increase in silico coverage over missed targets so that users can make more educate decisions in choosing these options.
In particular, information content now clearly specifies that only amplicons overlapping the regions missed by the standard solutions are subject to specificity relaxation, while the remaining amplicons in the design maintain their default high specificity level. Consequently, although lower specificity may result in increased off-target amplification for these amplicons, the effect is limited to the regions close to those missed by the default solution and not to the whole design.
A “Trouble Signing In” link on AmpliSeq.com login page points users to a new dedicated AmpliSeq FAQ section where solutions to the most common scenarios preventing users to sign in into their AmpliSeq.com account are provided.
Starting from this version, the pre-populated list of 12 gene expression assays in your AmpliSeq Made-to-Order Fusion designs is fixed (the default genes cannot be removed). As in previous versions, the gene list can be expanded to include further gene expression assay content. The 12 default genes are therefore always included in panel result files where they are configured as Expression Control assays for downstream analysis/QC purposes in Ion Reporter.
Note: Starting from v7.6.2 (Expected release date- end of June 2022), AmpliSeq.com will not be supported on Internet Explorer (any version). Please plan to switch to an alternative supported browser to access AmpliSeq.com.
A new Search & Compare tool is now available at the top of the Home page. The tool replaces the previous basic search tool and allows users to perform advanced content searching by keyword or by gene list throughout all panels available in their account. Searchable content includes custom DNA solutions, custom gene expression RNA solutions, designs shared by collaborators, Community panels and Ready-To-Use panels whose content is hosted on AmpliSeq.com (e.g. Cancer Hotspot Panel v2, Comprehensive Cancer Panel, etc.).
Search results are provided directly on the user interface as a list of panels matching the search criteria, organized in a sortable and filterable table.
The main details of each matching panel (e.g., formats available, number of pools, number of amplicons, application area, etc.) are available directly in the result table (“Details” button), together with direct links to access the corresponding panel page for a more detailed review and ordering of the panels.
Up to three panels in the search result list can be selected for a side-by-side comparison over their main features.
The “Search by Keyword” option allows searching designs available in the user account based on keywords, gene names, or symbols (free-text), performing an exact string match search (case insensitive) against panel descriptions, panel names, and gene names included in panel target list.
By default, results are provided as a list of the top 10 panels (with the option to show all results) matching the search criteria and ranked by relevance. Results can be filtered/sorted according to different criteria.
The “Search by Genes” option allows searching designs available in the user account based on their gene content. Search terms can be manually entered, pasted, or uploaded (CSV file) as a list of gene names, gene symbols, or synonyms (case insensitive). A mandatory Sample Criteria selection in the tool interface (“cfDNA”, “FFPE” or “Standard” for DNA panels; “Gene Expression” for RNA panels) focuses the search only to the panel's intended use and allows for a streamlined review of search results.
By default, results are provided as a list of the top 10 panels (with the option to show all results), matching the search criteria and ranked by the percentage of matched search genes. A detailed list of matched/missed genes is provided for each hit and results can be filtered/sorted according to different criteria.
The design of new custom panels of the relevant type given the selected sample criteria and based on the searched gene list can be launched directly from the search result page.
When comparing search-by-gene results (up to 3), the main details of each selected panel are provided side-by-side on the user interface, including the total number of genes (exportable as file) and the number of amplicons, the list of matching/missing genes, the number of pools, etc. A list of all matched and missed genes across compared solutions can also be exported as an Excel file for easier review.
Starting from this release, when a new custom design is created the RefGene version used to perform the panel design will be annotated in the header line of the panel bed files (“refGeneVersion” tag) for future reference.
The Help documentation for the Order Journey process and instrument selection options is currently under revision and will be updated in a future AmpliSeq Designer release.
The instrument selection options available in the Order Preview journey for all panels have been updated to align with products/solutions officially supported in Genexus Software 6.6. General guidelines on instrument support by panel type have been updated accordingly also in the “Ion Torrent Genexus System – Consumables” section in the AmpliSeq FAQ documentation.
A brief description of the tracks shown in IGV Lite tool for AmpliSeq On-Demand panels is now directly accessible within the panel page by clicking on the information icon located on the top-right corner of the IGV tool.
The Help documentation for the Order Journey process and instrument selection options is currently under revision and will be updated in a future AmpliSeq Designer release.
In this release, we have updated the Order Preview workflow to allow for an easier order configuration of all AmpliSeq custom panels, while also providing a more informative review of the selected panel format before proceeding with ordering. The main improvements include:
Among other things, the info displayed on the Order Preview is meant to help with:
Ordering format and special instructions for White Glove panels are displayed in details at the preview order stage within AmpliSeq.com, according to requirements pre-defined at the White Glove design request phase.
Note: The details provided in the Order Preview page are meant to enhance the user experience while configuring custom AmpliSeq panels for ordering. The ordering process, as well as the format, provided materials, manufacturing process and content of all panel types remain otherwise unchanged.
Inquiries related to AmpliSeq ordering can be sent by email to the following addresses (by region):
The FAQ search functionality is now case insensitive to allow for a more effective searching experience.
The Finalize Design functionality for AmpliSeq On-Demand panels is now executed within the panel page, removing the need to go through the panel order configuration journey.
Gene annotation employed for target submission by gene name (Made-To-Order designs) is now updated to RefGene v98 for hg19 and v99 for hg38. Gene annotation of AmpliSeq On-Demand panels remains unchanged at RefGene v74 to maintain consistency with pre-designed content. AmpliSeq On-Demand spike-in designs also remain unchanged at RefGene v74 for compatibility reasons. Three of the genes included in the Oncomine Tumor Specific inventory (TCEB1, HIST1H1E and HIST1H3B) have updated gene symbols (but otherwise unchanged coordinates) in RefGene v98. These genes are now reported with their updated gene symbols (ELOC, H1-4 and H3C2, respectively) in any new or unlocked designs (locked designs will maintain v74 gene symbols). Old gene symbols are still available as aliases / synonyms.
The SOS document content was revisited for addressing bug fixes and introduce usability improvements, including:
The Finalize Design functionality is now available also for AmpliSeq On-Demand panels. Once finalized, designs are locked from further editing and panel files (including BED files) are directly available for download. Only locked designs can be ordered, once configured in the desired format.
Notes: only genes selected when finalizing a design will be included in the final design and editing of locked designs is possible after creating a copy.
Embedded special instructions for White Glove designs, if any, are now automatically captured by the SOS document. However, the Preview Order workflow on the user interface does not show nor matches with embedded special instructions (if any) associated with White Glove designs. User interface improvements on special instructions handling for White Glove designs are in progress and will be made available in a future release.
Pricing information will now be available during the checkout process in AmpliSeq Designer without the need to proceed to the thermofisher.com Cart. List pricing will be displayed to customers at the Order Summary popup and the Pre-Cart page where additional optional consumables are available for selection.
FFPE designs with amplicon ranges between 125-175bp, also referred as “FFPE long”, may only be used with the 530 chip used by the Ion GeneStudio™ sequencing instruments. Designs with amplicon ranges between 75-125bp, which are considered “short”, are now considered to be “dual use” and may be used with all chips (530, 540, 550 and GX5), which includes the new Ion Torrent™ Genexus™ Integrated Sequencer. Dual use refers to the sample input compatibility which can be DNA extracted from liquid biopsy samples or FFPE stored material.
The gene LDB3 is now added to our GRCh38 genome reference. This can now be accessed by creating a new draft and typing the key word “LDB3” as the gene symbol.
All solid Oncomine tumor specific panels for cancer research focused on solid tumors can now be selected with a Solid Tumor RNA panel that enable detection of fusions with FusionSync. The Solid Tumor RNA panel cannot be selected with the Oncomine Lymphoma Research panel.
Easily create a new custom Oncomine tumor specific DNA panel from a gene list. Genes that are available in inventory, will be included in a new custom panel. All others will be listed in a downloadable file as either not in stock or invalid if the gene symbol is not recognized. The user will be able to either type the genes directly or upload them using a CSV file.
New and updated FAQs have been added to the Oncomine tumor specific panel help section, to help understand the behavior of this new functionality.
As part of our continuous improvement efforts, we have optimized the in-silico coverage for Spike-in panels created for AmpliSeq On-Demand designs.
Versions for the dbSNP are being updated for the hg19 and mm10 reference genomes. For hg19 the dbSNP version is now v153 and for mm10 the dbSNP version is v150.
To simplify the organization of all our panels with fixed content (Community and Ready-to-Use panels), we have reduced the number to the following 5 categories and preserving the DNA and RNA top level categories:
A new predesigned panel called Ion Torrent™ Oncomine™ Homologous Recombination Repair Pathway Predesigned Panel has been added to our collection of Oncomine tumor specific panels.
To improve the ease of working with Custom References, AmpliSeq Designer has adopted the NCBI genomic reference format, which allows any reference downloaded from the NCBI site to be uploaded to AmpliSeq.com without the need to further edit the file. In addition, contig names are now officially supported up to 200 characters in length, which covers most names found in references available from the NCBI.
In previous versions, users wanting to add or edit the polymorphism BED file had to re-upload the associated custom reference and provide the new BED files at the time of upload. With this release, we now enable the addition or editing of the polymorphism BED file, without the need to re-upload the custom reference.
A new section called "Ion AmpliSeq Designer – Custom References" has been added to our FAQs. This section describes the expected behavior when a design that is associated to a Custom References is transferred or shared to another user.
The Ion AmpliSeq SARS-CoV-2 Research Panel is now officially supported for the Ion Torrent Genexus System. The instrument selection option to include the Genexus System has been added as well for the Preview Order process.
To help with gathering feedback from our users, we have implemented a new survey tool where we will be asking a few brief questions. The survey is strictly optional, and participation is greatly appreciated.
Our newest design improvements for in-silico coverage, are now available for custom AmpliSeq HD designs. The magnitude of the improvement will vary from design to design and is dependent on the amplicon size and number of pools.
In addition, following the same practice as with custom AmpliSeq designs, the user will be prompted to select the “DNA Type” based on 2 amplicon sized options. Option 1 is for DNA with amplicon size range of 75-125bp, which has been optimized for cfDNA input material. Option 2 is for amplicon size range of 125-175bp, which works best for DNA sourced from FFPE material.
Advancements in our design logic have been incorporated to help reduce the likelihood of primer-dimer for designs with 500 amplicons per pool or less. Suspected amplicons likely to cause primer-dimer will be automatically shifted from one pool to the other (in the case of 2 pool designs) or removed completely from the design. In the case where amplicons have been copied from a design using the “Copy Amplicons” function, a file named “filtered.tsv” will be created to provide in-sight into the detected conflicting must have amplicons. The user will have the option to resolve the conflict by selecting one of the listed amplicons and re-running the creation of their design.
Additional 18 genes have been added to our inventory. Designs containing these genes will be automatically updated if they’re in the Results Ready state. For designs that have been ordered or locked, there will be a note to the user providing them with the guidance to clone the design in order to access the newly inventoried content.
Specific FAQs have been added to explain the behavior when copying amplicons from a specific DNA Type (e.g. FFPE) to an existing draft design with a pre-defined DNA type (e.g. cfDNA). Visit the “Ion AmpliSeq Designer How To”, for more information regarding rules around the Copy Amplicons function.
We have improved our ordering process to better reflect the options that the user has when ordering panels. Depending on the selected instrument, the library preparation method and the ordering format (e.g. tubes or tubes plus 384-well plates), the user will be provided with a new summary and the option to browse additional consumables. This improvement should make it easier to select the necessary consumables during the check out process.
We're extending our newest design improvements in in-silico coverage to designs being created from custom references or any of our pre-loaded genomes (e.g. Cow, Sheep, etc.) The magnitude of the increase will vary from design to design, and heavily depends on amplicon size and the number of pools.
Following further user feedback, we have incorporated a new parameter that allows the user to create design solutions for only the application of interest. This is captured as the "DNA Type" and provides the user with 4 amplicon sized options. Option 1, is for DNA with amplicon size range of 125-140bp. Option 2, is for designs with amplicon range of 125-175bp. Options 3 and 4, are for high quality DNA and gives the user the option for 125-275bp or 125-375bp amplicon range solutions respectively.
For our commonly designed genes, we have pre-loaded improved design solutions that combine automated and semi-automated methods to quickly generate designs with the highest possible quality and in-silico coverage.
For our Oncomine tumor specific panels, each gene in the panel now contains tumor type associations to help with interpretation.
We have now enabled bulk sharing of a design to multiple users, with an automated email notification alerting the recipients that a design has been shared to their account.
The login process has changed. Users need to provide their login credentials in a separate page prior to accessing the Home Page. This change is done as part of our continuous improvement of our internal systems to enhance the security of our site, and compatibility with single-sign-on.
In addition, a new mechanism for generating an Access Code has been provided under the "My Account" options. This Access Code will now be used for importing panel information in Torrent Suite and Ion Reporter.
Sharing of designs originating from a Custom Reference, is currently not supported. This feature will be supported in an upcoming release.
A new system for managing the sharing of designs has been created. The new management tool makes it easier to keep track which designs have been shared, and to whom they've been shared to. The recipient of the design must be registered in ampliseq.com for their email address to be recognized, and only one email can be input at a time. Support for bulk sharing to multiple emails will be provided in a future release.
The login process will be changing. Users will provide their login credentials in a separate page prior to accessing the Home Page. This change will be done as part of our continuous improvement of our internal systems to enhance the security of our site, and as a pre-requisite for future single-sign-on compatibility with corporate systems where available.
An issue with our 384-well plate files for all designs created for the Ion AmpliSeq™ HD technology was identified and is now fixed. This issue affected all designs with the prefix “IAH”, and was responsible for the incorrect mapping of the oligo location within each well. The 384-well plate files for designs created prior to March 17, 2019, will be fixed on a rolling basis. If you have ordered an Ion AmpliSeq HD design in the 384-well plate format before March 17, and you wish to do partial pooling, please contact your local support team or reach out to our global support for further guidance on how to deal with this issue.
Ion AmpliSeq™ Microsatellite Instability Research Panel
Ion AmpliSeq™ Methylation Panel for Cancer Research
This release of Ion AmpliSeq Designer unveils a brand new product called “Ion AmpliSeq™ HD technology” and includes new capabilities geared towards achieving ultra-high sensitivity and customization:
This release of Ion AmpliSeq Designer unveils a brand new product called “Ion AmpliSeq On-Demand” and includes an impressive array of new features:
After an On-Demand design is created, genes added using the Add Gene tool are not categorized correctly when using the “Group by: Disease Research Area” function. Currently the genes will be categorized under “Added” rather than their respective Disease Research Area group.
During the design review stage, the “Group by: Disease Research Area” option should list all the genes that have been pre-selected under the original Disease Research Area category. In the future, this will include both the genes that are available and not available in our On-Demand catalog. However, only the genes that are available in our On-Demand catalog will appear under this category at this time, while the unavailable genes will appear in the “Unclassified” category.
At this time, when an On-Demand panel is cloned, the genes that are available On-Demand will be re-selected while genes that are not available will be deselected by default. Preserving the user selections and de-selections after using the cloning option is currently not supported.
The filtering functionality in the IGV tool which allows users to view specific genomic positions based on Expected Coverage values is not working as expected at this time. Data ranges do not get correctly filtered.
When an incorrect gene symbol is uploaded via the Gene List option in the homepage or via the Upload file option after a panel has been already created, the user will have the option to download the list of unrecognized genes as a file. The downloaded file should contain the “.CSV” extension; however our current download does not include this extension. The user will need to add the CSV extension to the file and correct the gene symbol, prior to being able to upload the list into the Ion AmpliSeq Designer website.
These new panels provide greater focus for research and expand the breath for which the Ion AmpliSeq technology can be used for. To order, please use the “Add to Cart” or “Request quote” or “Request Information” buttons. For the request information button, you will need to provide your contact details and a representative of our team will be in touch shortly.
Update: Due to inventory backlog, the availability of trial sizes for the following research panels will be for early to mid-October:
The following recently released panels are now available in trial sizes for easier customer access:
Ion AmpliSeq™ Ebola Research Panel
Ion AmpliSeq™ TB Research Panel
Ion AmpliSeq™ Pharmacogenomics Panel
Ion AmpliSeq™ Inhered Diseases Research Panels
Ion AmpliSeq™ TB Research Panel
Ion AmpliSeq™ Pharmacogenomics Panel
Ion AmpliSeq™ Inherited Diseases Research Panels
Longer 375 bp design solutions are now available by default and will be selected by default for newly-submitted designs when the DNA type "Standard DNA" is selected. We recommend these 375 bp solutions be used with germline DNA and the Ion PGM™ System for Next-Generation Sequencing coupled with the use of our new Hi-Q™ enzyme. Our 275 bp design solutions will remain available for existing and new designs.
The HID-Ion AmpliSeq™ Identity Panel is one of the first Next-Generation Sequencing (NGS) solutions for human identification that provides discrimination of individuals similar to STR genotype match probabilities used by forensic analysts.
Improve in silico coverage by selecting designs with relaxed primer specificity.
Before: (91.57% coverage)
After: (95.13% coverage)
Greatly improved design times
Get all the details here: Migration Help Page
Introducing the Ion AmpliSeq™ Exome Panel panel. This is available under the "DNA Ready-to-use" panel tab.
Increased in silico coverage for all standard DNA designs. For better in silico coverage of your existing panels you will have to redesign them.
Ion Proton instrument supports short designs (125bp-175bp) for germline applications.
Detailed information can be viewed using the UCSC Browser button.
Two Ion AmpliSeq™ RNA Ready-to-Use Panels have been added to the Panels tab:
User selectable padding around exons
Up to 300 amplicons in a single pool
A cost-effective and easy-to-use human SNP genotyping panel comprising nine specially designed primer pairs that can be added prior to template amplification to generate a unique ID for each research sample during post-sequencing analysis.
Use the Ion Library Equalizer™ Kit to normalize your Ion DNA libraries without the need for dilution or quantification, or the need for any additional equipment.
You can now order designs that your colleagues have shared with you. Simply use the URL they’ve shared with you to review the design and then click the order button.
Any ordered custom design can now be submitted to Life Technologies for consideration as a Community Panel. To submit one of your designs please complete the form found in the Sharing option under More Actions button on the review page.
If you haven’t noticed yet, the AmpliSeq™ Training Videos have been updated to include even more great information. Check them and other great resources out under the Help tab. If you’re new to AmpliSeq™ Designer be sure to check out the getting started guide.
After receiving results from the AmpliSeq™ Designer pipeline you can now provide feedback to help us improve the application. You’ll find the feedback link in the top right corner of the review design page.
We’ve also included some minor fixes and user experience improvements.
Instantly compare designs with both 150bp and 200bp amplicon sizes. Simply click on “More solutions” to compare!
Review, order or customize Ion Ready-to-use Panels.
Share your designs with collaborators.
Many small bug fixes and user experience improvements
Integration with UCSC Genome Browser (click on magnifying glass icon in results ready view)
New Dashboard tab to quickly view all your panels, design status and key metrics
