Release Notes


5.6 (August 1, 2016)

New support for creating custom designs using the GRCh38 (hg38) genome.

  • We now support creation of custom designs using the latest publicly available human genome called hg38. Please note that support is limited to the consensus contig, and a new alternate contig containing the GSTT1 gene. This gene will no longer be located in Chr22 but on the new alternate contig. All other alternate contigs are not supported in this release.

Updates to the plan.json file for the Ion AmpliSeq Exome Hi-Q panel.

  • New updated parameters for the Ion AmpliSeq Exome Hi-Q are now available through a new version of the plan.json file, for improved variant calling.

Two new Ion AmpliSeq BRCA Community panels for cancer research now available.

  • The new Ion AmpliSeq BRCA Reflex, Hereditary Cancer Research Panel is a 2 pool panel with 610 amplicons, and contains 25 hereditary cancer-related genes which have a central role in DNA repair and mismatch repair pathway.
  • The new Ion AmpliSeq BRCA Plus, Extended Hereditary Breast and Ovarian Research Panel, is a 3 pool panel with 699 amplicons that targets 11 genes known to harbor mutations related to breast and/or ovarian cancer.

New set of RNA Pathway panels has been added to our collection of pre-designed RNA research panels

  • Ion AmpliSeq RNA MAPK Pathway Research Panel - this panel is involved in Cell Cycle & Proliferation, Virology and Signal Transduction.
  • Ion AmpliSeq RNA Human Cancer Pathways Research Panel - this panels includes a large number of genes that are involved in DNA repair, angiogenesis, cell adhesion and extracellular matrix, as well as cell cycle and apoptosis.
  • Ion AmpliSeq RNA Inflammation Response Research Panel - this panels targets numerous genes that are taking part in key pathways of inflammation response that include chemokines.
  • Ion AmpliSeq RNA WNT Signal Pathway Research Panel - this panel includes a list of genes that are responsible for the regulating the production of WNT signaling molecules.
  • Ion AmpliSeq RNA Pancreatic Adenocarcinoma Research Panel - this is a panel that targets genes known to be over-expressed in Pancreatic carcinoma.
  • Ion AmpliSeq RNA Breast Cancer Research Panel - this is a very comprehensive panel targeting over 1,100 genes involved in breast cancer development and progression.

5.4.2 (June 27, 2016)

New automated in-silico histogram for custom designs.

  • As part of our output files, we now include an in-silico histogram publication quality image to help visualize the amplicon insert size distribution of our custom designs. The image includes on the X-axis the Amplicon Insert Size in bp units, and the Amplicon Count on the Y-axis. Information on the total number of amplicons in the design and their size range is also provided.

5.4.1 (May 18, 2016)

Additional new Ion AmpliSeq™ Research Panels for Inherited Diseases Research Area.

  • Ion AmpliSeq Cardiac Arrhythmias and Cardiomyopathy Research Panel
  • Ion AmpliSeq Pulmonary Research Panel v2
  • Ion AmpliSeq Dysmorphia-Dysplasia Research Panel v2
  • Ion AmpliSeq Inborn Errors of Metabolism Research Panel v2
  • Ion AmpliSeq Primary Immune Deficiency Research Panel v2
  • Ion AmpliSeq Endocrine Research Panel v2
  • Ion AmpliSeq Gastrointestinal Research Panel v2
  • Ion AmpliSeq Deafness Research Panel v2
  • Ion AmpliSeq Renal Research Panel v2
  • Ion AmpliSeq Inherited Cancer Research Panel
  • Ion AmpliSeq Epilepsy Research Panel
  • Ion AmpliSeq Autism Research Panel
  • Ion AmpliSeq Ovarian Cancer Research Panel
  • Ion AmpliSeq Dermatology Research Panel v2

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.

5.4 (April 20, 2016)

  • Internal bug fixes and administrator enhancements

5.0 (October 6, 2015)

Improved workflow based user experience

  • Our new Ion AmpliSeq Designer 5.0 has been improved to bring a workflow based approach to creating, reviewing and ordering your designs. With this new version, you will find that navigating through the application has never been easier, and getting to where you need to go is only a click away.

Access to Ion AmpliSeq Research Panels with no log in

  • Our Ion AmpliSeq Research Panels known as Ready-to-use and Community Panels, have been reorganized by default to fit within common research areas where targeted sequencing is used.
  • You will now find direct links from the home page to important research areas which you may review without the need to register or log in. Once you’re ready to order, you will need to sign in to your account and proceed with the ordering process.

Support for our new Ion S5™ and S5™ XL Sequencers

  • As a reminder, the new S5 and S5 XL have been launched on September 1, and we provide full compatibility within Ion AmpliSeq Designer. The new S5 and S5 XL systems represent a new exciting offer for high performance bench top sequencers.

New trial sizes available for 4 Inherited Diseases Research panels and the Pharmacogenomics Research panel (Due early to mid-October)

Update: Due to inventory backlog, the availability of trial sizes for the following research panels will be for early to mid-October:

  • Ion AmpliSeq™ Cardio Panel – To be available in 8 reaction and 32 reaction Chef-ready-trial kits.
  • Ion AmpliSeq™ Hematology Panel – To be available in 8 reaction and 32 reaction Chef-ready-trial kits.
  • Ion AmpliSeq™ Neurological Panel – To be available in 8 reaction and 32 reaction Chef-ready-trial kits.
  • Ion AmpliSeq™ Ophthalmic Panel – To be available in 8 reaction and 32 reaction Chef-ready-trial kits.
  • Ion AmpliSeq™ Pharmacogenomics Research Panel – To be available in only 32 reaction Chef-ready.

Special pricing for Custom Gene Fusion panels

  • Based on customer demand, for a limited time, our Custom Gene Fusion panels will continue to be priced the same as traditional RNA Gene panel designs.
  • As a reminder, the variant analysis workflow for Custom Gene Fusions is exclusively provided by Ion Reporter™. For more information please visit the Ion Reporter™ site here.

4.4.9 (September 1, 2015)

Support for our new Ion S5™ and S5™ XL Sequencers

  • Full compatibility of AmpliSeq Designs
  • S5/S5 XL family of chips fully integrated
  • A new exciting offer for high performance bench top sequencers

Introducing the new Ion AmpliSeq™ Research Panels

  • Ion AmpliSeq™ TB Research Panel

    • The new Ion AmpliSeq™ TB Research Panel used for targeting genes associated with antimicrobial resistance is now available. This panel consists of 109 amplicons in 2 pools to provide a quick, accurate and cost effective means to identify variants in 8 genes (embB, eis, gyrA, inhA, katG, pncA, rpoB, rpsL) associated with antimicrobial resistance in Mycobacterium tuberculosis (TB).
  • Ion AmpliSeq™ Pharmacogenomics Panel

    • The new Ion AmpliSeq™ Pharmacogenomics Panel is a single pool panel of primers used to perform multiplex PCR for the preparation of amplicon libraries from genomic “hot spot” regions that play a critical role in DME genes. By focusing on 136 well documented SNP and indel variants that captures CYP2D6 copy number variations at both the gene level and the exon 9 rearrangement, the panel enables screening of a broad selection of haplotypes including *36. This targeted, ready-to use panel provides high value pharmacogenomics content while remaining flexible by allowing user customization.
  • Ion AmpliSeq™ Inherited Diseases Research Panels

    • We have added a collection of 13 new panels involved in various Inherited Disease areas to complement our existing offerings in this field. This new menu of Ion AmpliSeq Research Panels offers a broad selection of targeted panels that enable researchers to survey across collective sets of genes that have been scientifically curated as the most likely suspects for containing a candidate mutation based on criteria such as phenotype and disease. Panels represent a wide range of inherited conditions from cardiovascular to dermatological disease. Use of our Ion AmpliSeq™ Technology enables coverage of up to 766 genes employing a straightforward and rapid PCR based workflow requiring as little as 10 ng of input DNA. The panels can be used as-is or can be further customized through Ion AmpliSeq™ Designer to easily remove or add additional amplicons.

Browse Panels without logging in

  • The Ready-to-use and Community Panel interface has been redesigned to allow visitors easier access to our family of pre-designed panels. Site visitors can review the content of our panels without the need to register or log in to an Ion AmpliSeq™ Designer account.

Special pricing for Custom Gene Fusion panels

  • For a limited time, new Custom Gene Fusion panels will continue to be priced the same as traditional RNA Gene panel designs.

Analysis workflow exclusively provided by Ion Reporter™

  • Variant analysis workflows for Custom RNA Gene Fusion designs are exclusively provided by Ion Reporter™. For more information please visit the Ion Reporter™ site here.

4.4.10 (September 15, 2015)

Support for our new Ion S5 and S5XL Sequencers

  • Full compatibility of AmpliSeq Designs
  • S5/S5XL family of chips fully integrated
  • A new exciting offer for high performance bench top sequencers

New trial sizes available for 4 Inherited Diseases Research panels and the Pharmacogenomics Research panel.

The following recently released panels are now available in trial sizes for easier customer access:

  • Ion AmpliSeq™ Cardio Panel – Available in 8 reaction and 32 reaction Chef-ready-trial kits.
  • Ion AmpliSeq™ Hematology Panel – Available in 8 reaction and 32 reaction Chef-ready-trial kits.
  • Ion AmpliSeq™ Neurological Panel – Available in 8 reaction and 32 reaction Chef-ready-trial kits.
  • Ion AmpliSeq™ Vision Panel – Available in 8 reaction and 32 reaction Chef-ready-trial kits.
  • Ion AmpliSeq™ Pharmacogenomics Research Panel – Available in only 32 reaction Chef-ready

Introducing the new Ion AmpliSeq™ Research Panels

  • Ion AmpliSeq™ Ebola Research Panel

    • The new Ion AmpliSeq Ebola Panel was developed as a quick, accurate and cost effective method to identify the present of Ebola virus (EBOV). The panel contains 145 amplicons for targeting the Ebola gene.
  • Ion AmpliSeq™ TB Research Panel

    • The new Ion AmpliSeq™ TB Research Panel used for targeting genes associated with antimicrobial resistance is now available. This panel consists of 109 amplicons in 2 pools to provide a quick, accurate and cost effective means to identify variants in 8 genes (embB, eis, gyrA, inhA, katG, pncA, rpoB, rpsL) associated with antimicrobial resistance in Mycobacterium tuberculosis (TB).
  • Ion AmpliSeq™ Pharmacogenomics Panel

    • The new Ion AmpliSeq™ Pharmacogenomics Panel is a single pool panel of primers used to perform multiplex PCR for the preparation of amplicon libraries from genomic “hot spot” regions that play a critical role in DME genes. By focusing on 136 well documented SNP and indel variants that captures CYP2D6 copy number variations at both the gene level and the exon 9 rearrangement, the panel enables screening of a broad selection of haplotypes including *36. This targeted, ready-to use panel provides high value pharmacogenomics content while remaining flexible by allowing user customization.
  • Ion AmpliSeq™ Inhered Diseases Research Panels

    • We have added a collection of 13 new panels involved in various Inherited Disease areas to complement our existing offerings in this field. This new menu of Ion AmpliSeq Research Panels offers a broad selection of targeted panels that enable researchers to survey across collective sets of genes that have been scientifically curated as the most likely suspects for containing a candidate mutation based on criteria such as phenotype and disease. Panels represent a wide range of inherited conditions from cardiovascular to dermatological disease. Use of our Ion AmpliSeq™ Technology enables coverage of up to 766 genes employing a straightforward and rapid PCR based workflow requiring as little as 10 ng of input DNA. These panels are comprehensively designed and can be used as-is or can be easily customized with the power of Ion AmpliSeq™ Designer to create phenotype based focused sub panels. This collection of panels are 2-pool and have over 99% coverage.

Browse Panels without logging in

  • The Ready-to-use and Community Panel interface has been redesigned to allow visitors easier access to our family of pre-designed panels. Site visitors can review the content of our panels without the need to register or log in to an Ion AmpliSeq™ Designer account.

Special pricing for Custom Gene Fusion panels

  • For a limited time, new Custom Gene Fusion panels will continue to be priced the same as traditional RNA Gene panel designs.

Analysis workflow exclusively provided by Ion Reporter™

  • Variant analysis workflows for Custom RNA Gene Fusion designs are exclusively provided by Ion Reporter™. For more information please click visit the Ion Reporter™ help section here.

4.4 (May 28, 2015)

Support for RNA Gene Fusion designs

  • RNA Fusion designs creation has never been easier. Simply input and select your fusion(s) of interest and let Ion AmpliSeq™ Designer do the rest.
  • Support for gene fusion detection through highly targeted AmpliSeq™ assays is done using an extensive library of known fusion transcripts.

Special pricing for Custom Gene Fusion panels

  • For a limited time, new Custom Gene Fusion panels will be priced the same as traditional RNA Gene panel designs.

Panel search user interface revamp

  • The Ready-to-use and Community Panel search user interface has been redesigned to enhance the user experience and allow easier discovery of panels of interest.

Analysis workflow exclusively provided by Ion Reporter™

  • Variant analysis workflows for Custom RNA Gene Fusion designs are exclusively provided by Ion Reporter™. For more information please click visit the Ion Reporter™ help section here.

Known Limitations

  • Import of custom gene fusion panel files into Torrent Suite™ 4.4.3 will fail. Users are encouraged to create a generic run plan in Torrent Suite™ for any custom gene fusion run.
  • Full support of custom gene fusions will be available in Ion Torrent Suite™ 4.6. Please stay tuned for release updates.

4.2.3 (February 16, 2015)

Support for cell free DNA designs

  • Create designs for cell free DNA (cfDNA) targets with our new 140bp amplicon solutions.

New 8 reaction trial sizes now available for the following Ion AmpliSeq™ Community panels

  • Ion AmpliSeq™ RNA Lung Fusion Cancer Research Panel
  • Ion AmpliSeq™ CFTR Panel
  • Ion AmpliSeq™ TP53 Panel
  • Ion AmpliSeq™ Colon and Lung Cancer Research Panel v2
  • Ion AmpliSeq™ Hearing Loss Research Panel v1

4.2.2 (January 30, 2015)

Customize your panels!

  • Now the Ion AmpliSeq™ AML Research Panel and the Ion AmpliSeq™ Comprehensive Cancer Panel join the list of our panels that can be customized.

Upload even larger design reference files!

  • Our Custom Reference up-loader can support 2 GB uploads. However, users are encouraged to contact us to upload files of up to 4.0 GB if needed.

4.2 (December 18, 2014)

Customize your panels!

  • Re-use amplicons of interest from AmpliSeq Community Or Ready-to-use panels
  • Re-use amplicons of interest from previous AmpliSeq panels
  • Add new targets and mix new amplicons and re-used amplicons to form a new panel

New pre-loaded genomes now available!

  • Chinese Hamster (criGri1)
  • Dog (canFam3)

Upload larger design reference files!

  • Users may now upload files of up to 2.0 GB.

4.0 (September 19, 2014)

New AmpliSeq Assist!

  • Get expert help for your custom Ion AmpliSeq™ projects
  • A cost-effective way to support your entire project
  • For more information contact: Ion AmpliSeq Assist or visit the Ion Ampliseq Assist site for more information.

375 bp design solutions!

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.

New Agrigenomics and Any Reference design solutions!

  • Create designs for more organisms using new pre-loaded publicly available reference genomes. New genome references available for design
  • Is your genome not pre-loaded? No problem, load your own complete custom genomes or fragmented sequence contigs* and create your designs. * Additional help required for incomplete/fragmented genomes. Please contact ampliseq-designs@lifetech.com. Add custom reference page
  • Manage your new custom genomes using our new easy-to-use genome management dashboard. Custom references dashboard page
  • Use available primer specificity check options to ensure your design success.

New Live Chat!

  • Chat with one of our Product Information Specialists live to get help once you’re ready to place your order.

New/Updated Community Panels

  • Ion AmpliSeq™ RNA Fusion Lung Cancer Research Panel (released July 22, 2014)
    • Coverage: 100.00%
    • Number of amplicons: 85
    • Number of pools: 1
    • InputRNA: 10ng
  • Ion AmpliSeq™ AML Research Panel (released August 14, 2014)
    • Panel size: 21.97 kb
    • Coverage: 99.74%
    • Number of amplicons: 264
    • Number of pools: 4
    • Input DNA: 40ng

New/Updated Ready-to-Use Panels!

  • Ion AmpliSeq™ Transcriptome Human Gene Expression Research Panel (released September 5, 2014)
    • Coverage: >95% of RefSeq Genes
    • Number of amplicons: 20,802
    • Number of pools: 1
    • Input RNA: 10ng

3.6 (July 11, 2014)

New Custom Design Functionality!

  • New variant ID support for Hotspot designs
    • Add variants to your design using dbSNP or COSMIC IDs
    • Designer will automatically convert variant IDs to hg19 or mm10 coordinates
    • Provides option to enter either coordinates or supported variant IDs

New Ready-to-Use Panels!

  • A25642 - HID-Ion AmpliSeq™ Ancestry Panel (released June 27, 2014)
    • Number of amplicons: 168
    • Number of pools: 1
    • Input DNA: 1ng per tube
  • A25643 - HID-Ion AmpliSeq™ Identity Panel (released June 27, 2014)
    • Number of amplicons: 124
    • Number of pools: 1
    • Input DNA: 1ng per tube
  • Ion AmpliSeq™ RNA Apoptosis Panel (updated June 23, 2014)
    • Panel size: 267 genes
    • Number of amplicons: 267
    • Number of pools: 1
    • Input RNA: 10ng
    • Updated BED file

New Community Panels!

  • Ion AmpliSeq Hearing Loss Research Panel v1 (released June 30, 2014)
    • Panel size: 294.81kb
    • Coverage: 95.7378913
    • Number of amplicons: 2064
    • Number of pools: 2
    • Input DNA: 20ng
  • Ion AmpliSeq™ Colon and Lung Research Panel v2 (released May 28, 2014)
    • Panel size: 14.5kb
    • Coverage: 100
    • Number of amplicons: 92
    • Number of pools: 1
    • Input DNA: 10ng

3.4 (March 31, 2014)

New Community Panels!

  • Ion AmpliSeq™ TP53 Panel
    • Covers all coding exons (no UTRs)
    • 24 amplicons, 2 pools, 125-175bp design
    • Compatible with FFPE samples
  • Ion AmpliSeq™ CFTR Panel
    • Covers all protein coding regions including UTRs, intron/exon boundaries (20bp), 162 CFTR2.org mutations including 23 ACMG/ACOG mutations, four deep intronic mutations, and two large deletions (CFTRdele2,3 and CFTRdele22,23).
    • 102 amplicons, 2 pools, 125-225bp design

New Custom Design Functionality!

  • New hotspot design capability
    • Improved design algorithm to optimize coverage with a single-pool solution
      • Previous tiling methodology would favor multiple pool solutions to cover nearby hotspots. With current methodology, the algorithm looks for an optimal single pool solution avoiding amplicon overlap.
    • Hotspots are optimally positioned on amplicon insert for more robust variant calling
      • The new algorithm seeks to position the hotspot close to the center of the amplicon. The benefit is that reads are mapped with higher reliability, and a greater probability of having reads from the forward and reverse strands, fulfilling the requirement for variant calling.
  • Updated RefSeq
    • More up-to-date human RefSeq is used for defining gene targets
    • The human RefSeq has been updated to the latest reference available in January, 2014 (RefSeq v63). This provides an updated reference for gene design.

3.2 (February 7, 2014)

New Look and Feel!

  • Improved dashboard
    • Quick access to your custom designs, Ion Panels and Community Panels
    • Notifications on the progress of your custom designs
    • Quick access to support resources
  • Powerful search/filter capabilities to quickly find pre-designed panels.

New Community Panel

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.

3.0 (November 4, 2013)

New AmpliSeq™ custom design pipeline

  • Get close to 100% coverage on human exome targets
    • Rerun your designs to see the improvements
  • Improve in silico coverage by selecting designs with relaxed primer specificity.

    • Choose the recommended design for best on-target % of sequence reads.
    • Select the “increase coverage” button and immediately see higher coverage designs, if available.
    • These pre-computed designs deliver increased coverage in GC-rich regions, while seeking to minimize off-target amplification.

    Designs with relaxed primer specificity

    Before: (91.57% coverage)

    Before Boosting

    After: (95.13% coverage)

    After Boosting

  • Greatly improved design times

    • Smaller, gene-centric designs returned within minutes
    • Designs up to 1 Mb within a week

Share your own AmpliSeq custom panels with the world

  • See the first such panel, the Dementia Research Gene Panel, under Community Panels.
  • Share your own designs using the “Sharing” button: Screenshots showing workflow after clicking the Sharing button

2.2.2 (October 11, 2013)

  • Transition to single sign on system on LifeTechnologies.com and improved ordering experience To streamline the process of ordering Ion AmpliSeq™ Panels, AmpliSeq Designer is transitioning user accounts from Ion Community accounts to Life Technologies accounts.

Get all the details here: Migration Help Page

  • Benefits of Transitioning to Life Technologies accounts In one single checkout process add all the reagent kits and chips needed to complete your AmpliSeq experiment Order all AmpliSeq panels using the e-commerce solution on Life Technologies website See the details of the new experience: Ordering Process

2.2.1 (August 9, 2013)

RNA Panels

2.2 (June 27, 2013)

DNA Panels

  • Introducing the Ion AmpliSeq™ Exome Panel panel. This is available under the "DNA Ready-to-use" panel tab.

    • Comprehensive coverage of the protein-coding exons Screenshot of Ion AmpliSeq™ Exome Panel
  • Increased in silico coverage for all standard DNA designs. For better in silico coverage of your existing panels you will have to redesign them.

    • The amplicon range for standard DNA designs has increased to 275bp.
    • The same 200bp sequencing kits can be used to sequence the longer amplicons.
  • Ion Proton instrument supports short designs (125bp-175bp) for germline applications.

2.0.3 (May 22, 2013)

  • RNA AmpliSeq Designs now allow up to 1200 amplicons per pool
  • DNA design results display specific reasons why a design cannot be confidently covered by an amplicon.

Screenshot of the Coverage Dropouts dialog

Detailed information can be viewed using the UCSC Browser button.

Screenshot of the UCSC Genome Browser

  • Search across ready-to-use and community panels, including the panel name, description, and gene names.

Screenshot of the search results

2.0.1 (April 1, 2013)

Ion AmpliSeq™ RNA Ready-to-Use Panels

Two Ion AmpliSeq™ RNA Ready-to-Use Panels have been added to the Panels tab:

  • Ion AmpliSeq™ RNA Apoptosis Panel
  • Ion AmpliSeq™ RNA Cancer Panel

Screenshot of Ion AmpliSeq™ RNA Cancer Panel

2.0 (February 17, 2012)

New DNA AmpliSeq™ Custom Pipeline

  • Up to 3072 amplicons per pool (up to 5Mb submission)
  • User selectable padding around exons

    Screenshot of new exon padding feature

  • New iterative tiling algorithm for AmpliSeq™ DNA designs.

Custom Mouse Panels

  • Target your mouse genes of interest
  • The same proven Human design pipeline

Custom RNA AmpliSeq™ Panels

  • Relative quantification of your transcripts of interest
  • Up to 300 amplicons in a single pool

    Screenshot of new exon padding feature

Ready-to-Use RNA AmpliSeq™ Panels

Community Panels Available for Order

  • Ion AmpliSeq™ Colon and Lung Cancer Panel
  • Ion AmpliSeq™ BRCA1/2 Panel

Ion AmpliSeq™ Sample ID Panel

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.

Ion Library Equalizer™ Kit

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.

1.2.9 (December 19, 2012)

  • 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.

    Screenshot of submitting a custom design

  • 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.

1.2.8 (November 6, 2012)

  • Minor bug fixes and user experience improvements.
  • The Ion Panels tab is now called Panels and includes new AmpliSeq™ Community Panels designed with leading researchers. AmpliSeq™ Community Panels are currently being testing and verified for performance and will soon be available for order.

1.2.7 (October 7, 2012)

  • Minor bug fixes and user experience improvements.
  • Significant performance enhancements to improve turn around time designing your custom assays.
  • Profile tab is now called My Account, which has a new Order History page where see all your ordered designs in one place.

1.2.6 (September 10, 2012)

  • Custom AmpliSeq™ panels are only compatible with Ion PGM™ 200 Sequencing Kit.
  • Introduced a variety of performance enhancements and caching strategies to improve turnaround time.
  • Added significantly more help documentation.
  • Instantly compare designs with both 150bp and 200bp amplicon sizes. Simply click on “More solutions” to compare!

    Screenshot of More Solutions

  • Review, order or customize Ion Ready-to-use Panels.

    Screenshot of Ion Ready-to-use Panels

  • Share your designs with collaborators.

    Screenshot of Sharing

1.2.5 (August 17, 2012)

  • Minor bug fixes and user experience improvements.
  • Performance enhancements.

1.2.3 (July 27, 2012)

  • New designs that have 12-23 minimum amplicons per pool may now be ordered. Existing designs that have 12-23 minimum amplicons per pool must be resubmitted before they can be ordered.
  • The icon for the UCSC browser has been updated.

1.2.2 (June 22, 2012)

Many small bug fixes and user experience improvements

1.2 (May 2012)

New features

  • Improvements in algorithms and chemistry enable typical exon designs in just 2 pools
  • Targeted regions panel designs typically in just 1 pool
  • The maximum target size of submission has increased to 1 MB
  • Up to 3072 amplicons in a single pool
  • Integration with UCSC Genome Browser (click on magnifying glass icon in results ready view)

    Screenshot of UCSC integration

  • New Dashboard tab to quickly view all your panels, design status and key metrics

    Screenshot of dashboard tab

Notes