• Introduction to Ion AmpliSeq Designer
  • About Ion AmpliSeq Designer
  • Browser compatibility
  • Network and password security requirements
    • Network configuration and security
    • Password security
• Get started with Ion AmpliSeq Designer
  • Ion AmpliSeq Designer home page
  • Navigation bar
  • Manage my account
  • My Designs
  • Chip Calculator
  • View available reference genomes
  • Add a custom reference
  • Copy existing amplicons
    • Known limitations of the Copy Amplicons function
  • Instrument Compatibility
  • Basic and biological filtering
    • Filtering of repeat regions
    • Biological filtering ‑ GC content
• Oncomine tumor specific panels
  • Oncomine tumor specific panels
  • Workflow specifications
  • Panel design screen
  • Price tiers for the Oncomine tumor specific panels
  • Order a core or predesigned Oncomine tumor specific panel
  • Order a custom Oncomine tumor specific panel
  • Oncomine tumor specific panel files
• Ion AmpliSeq On‑Demand Panels
  • Start a new Ion AmpliSeq On-Demand design by manually entering a list of genes or uploading a CSV file
  • Start a new Ion AmpliSeq On-Demand design by browsing disease research areas
  • Order an Ion AmpliSeq On‑Demand Panel
  • Ion AmpliSeq On‑Demand panel files
• Ion AmpliSeq Custom panels
  • Start a new Ion AmpliSeq DNA Gene design
    • Ion AmpliSeq Custom panels: DNA gene design input specifications
  • Start a new Ion AmpliSeq DNA Hotspot design
    • Ion AmpliSeq Custom panels: DNA hotspot design input specifications
  • Start a new Ion AmpliSeq RNA Gene Expression design
    • Ion AmpliSeq Custom panels: RNA Gene Expression design input specifications
  • Start a new Ion AmpliSeq RNA Gene Fusion design
    • Ion AmpliSeq Custom panels: RNA Gene Fusion design input specifications
  • Order an Ion AmpliSeq custom panel
  • Ion AmpliSeq Custom panel files
  • Ion AmpliSeq Designer performance specifications for custom DNA panels
• Ion AmpliSeq HD Custom panels
  • Start a new Ion AmpliSeq HD DNA Gene design
    • Ion AmpliSeq HD Custom panels: DNA gene design input specifications
  • Start a new Ion AmpliSeq HD DNA Hotspot design
    • Ion AmpliSeq HD Custom panels: DNA hotspot design input specifications
  • Start a new Ion AmpliSeq HD RNA Gene Fusion design
    • Ion AmpliSeq HD Custom panels: RNA Gene Fusion design input specifications
  • Order an Ion AmpliSeq HD custom panel
  • Ion AmpliSeq HD Custom panel files
• Ion AmpliSeq Fixed Panels
  • Order Ion AmpliSeq Ready‑to‑Use and Community Panels
  • Ion AmpliSeq Fixed Panel files
• Supplemental information
  • Create a BED file from a list of variants
    • Create a custom BED file for input into Ion AmpliSeq Designer
    • Start from a list of dbSNP target identifiers
    • Use the UCSC Genome Browser to create a BED file with padded exons
  • Ion AmpliSeq panel design and CNV detection
  • Ion AmpliSeq On‑Demand Panel design and CNV detection
  • Manage shared designs
  • Get TaqMan assays
  • Generate and manage an Access Code
  • FASTA format requirements
  • Known polymorphism BED file requirements
  • Pipeline details
    • The design pipeline
    • Tiling algorithm
    • Pooling algorithm
    • Advantages of pooling and tiling
  • Hotspots pipeline
  • Ion Chip capacities for Ion AmpliSeq DNA libraries sequenced at equal depths
  • Ion Chip capacities for Ion AmpliSeq RNA libraries
  • Oncomine tumor specific panels: a complete list of targets
    • Oncomine Bladder Panel
    • Oncomine BRCA Expanded Panel
    • Oncomine Colorectal and Pancreatic Panel
    • Oncomine Gastric and Esophageal Panel
    • Oncomine Gynecological Panel
    • Oncomine HRR Pathway Predesigned Panel
    • Oncomine Kidney Panel
    • Oncomine Liver Panel
    • Oncomine Lymphoma Panel
    • Oncomine Melanoma Panel
    • Oncomine Prostate Panel
  • Ion AmpliSeq Made-to-Order designs: configuration options
  • Ion AmpliSeq HD Made‑to‑Order DNA and RNA panels: tubes only option
  • Ion AmpliSeq HD Made‑to‑Order DNA and RNA panels: plates only option
  • About Standard Order Sheet (SOS)
    • Order a design with more than 4,999 amplicons
  • Related Ion sequencing products
  • Helpful tools
  • Advanced features and tools
    • Minimize off-target hybridization
    • Determine GC content
    • Add coverageAnalysis plugin
• Screen descriptions
  • Design References
  • Ion Research Panels
  • Oncomine tumor specific panels for cancer research
  • Input gene list (Ion AmpliSeq On‑Demand Panels)
  • Browse Disease Research Areas (Ion AmpliSeq On‑Demand Panels)
  • Ion AmpliSeq On-Demand design screen
  • Start a new AmpliSeq design
  • Draft design screen – Ion AmpliSeq DNA Gene design
  • Draft design screen – Ion AmpliSeq DNA Hotspot design
  • Draft design screen – Ion AmpliSeq RNA Gene Expression design
  • Draft design screen – Ion AmpliSeq RNA Gene Fusion design
  • Results ready screen – custom Ion AmpliSeq designs
  • Start a new AmpliSeq HD design
  • Draft design screen – Ion AmpliSeq HD DNA Gene design
  • Draft design screen – Ion AmpliSeq HD DNA Hotspot design
  • Draft design screen – Ion AmpliSeq HD RNA Gene Fusion design
  • Results ready screen – custom Ion AmpliSeq HD design
• Documentation and support
  • Related documentation
  • Customer and technical support
  • Limited product warranty
• Legal