Agilent Technologies, Inc. · NYSE:A
Agilent Technologies — Technical Presentation (June 2017)
28 slides from Agilent Technologies's technical presentation, Jun 1, 2017
Slide 1: Advanced Custom NGS Panel Design with SureDesign
Advanced Custom NGS Panel Design with SureDesign Webinar Creating Complex NGS Designs June 1, 2017 PR
Slide 2: Topics for today’s presentation
Topics for today’s presentation For Research Use Only. Not for PR PR7000-0684 use in diagnostic procedures.
Slide 3: Enabling advanced features
Enabling advanced features Login to SureDesign For Research Use Only. Not for PR PR7000-0684 use in diagnostic procedures.
Slide 4: Advanced settings changes workflow
Advanced settings changes workflow Basic settings Advanced settings For Research Use Only. Not for PR PR7000-0684 use in diagnostic procedures.
Slide 5: Topics for today’s presentation
Topics for today’s presentation For Research Use Only. Not for PR PR7000-0684 use in diagnostic procedures.
Slide 6: Probegroups: when and how to efficiently use
Probegroups: when and how to efficiently use • A probegroup is a collection of baits that were designed using the same parameters • Use a probegroup as a sub-design (e.g., all of the genes related to inflammation that might be included in an infectious disease design as well as in a cancer design) •
Slide 7: Topics for today’s presentation
Topics for today’s presentation For Research Use Only. Not for PR PR7000-0684 use in diagnostic procedures.
Slide 8: Design approaches: tiling and probe reuse from other design(s)
Design approaches: tiling and probe reuse from other design(s) Tiling Reuse probes (catalog or custom) • Simple steps to design • More steps in SureDesign • Use performance metrics from previous runs of your design • Agilent catalog designs empirically optimized • Likely increase bait counts conside
Slide 9: Tiling design considerations (long regions)
Tiling design considerations (long regions) Long tiled regions may get covered “too well” in the middle (about 700 bp) 4X tiling 760 reads at peak Remove some of the baits in the center of the region Staggered baits result in fewer reads; more even coverage For Research Use Only. Not for PR PR7000-0
Slide 10: Tiling design considerations (short regions)
Tiling design considerations (short regions) Similarly, tiling short regions may not provide enough coverage (110 bp) Need to add more copies of each bait in shorter regions 16 replicates of each bait to get 56X coverage For Research Use Only. Not for PR PR7000-0684 use in diagnostic procedures.
Slide 11: Topics for today’s presentation
Topics for today’s presentation For Research Use Only. Not for PR PR7000-0684 use in diagnostic procedures.
Slide 12: Optimizing SureSelect designs (design gaps)
Optimizing SureSelect designs (design gaps) • Identify “missed” regions by downloading the design and examining the AllTracks.bed file • Because fragments can extend outside the bait, small regions outside the baits will likely be captured. Don’t be concerned with gaps smaller than 40 bp • Relax the
Slide 13: Optimizing SureSelect designs (performance)
Optimizing SureSelect designs (performance) • If you have an existing design and sequencing performance metrics, you may selectively increase the bait replication factor (individually or probegroup replicates) or selectively delete baits from an existing design (see previous tiling slides) • You may
Slide 14: Optimizing HaloPlex and HaloPlex HS designs
Optimizing HaloPlex and HaloPlexHS designs • SureDesign allows few optimizations for HaloPlex designs within the tool. Most optimizations would have to be performed by Agilent personnel using tools outside of SureDesign. • Use the FFPE design option to add probes to both strands (Illumina). • If amp
Slide 15: Topics for today’s presentation
Topics for today’s presentation For Research Use Only. Not for PR PR7000-0684 use in diagnostic procedures.
Slide 16: Design visualization
Design visualization Or download AllTracks.bed file to view Targets, Covered, and Missed regions and upload into your favorite genome browser UCSC View link at design level shows Covered.bed file for design For Research Use Only. Not for PR PR7000-0684 use in diagnostic procedures.
Slide 17: While on the subject of design files…..simple or catalog designs
While on the subject of design files…..simple or catalog designs Target, Covered, Missing Union of all regions covered by baits Covered.bed ± 100 bp Chromosomal coordinates of targets List of design targets Use Covered.bed for on-target metrics but use Padded.bed file for SNP calling For Research Us
Slide 18: Design files….complex designs with probegroups
Design files….complex designs with probegroups Top level files for design; must create your own padded.bed file from Covered.bed file One set of files per probegroup. If designed hierarchically (use targets and then try to close gaps for same targets), you will have to look at the last probegroup’s
Slide 19: Topics for today’s presentation
Topics for today’s presentation For Research Use Only. Not for PR PR7000-0684 use in diagnostic procedures.
Slide 20: Collaborations and sharing designs
Collaborations and sharing designs • Your custom designs are private; even Agilent field employees cannot see the details nor can anyone else order them • If you wish to share designs with a coworker, collaborator, or an Agilent employee, you must create a collaboration and invite members to join us
Slide 21: Creating a collaboration in SureDesign
Creating a collaboration in SureDesign 1) From Home Screen, Find Designs>SureSelect DNA 2) Click on Collaborations Tab First time message 3) In left panel, select Collaborations>Manage Collaborations 4) Select Add at bottom of screen 5) On next screen, enter Name and Save, Invite using SureDesign lo
Slide 22: Designs can be created in collaboration space
Designs can be created in collaboration space Your default folder or workspace All probegroups must reside in the same workspace or collaboration For Research Use Only. Not for PR PR7000-0684 use in diagnostic procedures.
Slide 23: Topics for today’s presentation
Topics for today’s presentation For Research Use Only. Not for PR PR7000-0684 use in diagnostic procedures.
Slide 24: Tips & Tricks (specifying Targets)
Tips & Tricks (specifying Targets) • Targets can be a mixture of gene names, genomic coordinates, SNP IDs, Entrez IDs • Targets can be cut and pasted into the window • Targets may be in a file that gets Uploaded • After selecting Next, SureDesign translates Targets into Regions which you can immedia
Slide 25: Tips & Tricks (specifying targets)
Tips & Tricks (specifying targets) Coding Regions + UTRs must be selected for noncoding RNAs (antisense tx, lncRNA, Choose databases microRNAs) wisely. Different levels of curation for each database. If UTR specified with all databases selected, the UTR Allow Synonyms should only be regions will use
Slide 26: Tips & Tricks (SureDesign extras)
Tips & Tricks (SureDesign extras) Some SureSelect and HaloPlex catalog design files contain sample data for download HaloPlex designs also contain the QC BioAnalyzer trace PR PR7000-0684
Slide 27: Topics for today’s presentation
Topics for today’s presentation For Research Use Only. Not for PR PR7000-0684 use in diagnostic procedures.
Slide 28: Further information
Further information Register for SureDesign account at link provided in chat (designing or quote requests) 3 ways to create custom designs 1) Design it yourself using SureDesign 2) Consult your local Field Application Scientist 3) Contact Agilent Design Services through your account manager So
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