agriseq™ targeted gbs panel for determination of canine ...€¦ · new customer facing slide...
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The world leader in serving science
Christopher Adams, Ph.D. Business Development Manager/ Agrigenomics Austin TX
AgriSeq™ Targeted GBS Panel for Determination of Canine Parentage and Genetic Health
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Thermo Fisher Scientific Offers Multiple Genotyping Technologies Across the Application Continuum
New Thermo Fisher Scientific Agrigenomics Business • Started in January 2016, based in Austin (Texas) • Have dedicated R&D resources • Focused on technologies for plant and animal genotyping
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Both STR and SNP Genotyping Approaches for Assessing Parentage Have Merit
Advantages: • Fast <1day • Economical • Simple Disadvantages: • Less Accurate • Subjective data interpretation • Not Scalable (<25 Markers) • Not correlated with phenotypes
Advantages: • Scalable (50-5000 markers/assay) • Flexible
Parentage, Breeding & Inherited Diseases
• High Accuracy Disadvantages: • ~2 day workflow
VS.
Seeing transition from STR-based to SNP-based genotyping
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There are Currently 2 Categories of Genetic Markers Employed for Determining Animal Parentage (Heredity): STRs (Microsatellites) or SNPs (mutations)
Bovine
Equine
Canine
SNPs
SeqStudio Genetic Analyzer Capillary Electrophoresis (Sanger)
Next-Generation Sequencing (NGS)
• New Canine 22-plex STR Genotyping Kit
• New Canine 372 Marker AgriSeq GBS panel for Parentage and Genetic Defects in development
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Excellent multiplexing performance
Fast, high throughput workflow
Customizable and flexible solutions
Ultra low pricing for agricultural
AgriSeq™ Targeted Genotyping by Sequencing Solutions
¢
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Genotyping by Sequencing (GBS) Can Represent Different Technical Approaches
GBS
Targeted GBS
Restriction Enzyme Mediated (RAD-Seq)
Common features: • Complexity of genome reduced
• SNP discovery
Key Differences
Up to 100,000s Number of SNPs interrogated/sample Up to 5,000
Med (20-80%) Consistency of markers called between sample High >95%
Random Types of markers identified Targeted – user selected
Discovery Best fit for … Mapping/Screening
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~ 2 day AgriSeq™ workflow with minimal hands on time
Hands on time <3 hours <15 minutes <15 minutes <15 minutes
96 or 384 format
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AgriSeq GBS has proven performance
Species Markers Sample Call Rate (%) Uniformity (%) On Target Reads
(%) Bovine 190 99.7% 98% 97.6% Canine 229 99.2% 99% 98.8% Feline 62 99.8% 99% 96.6%
Porcine 3000 96.2% 98% 99.3% Soybean 1134 98.3% 97% 98.9%
Cucumber 2804 91.4% 97% 99.7% Maize 1079 87.5% 87% 97.7%
• 50 plus panels designed across 19 Ag species • Excellent genotype call rates across samples & panel sizes • High uniformity & specificity
• >99.9% reproducibility intra and inter run assay • 99.4 % concordance to orthogonal genotyping technologies
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AB AgriSeq™ Target Enrichment Provides Workflow Flexibility
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Pool A (parentage/ traceability)
Pool B (gene defects)
Pooled panels
Additional markers
Panels can be pooled and/or markers can be added (spiked into existing panels) to meet customers needs
Panel Species B
Panel Species A
Libraries from multiple species can be pooled for templating and sequencing to help maximize run efficiency
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• Panels Designed using Canis lupus familiaris (CanFam3.1) reference • Chromosomes: 39 sequences (including X) • Other: 3229 sequences (unplaced scaffolds and mitochondrion)
Summary of Canine Genetic Health/Defects and ISAG Parentage Panels Tested
Background: Defects: Parentage: Combo: Samples Tested 192 192 192 Panel Size (Markers) 143 200 343
Experimental Design
• Combining panels reduces library preparation time and costs
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Genetic Defect Panel Marker Call Rate (97.3%)
Marker
Call
Rate
%
• Majority of markers (133) have >95% call rate
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Canine Parentage Panel Marker Call Rate (97.8%)
Marker
Call
Rate
%
• Majority of markers (200) have >95% call rate
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Combined Genetic Defect & Parentage Panel Marker Call Rate Comparison
Marker
Call
Rate
%
• Markers perform similar regardless of whether stand-alone or combo panel. • Underperforming markers have lower call rates (on average) in the combo panel compared to the stand-alone
panels.
Defect Panel Parentage Panel Combo Panel 97.4% Avg Call Rate
Y-chromosome
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Canine SNP Panel Non-Hot Spot SNPs
• 192 samples run • 514 additional variants identified with varying frequency (1-191) • Average 1133 additional variants identified across samples (22-161)
Num
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var
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Num
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Varia
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per s
ampl
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Num
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var
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Known SNP
Unknown/Known SNP
200bp sequence read
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Summary of Canine Panel Performance
Background: Defect: Parentage: Combo: Samples Tested 192 192 192 Panel Version Tested 2 2 2/2 Panel Size (Markers) 143 200 343 Quality: Reads Per Chip 75 M 83 M 64 M Mapped Reads 98.5 % 99.6 % 99.2 % Mean Read Length 154 bp 162 bp 156 bp Performance: Average Coverage 2389 X 1729 X 806 X Average Call Rate 97.3 % 97.8 % 97.4 % Markers With Call Rate Above 95% 93.0 % 93.0 % 93.0 %
• Panels can be combined without impacting individual panel performance
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Evaluate AgriSeq® GBS genotyping data with your samples for selected panels at no cost to you - get details at the Thermo Fisher Scientific Booth #9
• Bovine ISAG SNP 200 Parentage Panel (2013)
• Canine Neogen Primary and Secondary Panel
The Power of AgriSeq GBS: Experience It On Us
• Sign up times and more details at the booth: • Monday 15:00-17:00 • Tuesday 11:00-13:00 • Wednesday 9:00-12:00 • Friday 8:00-10:00
Interested in other species or markers? Let us scope a custom project for you!
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Summary
Thermo Fisher Scientific is committed to scientific partnership Targeted GBS solutions help improve sample throughput and simplify workflow while reducing cost per sample
• Flexible technology • Custom content
We support the complete Agrigenomics workflow from discovery to production with accurate, robust, fit for purpose technologies
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Marketing Materials – Sales Hub
New Customer Facing Slide Deck New AgriSeq Sales Flyer
Rebranded literature App Notes
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Thermo Fisher R&D: • Angela Burrell • Michelle Swimley • Chris Willis
Bioinformatics • Adam Allred • Prasad Siddavatam
VHL
• Maarten de Groot • Wim van Haeringen
Acknowledgements
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Thanks for your attention!!
[email protected] – Business Development [email protected] Product Management [email protected] - Agrigenomics Business Leader
Key Contacts:
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