Agrigenomic research is difficult enough without having to coerce software designed for human genetics to work with the plant or animal species you're studying. Not anymore. In this webcast, Greta Linse Peterson will present updated workflows in SNP & Variation Suite 8 (SVS) and GenomeBrowse for agricultural genetic research. SVS includes a robust suite of analytical tools and a revolutionary genome browser in one program to support a wide-variety of species including plant, animal, and parasites. New tools make it easy to adjust for inbreeding and incomplete pedigrees, making it even easier than before to identify variants related to pest and disease resistance, increased feed efficiency, milk production, and more. Topics to be covered include: supported file formats for importing data (including imputation sources like FindHap, Fimpute, and Impute2), comprehensive sequencing and GWAS workflows to take your analysis from QA to finding putative variants or SNPs of interest, common pitfalls to avoid and precautions when working with agrigenomic data, and visualizing results seamlessly in an integrated genome browser.

1. Advancing Agrigenomic
Discoveries with
Sequencing &
GWAS Research
January 8, 2014
Greta Linse Peterson
Director of Product Management and Quality

2. Use the Questions pane in
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Questions during
the presentation

3. Agenda
GWAS for Agrigenomics
Conclusion
2
3
4
DNA-Seq for Agrigenomics
Overview1

4. Agrigenomic Strategic Relationships

5. Core
Features
Packages
Core Features
 Powerful Data Management
 Rich Visualizations
 Robust Statistics
 Flexible
 Easy-to-use
Applications
 Genotype Analysis
 DNA sequence analysis
 CNV Analysis
 RNA-seq differential
expression
 Family Based Association
SNP & Variation Suite (SVS)

6. GenomeBrowse
 Free sequencing visualization tool
 Launched in 2011
 Makes the process of exploring
DNA-seq and RNA-seq pile-up and
coverage data intuitive and powerful
 Stream public annotations via the
cloud
 Use it to validate variant calls, trio
exploration, de Novo discovery, and
more

7. Merging of Two Great Products

8. Species Supported
 Bovine
 Canine
 Equine
 Gallus gallus
 Mus musculus
 Ovine
 Porcine
 Rhesus macaque
 And over 16 more
plant and animal
genomes

9. Agenda
Conclusion
2
3
4
DNA-Seq for Agrigenomics
1 Overview
GWAS for Agrigenomics

10.  Sheep HapMap
SNP50_Breedv1 dataset
 Illumina 50k SNP array
 49,034 markers were left
after filtering by the
consortium
 110 unmapped markers
 Only 1 marker in Chr Y
First a little about the dataset…

11. GWAS Workflow
Phenotype Distribution
Sample Quality
SNP Quality
Population Structure
Correlation/Trend Test
Linear Regression with
PCA Correction
EMMAX (Mixed Linear
Model Analysis)
QQ Plots
Manhattan Plots and
Annotation Sources in
GenomeBrowse
Quality Assurance Analysis Visualization

12. [Demonstration]

13. [Poll]

14. Agenda
Conclusion
2
3
4
DNA-Seq for Agrigenomics
1 Overview
GWAS for Agrigenomics

15.  2 Bovine Partial Exomes +
1 Bison Partial Exome
 All female
 From Sequence Read
Archive (SRP007095)
 Illumina Genome
Analyzers for sequencing
 GATK for alignment and
variant calling
 UMD_3.1 Reference
Sequence
First a little about the dataset…

16. DNA-Seq Workflow – Unrelated Samples
Alternate Read Ratio
Read Depth
Genotype Quality
Exon Region Filter
Examine Variant Sharing
Between Samples
Sample Pattern Filtering
Variant Classification
Candidate Variants
VCFs
BAMs
Annotation Sources
Quality Assurance
Filtering and
Analysis
Interrogation

17. [Demonstration]

18. Agenda
Conclusion
2
3
4
DNA-Seq for Agrigenomics
1 Overview
GWAS for Agrigenomics

19. Questions or
more info:
 Email
info@goldenhelix.com
 Request an evaluation of
the software at
www.goldenhelix.com

20. Questions?
Use the Questions pane in
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