Sneak peak at SNP III presentation

1. SNP Workshop III

2. NGS and SNP Discovery

3. NGS and SNP Discovery
!

4. Challenges

5. Sharing

6. NGS and SNP Discovery

7. NGS and SNP Discovery

8. NGS and SNP Discovery
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9. NGS and SNP Discovery
credit: NOAA

10. SNP Discovery in Pacific herring using 454
transcriptome sequencing
Steven Roberts, Jim Seeb, Lisa Seeb, Lorenz Hauser,
University of Washington
School of Aquatic and Fishery Sciences
William Templin
Alaska Division of Fish and Game
Division of Commercial Fisheries
Exxon Valdez Oil Spill Trustee Council

11. Credit: EXXON VALDEZ Oil Spill Trustee Council

12. Prince
Togiak William Sound
Kodiak
Sitka

13. Approach
• Pooled Individuals to
generate 2 libraries
• Liver
• Testes
• De novo Assembly
• Annotation
• SNP Discovery

14. Sequencing Output (combined)
Reads: 1.9 million
Average Length: 272 bp
Matched: 1.7 million
Contigs: 47,267
Average Length of
Contigs: 728 bp

15. Comparing Tissues
10622 features
not expressed
in Liver
14190 features
not expressed
in Testes

16. Annotation (combined)
!

17. SNP Discovery
16,000 SNPs
per library - ~9300 SNPs
Annotation of
= corresponding
features
!
!
all features

18. transversions transitions
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19. transversions transitions
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tinyurl.com/herringSNP

20. Targeting SNPs
xenobiotic response

21. Synonymous and NonSynonymous workflow
consensus EMBOSS
sequences getorf
SNP reference
Detection assembly
2514 NonSynonymous
Annotate Filter based
SNP Positive
on e-value
Features 7017 SNPs

22. Synonymous and NonSynonymous workflow
2514 NonSynonymous

23. NonSynonymous

24. NonSynonymous
stress response