1. Genome Biology & Applied Bioinformatics Mehmet Tevfik DORAK, MD PhD
SNPs
Mehmet Tevfik DORAK, MD PhD

2. Schedule

3. Individual SNP Analysis Functionality Scores for the Whole Genome
Outline
Individual SNP Analysis
(SNiPA, rVARbase)
Multiple SNP Analysis
(PheGenI, SNPnexus)
eQTL Resources
Browsers
Functionality Scores for the Whole Genome

4. Interpretation of GWAS Findings: Individual SNPs
SNiPA: For individual SNP analysis, SNiPA is a very comprehensive tool. Variant Annotation is the section which provides basic information, conservation and functionality scores (CADD included), eQTL results for multiple tissues, chromatin modifications, GWAS associations and regulatory effects summary. Results can be saved as a single PDF file.

5. Interpretation of GWAS Findings: Individual SNPs
Link:
rVARbase compiles information from a variety of sources mainly for regulatory effects of individual SNPs. Results include CCC analysis, miRNA and lncRNA effects, and downloadable.

6. Interpretation of GWAS Findings: Multiple SNPs
SNPnexus:
Up to 100 thousand SNPs can be analyzed in one go!

7. Interpretation of GWAS Findings: Multiple SNPs
SNPnexus:
Results can be saved as a single Excel file (may be too large for a large number of SNPs).

8. Interpretation of GWAS Findings: Multiple SNPs
PheGenI:
Multiple SNPs can be analyzed in one go, but no more than around 400. Also provides eQTL results, but only for lymphoblastoid cells. Each component of the results is downloadable.

9. Results from multiple tissues from the same persons
eQTL Resources: GTEx
Results from multiple tissues from the same persons
GTEx:
Paper:

10. eQTL Resources: GTEx
Link:

11. eQTL Resources: GTEx
Link:

12. Address: http://www.gtexportal.org/home/bubbleHeatmapPage/ACTN3
eQTL Resources: GTEx
Link:
Address:

13. Address: http://www.gtexportal.org/home/gene/RASSF2
eQTL Resources: GTEx
Address:
Link:

14. eQTL Resources
Link:

15. eQTL Resources
GTEx is not the only eQTL resource. Many others are available and can be reached via

16. eQTL and meQTL Expression Quantitative Trait Locus: eQTL
Methylation Quantitative Trait Locus: meQTL
(most relevant in complex diseases)
* * * *
Non-synonymous (missense) or non-sense mutations directly affect protein structure or translation
(more relevant in Mendelian than complex diseases)

17. BIOS QTL Browser for eQTL/meQTL analysis
Assesses both eQTL and meQTL status of a SNP
BIOS QTL Browser:
Paper:

18. mQTLdb for meQTL analysis Results from five life stages
Paper:

19. Browsers UCSC: http://genome-euro.ucsc.edu
Ensembl:
1KG:
HapMap:
Swiss Regulon:

20. Functionality Scores for the Whole Genome
CADD scores:
DANN scores:
EIGEN scores:
RegulomeDB scores:
dbWGFP Scores:
Pre-computed Structure-PPi scores for COSMIC and 1KG mutations:

21. Functionality Scores for the Whole Genome
Links:
GeneCanyon:
Paper:
22 different annotations corresponding to either conservation score or biochemical activity, including 2 genomic conservation measures, 2 indicators of open chromatin, 8 histone modifications, and 10 TFBS peaks.

22. Functionality Scores for the Whole Genome
Links:
GeneCanyon:
Paper:
22 different annotations corresponding to either conservation score or biochemical activity, including 2 genomic conservation measures, 2 indicators of open chromatin, 8 histone modifications, and 10 TFBS peaks.

23. … Looking forward …..

24. Course material: http://www.dorak.info/genbiol/course.html