Exploring genomic databases: Practical session "

Transcription

1 Exploring genomic databases: Practical session Work through the following practical exercises on your own. The objective of these exercises is to become familiar with the information available in each database and how to access it. We will look at automated variant annotation in the next session.

2 (1) EXPLORING ALLELE FREQUENCY Search for rs in the ExAC, ESP6500 and dbsnp databases Which populations are allele frequency data available for in each of the databases? Does this SNP have the same allele frequency distribution in all populations? Compare allele frequency data across the different databases Is it the same? If it s different, can you explain why? Which genome build co-ordinates does each database use to describe the SNP s chromosomal location? Why is this important to know when exploring SNPs from your.vcf file?

3 (2) EXPLORING GENOMIC CONTEXT Search for rs in dbsnp and Ensembl What are the Reference and Alternate alleles for this SNP? Does this SNP fall within a coding region of the genome? (i.e. is it exonic, intronic, intergenic etc?) What is the closest gene? Does this SNP result in an amino acid change or is it synonymous? What is the genomic function of this SNP? You have a novel variant (no dbsnp ID!) in your.vcf file which you want to explore using it s chromosomal co-ordinates. You used hg19 as the reference genome for your alignment. Using Ensembl, how do you figure out which gene it is in?

4 (3) EXPLORING VARIANT FUNCTION Explore the following.vcf file record in SIFT: hp://si(.jcvi.org/www/sift_chr_coords_submit.html CHROM POS ID REF ALT QUAL FILTER C T 8857 PASS Click here to check the required format for submivng your SNP (Be sure to check which genome build co-ordinates you need the one above is GRCh37) Before submivng, scroll down to OUTPUT OPTIONS: Select any addi\onal informa\on you want in the output Click through to the Results page Click on View results for the complete dataset

5 (3) EXPLORING VARIANT FUNCTION The SNP at position 19: is rs Check that the dbsnp id SIFT returned is correct? What is the SIFT score and prediction? Look up this SNP in Ensembl. Click through to the See all predicted consequences tab. Does the SIFT score prediction match that returned by SIFT directly?

6 (3) EXPLORING VARIANT FUNCTION Check the functional prediction for this same variant in PolyPhen-2 using the dbsnp rs ID: hp://gene\cs.bwh.harvard.edu/pph2/ When the job status changes to Completed, click through to View under results

7 (3) EXPLORING VARIANT FUNCTION What is the score and func\onal predic\on returned for this SNP? Click on the + next to HumVar. Is the output different to HumDiv? Why? If you are inves\ga\ng this SNP as part of a study on the genomics of Myocardial Infarc\on (a mul\factorial condi\on), which score would you use? How confident would you be with this predic\on? Is it similar to that predicted by SIFT? Does it match the PolyPhen score reported in Ensembl?

8 Expected SIFT results: (3) EXPLORING VARIANT FUNCTION Expected PolyPhen-2 results:

9 (3) EXPLORING VARIANT FUNCTION rs is a UTR variant (20: ; A/G) in the GDF5 gene that is associated with osteoarthritis Use Ensembl to find the SIFT and PolyPhen-2 scores for this variant. Can you explain this result? Use the non-coding algorithm from FATHMM to predict the functional consequence of this variant. Click here to check the required format you need to submit your SNP

10 (3) EXPLORING VARIANT FUNCTION On the results page, scroll down to see the output What is the non-coding score for this variant? You will see leer codes under the Non-coding groups. Go back to the input page, and follow the steps below to find out what the codes indicate. Click on the Help tab Click on Predic\on Interpreta\on and read the documenta\on explaining the codes and scores

11 (3) EXPLORING VARIANT FUNCTION Search for rs in RegulomeDB Click through to the results here What does this RegulomeDB score mean? Scroll down to the Protein binding and motifs tabs Is this SNP in a region associated with protein binding? Is this SNP located in a transcription factor binding site?

12 (3) EXPLORING VARIANT FUNCTION Go to the SNPedia homepage: hps:// Scroll down to the Popular sec\on and click through to a SNP of interest What gene is this variant located in? What is the genomic context of the SNP? Scroll through the text snippets and click through (using the PMID link) to the PubMed entry of an interes\ng publica\on. Scroll down to Categories. Which SNP chips is this SNP included on?

13 (3) EXPLORING VARIANT FUNCTION Look at the informa\on panel on the right: What is the rela\onship between genotype & phenotype? Click through to Mag to read more about the measure of magnitude for this SNP Click through to the cross-referenced page for: - pharmgkb to inves\gate PGx associa\ons - ExAC to inves\gate popula\on specific allele frequencies - GWAS Ctlg to see if it has been implicated in any GWAS findings

14 (3) EXPLORING VARIANT FUNCTION Search for rs6025 in PharmGKB hps:// Explore the Clinical PGx associa\ons with this SNP Click on the? in the level of evidence block to explore the evidence annota\ons

15 (3) EXPLORING VARIANT FUNCTION Search for rs6025 in PharmGKB hps:// Explore the PGx research publica\ons which cite this SNP How many different publica\ons in PubMed refer to PGx effects in this SNP? Click through to the 1 st entry to read about the observed associa\on in more detail

16 (4) EXPLORING CANDIDATE GENES Search for the APOE gene in OMIM What phenotypes are associated with this gene? What is the inheritance paern for these phenotypes? Click through to explore the different categories of phenotypes associated with this gene. Are there any cardiovascular phenotypes associated with this gene?

17 (4) EXPLORING CANDIDATE GENES Click through to Descrip\on on the le( What is the molecular basis of human apolipoprotein E polymorphisms? Click through to popula\on gene\cs on the le( Are there any popula\on specific allele distribu\ons in this gene?