My presentation at Bioinformatics Got Talent - the first public Bioinformatics Competition and workshop in Egypt to be held at Nile University on 24th of August 2019. Materials are collected from NCBI tutorials, webinars and help pages.

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Gene-Disease Association using
NCBI Gene Database and
Variation Viewer

2. Gene-Disease Association using
NCBI Gene Database and
Variation Viewer
Eng. Asmaa Ali Abdelwahab
B.Sc. in Computer Engineering
Postgraduate Student at Nile University
Data Scientist at Rosettastein Consulting GmbH,
Germany

3. • 3
Agenda
• Why to use NCBI Gene database ?
• How to locate the gene of interest.
• NCBI Gene record.
• Case Study.
• NCBI Variation Viewer.
• Case study.

4. • 4
Why NCBI Gene Database?

5. NCBI Gene Database

6. Locate the gene of interest

7. Gene record

8. Case Study
(NCBI Gene database)

9. • What diseases can be caused by
variations in the tyrosine hydroxylase
gene? Can I get a list of all disease
causing single nucleotide variants that
affect the coding regions with their
positions?
Case Study

10. NCBI Gene Database - Video tutorial

11. NCBI Variation Viewer

12. NCBI Variation Viewer
https://www.ncbi.nlm.nih.gov/clinvar/

13. NCBI Variation Viewer
https://www.ncbi.nlm.nih.gov/variation/view/

14. Case Study
(NCBI Variation Viewer)

15. Our Case Study
• Your collaborator gave you a VCF with 3 suspect variants
from a patient exhibiting a phenotype suggestive of severe
combined immunodeficiency (SCID), suggesting the ADA
gene might be involved. Variant calls made on GRCh37
(hg19), but your collaborator has also provided you with a
VCF in which the results have been remapped to GRCh38
(hg38).
• The patient also suffers from irritable bowel disease (IBD)
• How can you use Variation Viewer to evaluate and
prioritize these variants?
• Is there any evidence to suggest the IBD is associated with
the SCID-like phenotype?

16. NCBI Variation Viewer - Video tutorial

17. Summary: Variant review in Variation Viewer
• Used Variation Viewer to review 3 variant calls in ADA
– 1. discounted as artifact of GRCh37 assembly error.
– 2. candidate SNPs
• Exonic missense variant
• Intronic variant
• Accessed additional data in ClinVar and PubMed to determine
exonic variant is putatively pathogenic and in an ADA mutation
hotspot.
• Used Biological Regions track to identify putative functional
implications for intronic variant.
• Looked for GWAS studies associated with possible secondary
IBD phenotype
– Found strong association of SNP with Ulcerative Colitis

18. THANK YOU!
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