How will you identify gene for a particular disease in silico . this is described here

1. S.Prasanth Kumar, Bioinformatician Identification of Disease Genes Pharmacogenomics & Drug Design S.Prasanth Kumar, Bioinformatician S.Prasanth Kumar Dept. of Bioinformatics Applied Botany Centre (ABC) Gujarat University, Ahmedabad, INDIA www.facebook.com/Prasanth Sivakumar FOLLOW ME ON ACCESS MY RESOURCES IN SLIDESHARE prasanthperceptron CONTACT ME [email_address]

2. From Scratch Patient New Symptom Phenotype Genotype Molecular Biologist Bioinformatics

3. Note of Caution !!! Before we progress You are entitled to study the following programs/tools/web server and its working methodology NCBI – Entrez GenBank BLAST and its types MapViewer OMIM dbSNP And other available programs of NCBI

4. Molecular Biologist Point of View KEY POINT A phenotype is expressed by a Genotype Patient developed new symptom Disease Collect tissue or cells representing a developmental stage Isolate mRNA Produce cDNA Insert this cDNA into a suitable vector Produce cDNA clones Sequence these cDNA insert from either end Expressed Sequence Tags (ESTs)

5. Finding a Disease Gene EST Single pass, short 300–500 nucleotide sequences cDNA clones cDNA inserted into vector cDNA RTase mRNA RE Sequencing

6. Finding a Disease Gene Human Genome Search ESTs Results XYZ gene XYZ gene XYZ gene KEY POINT The XYZ gene expresses these ESTs.

7. Finding a Disease Gene XYZ Normal gene T XYZ gene variants C A G T SNPs Normal Genetics & Pharmacogenomics

8. To obtain information about the gene(s) causing the phenotype Unknown EST collected from patient Human Genome Which BLAST to use ? BLAST (human genome) Genome (reference only) database Annotated Human Genome Assembly MegaBlast EST matches with a Contig Query

9. What is a Contig ? NCBI assembles component sequences from the human genome sequencing project into longer sequences called contigs whose accession numbers begin with prefix “NT_” Annotated Human Genome Assembly Component Sequences Sequencing Projects Assembly

10. Compare ESTs to The Human Genome EST matches with a Contig a real SNP or a sequencing error Position 16951392

11. Identify the Genes Expressing the ESTs “ Known” genes annotated by alignment of EST and/or mRNA sequences to the assembly The assembled genome contig sequence in the region The Ab initio model genes predicted by the NCBI’s program Gnomon The alignments of the known alternatively spliced transcripts

12. Genes_seq Map as a master map Exons Introns BLAST hit HFE gene Arrow downward = forward strand Arrow upward = reverse strand The HFE gene is annotated on the forward strand of chromosome 6 sv (Sequence Viewer), pr (Reference Proteins), dl (Download Sequence), ev (Evidence Viewer), mm (Model Maker), and hm (Homologene)

13. Variation Map as a master map SNPs Can you tell which SNPs corresponds to Exons and Introns ? Click any of the links and obtain information about the location and the nucleotide variation

14. “ Fasta sequence” and “Integrated maps” panels SNP entry rs1800562 The location of the SNP, nucleotide position 16951392 on the contig NT_007592.14 of the reference assembly

15. Is the SNP non-synonymous ? GeneView Panel The query EST sequence contains a known SNP in the HFE gene that results in a cysteine to tyrosine change in the 282nd amino acid (Cys282Tyr) of the protein expressed by the longest HFE transcript variant Gene Alternatively Spliced Variants (mRNA) SNPs …… ..TAC…... …… ..U G C…… Gene mRNA SNP Tyrosine Cysteine

16. Whether the HFE Gene Variant is Known to Cause a Disease Phenotype The Cys282Tyr variant is reported to be associated with hemochromatosis

17. GeneSeeker Cytogenetic Localization Phenotype Expression Patterns Genes underlying human genetic disorders List of Candidate Genes

18. GeneSeeker Methodology DB Group-1 Localization dbs (Human)

19. GeneSeeker Methodology DB Group-2 Localization dbs (Mouse)

20. GeneSeeker Methodology DB Group-3 Phenotype & Expression Patterns

21. GeneSeeker Interface

22. GeneSeeker Result Page

23. Have a look at this Research Article * Exhibition for Academic Studies *

24. References Identification of Disease Genes Thank You For Your Attention !!! It is freely available in HTML format NCBI Bookshelf