Pharmacogenomics & Drug Design

Identification of Disease Genes

CONTACT ME

S.Prasanth Kumar,prasanthbioinformatics@gmail.com
Bioinformatician
ACCESS MY RESOURCES IN SLIDESHARE
S.Prasanth Kumar prasanthperceptron
Dept. of Bioinformatics
Applied Botany Centre (ABC) FOLLOW ME ON
Gujarat University, Ahmedabad, INDIA www.facebook.com/Prasanth Sivakumar
From Scratch

Patient New Symptom

Phenotype

Genotype Molecular Biologist

Bioinformatic
s
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
Molecular Biologist Point of View

Patient developed new symptom

Disease
Collect tissue or cells representing a
KEY POINT developmental stage
A phenotype is Isolate mRNA
expressed by a
Genotype Produce cDNA
Insert this cDNA into a suitable vector
Produce cDNA clones
Sequence these cDNA insert from
either end
Expressed Sequence Tags (ESTs)
Finding a Disease Gene

mRNA
RTase
cDNA clones
cDNA

cDNA inserted into vector RE

EST
Single pass, short 300–500
nucleotide sequences Sequencing
Finding a Disease Gene

Search
Human Genome

ESTs

XYZ gene

KEY POINT XYZ gene

The XYZ gene Results
expresses these XYZ gene
ESTs.
Finding a Disease Gene

XYZ Normal gene

T

XYZ gene variants

Normal T
C
G SNPs
A

Genetics & Pharmacogenomics

To obtain information about the gene(s) causing the phenotype

Unknown EST collected from patient Query

Human Genome

Which BLAST to use ?

MegaBlast

BLAST (human genome) EST matches with a Contig

Genome (reference only) database

Annotated Human Genome Assembly
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_”

Sequencing Projects

Component Sequences

Assembly

Annotated Human Genome Assembly

Compare ESTs to The Human Genome

EST matches with a Contig

a real SNP or a sequencing error

Position 16951392
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
 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)
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
“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
Is the SNP non-synonymous ? GeneView Panel

Gene SNPs
Tyrosine

……..TAC…... Gene
Alternatively Spliced Variants (mRNA) ……..UGC…… mRNA

Cysteine SNP

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
Whether the HFE Gene Variant is Known to Cause a Disease Phenotype

The Cys282Tyr
variant is reported
to be associated
with
hemochromatosis
GeneSeeker

Genes underlying human genetic disorders

Cytogenetic Localization
Phenotype
Expression Patterns

List of Candidate Genes

GeneSeeker Methodology

DB Group-1 Localization dbs (Human)

GeneSeeker Methodology

DB Group-2 Localization dbs (Mouse)

GeneSeeker Methodology

DB Group-3 Phenotype & Expression

Patterns
GeneSeeker Interface
GeneSeeker Result Page
Have a look at this Research Article

* Exhibition for Academic Studies

References

Identification of Disease Genes

It is freely available in HTML format

NCBI Bookshelf

Thank You For Your