Snp

1. “SINGLE NUCLEOTIDE
POLYMORPHISM”
PRESENTED BY
SAIMA FAZAL
BS MT 3
RD
YEAR 6
TH
SEMESTER

2. POLYMORPHISM
•Polymorphism is a generic term that
means 'many shapes‘
•It is the ability to appear in different form

3. SINGLE NUCLEOTIDE POLYMORPHISM
•Single nucleotide polymorphisms or SNP
(pronounced “snips”), are the most common type
of genetic variation among peoples.
•Each SNP represents a difference in a single
DNA building block, called a nucleotide

4. •It is a DNA sequence
variation occurring when a
single nucleotide A, T, C, or
G in the genome differs
between members of a
species
•For example, two sequenced
DNA fragments from different
individuals, AAGCCTA to
AAGCTTA, contain a
difference in a single
nucleotide

6. Some Facts
•In human beings, 99.9 percent bases are same.
•Remaining 0.1 percent makes a person unique.
–Different attributes / characteristics / traits
•how a person looks,
•diseases he or she develops.
•These variations can be:
–Harmless (change in phenotype)
–Harmful (diabetes, cancer, heart disease,
Huntington's disease, and hemophilia )
–Latent (variations found in coding and regulatory
regions, are not harmful on their own, and the change
in each gene only becomes apparent under certain
conditions e.g. susceptibility to lung cancer)

7. SNPs facts
•SNPs are found in
–coding and (mostly) non coding regions.
•Occur with a very high frequency
–about 1 in 1000 bases to 1 in 100 to 300 bases.
•The abundance of SNPs and the ease with which they
can be measured make these genetic variations
significant.
•SNPs close to particular gene acts as a marker for that
gene.
•SNPs in coding regions may alter the protein structure
made by that coding region.

8. SNP MAPPING
•Sequence genomes of a large number of people

•Compare the base sequences to discover SNPs.
•Generate a single map of the human genome
containing all possible SNPs

9. TYPES OF SNP
Following are the types of
SNP
•Non-coding region
•Coding region
–Synonymous
–Non synonymous
•Missense
•Nonsense

10. NON-CODING REGION
A segment of DNA that does comprise a gene and
thus does not code for a protein .
CODING REGION
Regions of DNA/RNA sequences that code
for proteins

11. Synonymous
A SNP in which both forms lead to the same
polypeptide sequence is termed synonymous
(sometimes called a silent mutation).
Non synonymous
If a different polypeptide sequence is produced they
are non synonymous . A non synonymous change
may either be missense or nonsense, where a
missense change results in a different amino acid,
while a nonsense change results in a premature
stop codon.

12. Effect of SNP
Silent
Alter the function of the protein
• Directly : alter an amino acid sequence
• indirectly : alter the function of the
regulatory sequence

13. Role of SNPs in Disease predisposition
•The Common disease are multifactorial
•The Genetic differences between human
populations make one population more
susceptible to particular disease.

14. SNPs and Cancer
•SNPs in genes involved in DNA repair and drug
metabolizing enzymes which responsible for
metabolism & detoxification of Carcinogens can act
as cancer susceptibility genes
Through
•Increase activation of chemical carcinogens
•Decrease ability of cells to detoxify & repair
mutagenic damage

15. A) Detection of known SNPs
B) Identification of new SNPs
Methods of identification SNPs

16. Detection of known SNPs
a) Gel-Based genotyping methods
1-PCR with restriction enzyme coupled analysis.
2-Amplification refractory mutation system (ARMS).
3-Oligonucleotide ligation assay.
4-Minisequencing.

17. Detection of known SNPs
b) Non-Gel-based High throughput Genotyping
Technologies
1- hybridization using fluorescence resonance
energy transfer detection (TaqMan genotyping,
Molecular beacons).
2- High-density chip array.

18. B)Identification of new SNPs
It involves two steps:
1- Conformation-based mutation scanning.
2-Direct DNA sequencing.

19. Conformation-based mutation scanning
•Single-strand conformation polymorphism
(SSCP).
•most widely used methods.
Principle:
Single strand DNA tend to fold into complex
structure which determines the mobility of the
DNA strand in non denaturating gel.

20. Use and importance of SNPs
•Variations in the DNA sequences of humans can
affect how humans develop diseases and
respond to pathogens, chemicals, drugs,
vaccines, and other agents.

•SNPs are also thought to be key enablers in
realizing the concept of personalized medicine

21. SNP Applications
•Gene discovery and mapping
•Association-based candidate polymorphism
testing
•Diagnostics/risk profiling
•Response prediction
•Homogeneity testing/study design
•Gene function identification

22. summary
•A single-nucleotide polymorphism is a DNA sequence
variation occurring when a single nucleotide genome
differs between members of a species.
•They can act as biological markers, helping scientists
locate genes that are associated with disease. When
SNPs occur within a gene or in a regulatory region near
a gene, they may play a more direct role in disease by
affecting the gene’s function.