Single Nuclotide Polymorphism (snps) By Sujata Dandale Deptt of Pplant Pathology, PDKV,Akola

2. Department of Plant Pathology ,
Dr. Panjabrao Deshmukh Krishi Vidyapeeth, Akola (MH)
444104
Doctoral Seminar
Single Nucleotide Polymorphism
On
Course Title : Doctoral Seminar Ist
Course Credit : 0+1
Seminar In charge
Dr. S. S. Mane
PRESENTED BY
Dandale Sujata Nandkumar
Ph. D (Agri.) 2nd Year

3. Advisory Committee
• Chairman Dr. S. S. Mane
• Member Dr. S. T. Ingle
• Member Dr. R. S. Nandanwar
• Member Dr. A. N. Patil
• Member Dr. P. V. Jadhav

4. Content
• Introduction
• Characteristics of SNP
• SNP as genetic markers
• Emergence of SNPs in genetic analysis
• Types Of SNP
• SNP Genotyping
• Effect of SNP
• Advantages
• Disadvantages
• Use and importance of SNPs
• Application
• Conclusions

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

6. INTRODUCTION
• It pronounced as “snips”.
• And are the most common type of genetic
variation among peoples.
• SNP: Commonly biallelic
• Each SNP represents a difference in a single DNA
building block, called a nucleotide
• A single nucleotide polymorphism (SNP) is a DNA
sequence variation occurring when a single
nucleotide - A, T, C, or G - in the genome differs
between members of a species (or between
paired chromosomes in an individual).
A. A. Komar , H. Press,2009

7. • Single nucleotide polymorphisms
or SNP, are the most common
type of genetic variation among
species.
• Each SNP represents a
difference in a single DNA
building block, called a
nucleotide .
• For example, two sequenced
DNA fragments from different
individuals, AAGCCTA to
AAGCTTA, contain a difference
in a single nucleotide .

8. CHARACTERISTICS OF SNP
• 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, and
hemophilia).

9. SNP AS GENETIC MARKERS
• 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.

10. • Abundance :The high frequency with which SNPs
are found on the genome gives them definite
utility for trait or disease gene discovery purposes.
• Position :SNPs are found throughout the genome,
e.g. in exons, introns, intergenic regions, in
promoters or enhancers.
• Origins and haplotypic patterns: Because new
SNP alleles arise as mutations at different loci
and at different points in time, and because they
occur with such great abundance over the
genome, groups of neighboring SNPs may have
alleles that show distinctive patterns of linkage
disequilibrium
Emergence of SNPs in genetic analysis

11. • Ease of genotyping : Because of their simple
structure as base changes, microarray .
• Allele frequency drift : SNPs will have allele
frequencies that will ‘drift’ as a function of the
dynamics of different populations.
• Less mutable: SNPs generally are less mutable
than other forms of polymorphism
Schork et al,2000

12. TYPES OF SNP

13. 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

14. 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.
Khlestkina, Salina ,2006

15. • •Reverse Dot Blots
• •Direct Sequencing
• •HPLC Genotyping
• •TaqMan Assay
• •Fluorescence Polarization (FP)
• •Mass Spec
• •Microchips
• •Pyrosequencing
• •Allele Specific Hybridization
• •SNaPshot
SNP GENOTYPING

16. Development of snp
( DIRECT SEQUENCING METHOD)
A B C (individuals)
xa,ya,za xb,yb,zb xc,yc,zc.
(genes)

17. RNA is taken from each individual.( particular gene)
cDNA
PCR
Electrophoresis of each PCR product.
Gel extraction
Sequencing (Sanger di-deoxy method.)

18. Sanger di-deoxy method

20. Alignment of the sequence
• For alignment of the genes a bioinfomatics tool
BLAST (Basic Local Alignment Search Tool) is
used.
• Xa = AAGCCTAGATAGCT.
• XB = AAGCTTAGATAGCT.
• XC = AAGCATAGATAGCT.

21. Taq Man Assay
•Uses a probe that binds to center of DNA sequence
you are amplifying
•Probe contains both:
–Reporter dye
–Quencher dye –stops reporter from fluorescence
•Whenever two dyes break apart ,we see
fluorescence of reporter dye
•Probe is allele specific so that it will only break upon
copying exact DNA sequence

23. Microchips
• Silicon chip has thousands of oligo probes attached
to it.
-Exact position of each probe is known
-Probes are allele specific
• PCR products are labeled with fluorescent dyes.
• Washed over microchips.
• Product will bind to specific probe based on
complimentary base pairing –Position of label will
show which probe bound.

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

27. ADVANTAGES
• It is a co- dominant marker. They will
identify one allele in homozygous individual
and two alleles in heterozygous individual.
• PCR products can be very small:–Markers
will work with extremely degraded DNA
samples.
• More common in genome.
• Sample processing may be completely
automated.

28. • They are neutral markers. They are not under
selective pressure.
• They are stable markers. They are found in all
proportion of population.
• They are independent markers. They are not
linked they assort independently or randomly
among mendalian traits.
• They are multiallelic and they are controlled by
more than one allele.
• Small amount of DNA is required. No radioactive
isotopes are used.

29. DISADVANTAGES
• Its PIC (polymorphic information content)
is lower than microsatellite markers because,
it is a bi-allelic.
• Technical expertise is required.
• Developmental and genotyping are very
costly.

30. 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

31. APPLICATION
• Genetic variation between the members of
same species.
• Gene discovery and mapping.
• Diagnostics/risk profiling.
• Response prediction.
• Homogeneity testing/study design.
• Gene function identification.

32. • Single nucleotide polymorphisms (SNPs) are
the most abundant type of molecular genetic
marker and can be used for producing high-
resolution genetic maps, marker-trait
association studies and marker-assisted
breeding.

34. CONCLUSIONS
• 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.
• Also, check the molecular variability among different
isolates.
• Also studied expression profile of gene .