This document discusses single nucleotide polymorphisms (SNPs) and methods for identifying and analyzing them. It defines SNPs as variations in a single nucleotide that can differ between members of a species. Several methods are described for identifying known and new SNPs, including gel electrophoresis, mass spectrometry, and DNA sequencing. SNPs can serve as biological markers and help locate genes associated with diseases. While they provide useful information, SNPs have less informative power than other genetic markers due to fewer alleles.

1. SERBT- 3.2:-OMICS:GENOMICS,TRANSCRIPTOMICS, PROTEOMICS AND BIOINFORMATICS
A SEMINAR ON
CONSTRUCTION OF SNP LINKAGE MAP
Presenter:
NARASIMHA MURTHY S V
MSc 3rd SEMESTER
SERICULTURE AND SERIBIOTECHNOLOGY
DOS IN SERICULTURE SCIENCE
MANASAGANGOTRI MYSURU-06
REG NO:SS200018
Guide:
DR.H.B.MANJUNATHA
PROFESSOR AND CHAIRMAN
DOS IN SERICULTURE SCIENCE
MANASAGANGOTRI MYSURU

2.  INTRODUCTION
 SOME FACTS
 TYPES OF SNPs
 METHODS OF IDENTIFICATION SNPs
 SNP ANALYSIS
 ADVANTAGES OF SNPs
 DISADVANTAGES OF SNPs
 SUMMARY
 REFERENCES

3.  A SNP is defined as a single base change in a DNA sequence that
occurs in a significant proportion (more than 1 percent) of a large
population.
• Polymorphism is a generic term that means ‘many shapes’
• It is the ability to appear in different form.
What is SNP ?
POLYMORPHISM
INTRODUCTION
In genetics,
 A single-nucleotide polymorphism (SNP) is a germline substitution
of a single nucleotide at a specific position in the genome.

4.  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).
 Single nucleotide polymorphisms or SNP, are the most common type
of genetic variation among species.

5.  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
haemophilia).
-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).

6. TYPES OF SNPs
Non coding region Coding region
Synonymous Non- Synonymous
Missense Nonsense

7. 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.
Synonymous
A SNP in which both forms lead to the same polypeptide sequence is termed
synonymous (sometimes called a silent mutation).

8. 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..
 Missense
In genetics, a missense mutation is a point mutation in which a single
nucleotide change results in a codon that codes for a different amino acid. It is a
type of nonsynonymous substitution.
 Nonsense
In genetics, a nonsense mutation is a point mutation in a sequence of DNA that
results in a premature stop codon, or a nonsense codon in the transcribed mRNA,
and in a truncated, incomplete, and usually nonfunctional protein product.

9.  SNPs are found in - coding and (mostly) noncoding 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. Methods of Identification SNPs
A) Detection of known SNPs
B) Identification of new SNPs
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.

11. b) Non-gel-based high through put genotyping technologies
1.Hybridization using fluorescence resonance energy transfer detection
(TaqMan genotyping, Molecular beacons).
2.High-density chip array.
B)Identification of new SNPs
It involves two steps:
1- Conformation-based mutation scanning.
2- Direct DNA sequencing.

12. RNA is taken from each individual (particular gene).
cDNA
PCR
Electrophoresis of each PCR product
Gel extraction
Sequencing (Sanger di-deoxy method).
Development of SNPs in direct sequencing method

13.  Reverse Dot Blots
 Direct Sequencing
 HPLC Genotyping
 TaqMan Assay
 Fluorescence Polarization (FP)
 Mass Spectrometer
 Microchips
 Pyrosequencing
 Allele Specific Hybridization
SNP GENOTYPING

14.  DNA sequencing.
 Mass spectrometry.
 Single-strand conformation polymorphism (SSCP).
 Electrochemical analysis.
 Capillary electrophoresis.
 Denaturating HPLC and gel electrophoresis.
 Restriction fragment length polymorphism.
 Hybridization analysis.
SNP analysis
Analytical methods to discover novel SNPs and detect known SNPs include:

15. It is a method for separation and analysis of
macromolecules and their fragments Nucleic acid
molecules are separated by applying an electric field to
move the negatively charged molecules through a matrix
of agarose or other substances.
Shorter molecules move faster and migrate farther than
longer ones.
This phenomenon is called sieving.
Procedure:
Step 1:-Place DNA into tubes...
Step 2:-The polymerase chain reaction uses a machine
called thermocycler to quickly copy a piece of DNA.
GEL ELECTROPHORESIS

17. Step 3:- Place restriction enzyme will cut DNA into different sizes according to its
sequence.
Step 4:- Dye DNA and add into gel, the gel is made of agarose.
Step 6:-DNA is negatively charged and hence will move towards the positive
charged end of the gel. Smaller pieces of DNA travel faster than larger
pieces of DNA.
Step 5:- Run electric current through gel.

18. Single-Strand Conformation Polymorphism
1) Polymerase chain reaction (PCR) amplification of DNA sequence of
interest.
2) Denaturation of double-stranded PCR products.
3) Cooling of the denatured DNA (single-stranded) to maximize self-
annealing;
4) Detection of mobility difference of the single-stranded DNAs by
electrophoresis under non-denaturing conditions.
5) Several methods have been developed to visualize the SSCP mobility
shifts.
Procedure:

19.  SNPs are the most frequent form of variation.
 They are disease causing mutations in many genes.
 They are abundant and slow mutation rates.
 May work as the next generation of genetic markers.
MEDICATION & DIAGNOSIS AT INDIVIDUAL LEVEL
 IN DISEASE DIAGNOSIS.
 IN DRUG DISCOVERY & DEVELOPMENT.
 IN DRUG RESPONSE INVESTIGATION OF MIGRATION PATTERNS.
Advantages of SNPs

20.  Less alleles.
 Each marker is less informative.
 Therefore have to genotype many more SNPs to get same level of
information about DNA sample.
A wide range of diseases occurred by this in humans
 Sickle cell anaemia
 B thalassemia
 Diabetes
Disadvantages of SNP

21. • 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.

22.  Molecular Cell Biology
By Harvey Lodish, Arnold Berk, Chris A. Kaiser, Monty
Krieger, Anthony Bretscher, Hidde Ploegh, Angelika
Amon, Kelsey C. Martin · 2016
 https://www.genome.gov/genetics-glossary/Single-Nucleotide-
Polymorphisms
 https://en.wikipedia.org/wiki/Single-nucleotide_polymorphism
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