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  2. 2. POLYMORPHISM <ul><li>Polymorphism is a generic term that means 'many shapes‘ </li></ul><ul><li>I t is the ability to appear in different form </li></ul>
  3. 3. SINGLE NUCLEOTIDE POLYMORPHISM <ul><li>Single nucleotide polymorphisms or SNP (pronounced “snips”), are the most common type of genetic variation among peoples. </li></ul><ul><li>Each SNP represents a difference in a single DNA building block, called a nucleotide </li></ul>
  4. 4. <ul><li>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 </li></ul><ul><li>For example, two sequenced DNA fragments from different individuals , AAGC C TA to AAGC T TA, contain a difference in a single nucleotide </li></ul>
  5. 6. Some Facts <ul><li>In human beings, 99.9 percent bases are same . </li></ul><ul><li>Remaining 0.1 percent makes a person unique. </li></ul><ul><ul><li>Different attributes / characteristics / traits </li></ul></ul><ul><ul><ul><li>how a person looks, </li></ul></ul></ul><ul><ul><ul><li>diseases he or she develops. </li></ul></ul></ul><ul><li>These variations can be: </li></ul><ul><ul><li>Harmless (change in phenotype) </li></ul></ul><ul><ul><li>Harmful (diabetes, cancer, heart disease, Huntington's disease, and hemophilia ) </li></ul></ul><ul><ul><li>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 ) </li></ul></ul>
  6. 7. SNPs facts <ul><li>SNPs are found in </li></ul><ul><ul><li>coding and (mostly) non coding regions. </li></ul></ul><ul><li>Occur with a very high frequency </li></ul><ul><ul><li>about 1 in 1000 bases to 1 in 100 to 300 bases. </li></ul></ul><ul><li>The abundance of SNPs and the ease with which they can be measured make these genetic variations significant. </li></ul><ul><li>SNPs close to particular gene acts as a marker for that gene. </li></ul><ul><li>SNPs in coding regions may alter the protein structure made by that coding region. </li></ul>
  7. 8. SNP MAPPING <ul><li>Sequence genomes of a large number of people </li></ul><ul><li>Compare the base sequences to discover SNPs. </li></ul><ul><li>Generate a single map of the human genome containing all possible SNPs </li></ul>
  8. 9. TYPES OF SNP <ul><li>Following are the types of SNP </li></ul><ul><li>Non-coding region </li></ul><ul><li>Coding region </li></ul><ul><ul><li>Synonymous </li></ul></ul><ul><ul><li>Non synonymous </li></ul></ul><ul><ul><ul><li>Missense </li></ul></ul></ul><ul><ul><ul><li>Nonsense </li></ul></ul></ul>
  9. 10. <ul><li>NON-CODING REGION </li></ul><ul><li>A segment of DNA that does comprise a gene and thus does not code for a protein . </li></ul><ul><li>CODING REGION </li></ul>Regions of DNA/RNA sequences that code for proteins
  10. 11. <ul><li>Synonymous </li></ul><ul><li>A SNP in which both forms lead to the same polypeptide sequence is termed synonymous (sometimes called a silent mutation ). </li></ul><ul><li>Non synonymous </li></ul><ul><li>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 . </li></ul>
  11. 12. Effect of SNP <ul><li>Silent </li></ul><ul><li>Alter the function of the protein </li></ul><ul><li>Directly : alter an amino acid sequence </li></ul><ul><li>indirectly : alter the function of the regulatory sequence </li></ul>
  12. 13. Role of SNPs in Disease predisposition <ul><li>The Common disease are multifactorial </li></ul><ul><li>The Genetic differences between human populations make one population more susceptible to particular disease. </li></ul>
  13. 14. SNPs and Cancer <ul><li>SNPs in genes involved in DNA repair and drug metabolizing enzymes which responsible for metabolism & detoxification of Carcinogens can act as cancer susceptibility genes </li></ul><ul><li>Through </li></ul><ul><li>Increase activation of chemical carcinogens </li></ul><ul><li>Decrease ability of cells to detoxify & repair mutagenic damage </li></ul>
  14. 15. <ul><li>A) Detection of known SNPs </li></ul><ul><li>B) Identification of new SNPs </li></ul>Methods of identification SNPs
  15. 16. Detection of known SNPs <ul><li>a) Gel-Based genotyping methods </li></ul><ul><li>1-PCR with restriction enzyme coupled analysis. </li></ul><ul><li>2-Amplification refractory mutation system (ARMS). </li></ul><ul><li>3-Oligonucleotide ligation assay. </li></ul><ul><li>4-Minisequencing. </li></ul>
  16. 17. Detection of known SNPs <ul><li>b) Non-Gel-based High throughput Genotyping Technologies </li></ul><ul><li>1- hybridization using fluorescence resonance energy transfer detection (TaqMan genotyping, Molecular beacons). </li></ul><ul><li>2- High-density chip array. </li></ul>
  17. 18. B)Identification of new SNPs <ul><li>It involves two steps: </li></ul><ul><li>1- Conformation-based mutation scanning. </li></ul><ul><li>2-Direct DNA sequencing. </li></ul>
  18. 19. Conformation-based mutation scanning <ul><li>Single-strand conformation polymorphism (SSCP). </li></ul><ul><li>most widely used methods. </li></ul><ul><li>Principle: </li></ul><ul><li>Single strand DNA tend to fold into complex structure which determines the mobility of the DNA strand in non denaturating gel. </li></ul>
  19. 20. Use and importance of SNPs <ul><li>Variations in the DNA sequences of humans can affect how humans develop diseases and respond to pathogens , chemicals , drugs , vaccines , and other agents. </li></ul><ul><li>SNPs are also thought to be key enablers in realizing the concept of personalized medicine </li></ul>
  20. 21. SNP Applications <ul><li>Gene discovery and mapping </li></ul><ul><li>Association-based candidate polymorphism testing </li></ul><ul><li>Diagnostics/risk profiling </li></ul><ul><li>Response prediction </li></ul><ul><li>Homogeneity testing/study design </li></ul><ul><li>Gene function identification </li></ul>
  21. 22. summary <ul><li>A single-nucleotide polymorphism is a DNA sequence variation occurring when a single nucleotide genome differs between members of a species. </li></ul><ul><li>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 . </li></ul>