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Single Nucleotide Polymorphism
- 1. Single Nucleotide Polymorphism Authors FAZEEHA AMJAD AYESHA BUTT AYESHA SADIQA AROOJ SAEED Department of Biotechnology
- 3. SINGLE NUCLEOTIDE POLYMORPHISM • The variations in DNA sequence that occurs when single nucleotide ( A, T G, C) in the genome sequence is altered, is called single nucleotide polymorphism.
- 4. Frequency of SNPs • ~ 1.5 million sites in the human genome where SNPs could occur. • ~ 3.8 million SNPs are catalogued in 270 individuals. • ( ~ 1 SNP/ 1000 bases) • ~ each person has ~3.5 million common SNPs (inherited) and ~30 new mutations have arisen (mutation rate of 10-8 /base/ generation)
- 5. Factors
- 6. Difference b/w mutation & SNP SNP persistence in a population Frequency more than 1% Mutation Occurrence in an individual Frequency less than 1%
- 7. SNP Coding Region Affect protein Structure Synonymous Same polypeptide sequence produced Non-synonymous Different polypeptide sequence produced Non Coding Region Don’t effect protein structure But act as promoter or enhancer Non-Sense Premature stop codon Missense Leads to amino acid sequence Types Of SNP
- 8. Uses In Biotechnology 1) Genome mapping 2) Genome wide association studies of complex diseases 3) specific genetic traits 4) classifying patients in clinical trials 5) genetic markers for other traits 6) pharmacogenomics
- 9. Applications SNP discovery in crop species e,g • corn • soyabean SNP in industrial yeast In human genome project
- 10. Importance • variation in population. • Newer characteristic. • In therapeutic purposes. • In genealogical analysis of DNA
- 11. disadvantages The non coding SNPs cause many diseases in living organisms e.g • Cancer • Osteoporosis • Rheumatoid arthritis
- 12. Analytic Techniques •Reverse Dot Blots •DNA Sequencing •HPLC Genotyping •TaqMan Assay •Fluorescence Polarization (FP) •Mass Spec •Microchips •Pyrosequencing •Allele Specific Hybridization •SNaPshot
- 13. DNA Sequencing • Requirements template DNA free nucleotides (deoxy & dideoxy) Enzyme primer
- 15. initiation Formation of complementary strand & termination Gel Electropherosis
- 16. Microchip
- 17. • Two probes are introduces in solution;ASO and LSO. • LSO binds to 3’ and ASO to 5’ direction of SNP to hybridize; 1. LSO(locus specific nucleotide)-stops before SNP 2. ASO(Allele specific nucleotide)- contain base complimentary to SNP. • Positive result: Last base of ASO similar to SNP base-ligase binds LSO and ASO. • Negative result: Last base of ASO dissimilar to SNP base-ligase doesn’t bind two probes. • Positive result detect the presence of SNP. • Amplify to study the region Oligonucleotide ligation reaction
- 18. HPLC • HPLC stands for High Performance Liquid Chromatography • HPLC is characterized by the use of high pressure to push a • mobile phase solution through a column of stationary phase • allowing separation of complex mixtures with high resolution.
- 19. Separations 19 Separation in based upon differential migration between the stationary and mobile phases. Stationary Phase - the phase which remains fixed in the column, e.g. C18, Silica Mobile Phase - carries the sample through the stationary phase as it moves through the column. Injector Detector Column Solvents Mixer Pumps High Performance Liquid Chromatograph Waste
- 20. Separations 20 Injector Detector Column Solvents Mixer Pumps Chromatogram Start Injection mAU time High Performance Liquid Chromatograph
- 21. Separations 21 Injector Detector Column Solvents Mixer Pumps Chromatogram Start Injection mAU time
- 22. Separations 22 Injector Detector Column Solvents Pumps Mixer Chromatogram Start Injection mAU time
- 23. Separations 23 Injector Detector Column Solvents Pumps Mixer Chromatogram Start Injection mAU time
- 24. Separations 24 Injector Detector Column Solvents Pumps Mixer Chromatogram Start Injection mAU time
- 25. Separations 25 Injector Detector Column Solvents Pumps Mixer Chromatogram Start Injection mAU time
- 26. Separations 26 Injector Detector Column Solvents Pumps Mixer Chromatogram Start Injection mAU time
- 27. Separations 27 Injector Detector Column Solvents Pumps Mixer Chromatogram Start Injection mAU time
- 28. Separations 28 Injector Detector Column Solvents Pumps Mixer Chromatogram Start Injection mAU time
- 29. Separations 29 Injector Detector Column Solvents Pumps Mixer Chromatogram Start Injection mAU time
- 30. Separations 30 Injector Detector Column Solvents Pumps Mixer Chromatogram Start Injection mAU time
- 31. Separations 31 Injector Detector Column Solvents Pumps Mixer Chromatogram Start Injection mAU time
- 32. Separations 32 Injector Detector Column Solvents Pumps Mixer Chromatogram Start Injection mAU time
- 33. Separations 33 Injector Detector Column Solvents Pumps Mixer Chromatogram Start Injection mAU time
- 34. Separations 34 Injector Detector Column Solvents Pumps Mixer Chromatogram Start Injection mAU time
- 35. Separations 35 Injector Detector Column Solvents Pumps Mixer Chromatogram Start Injection mAU time
- 36. Refferences • http://biochem218.stanford.edu/16SNPs.pdf • http://www.sciencedirect.com/science/article • http://www.researchgate.net/post/What_is_the_diff erence_between_a_SNP_and_a_mutation