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Single Nucleotide Polymorphism
- 1. Single Nucleotide Polymorphism Authors FAZEEHAAMJAD 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)
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- 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 proteinStructure 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 incrop species e,g • corn • soyabean SNP in industrial yeast In human genome project
- 10. Importance • variation inpopulation. • Newer characteristic. • In therapeutic purposes. • In genealogical analysis of DNA
- 11. disadvantages The non codingSNPs cause many diseases in living organisms e.g • Cancer • Osteoporosis • Rheumatoid arthritis
- 12. Analytic Techniques •Reverse DotBlots •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
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- 17. • Two probesare 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 standsfor 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 basedupon 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
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- 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