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SNPs

Introduction. The human genome consists of 3 billion nucleotides ('base pairs') of DNA.Everyone shares about 99.9 per cent of this DNA.But ~ 0.1 per cent difference is what makes each one unique. SNPs (pronounced ?snips") are a key part of this variation.The variation makes us look different .

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SNPs

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    1. SNPs Karthikeyan Narayanan

    2. Introduction The human genome consists of 3 billion nucleotides ('base pairs') of DNA. Everyone shares about 99.9 per cent of this DNA. But ~ 0.1 per cent difference is what makes each one unique. SNPs (pronounced “snips”) are a key part of this variation. The variation makes us look different

    3. What are SNPs? Single nucleotide polymorphisms or SNPs are DNA sequence variations that occur when a single nucleotide (A,T,C,or G) in the genome sequence is altered. Example:- A SNP might change the DNA sequence AAGGCTAA to ATGGCTAA.

    4. Why SNPs? Number of Available Markers SNPs 1 in 1,000 bp ~ 3,000,000 Markers Diallelic - Nucleotide Substitutions Number of High Throughput Typing Methods Found in Coding and Non-Coding Regions Potential Association with Functional Variation

    5. How are SNPs generated?

    6. Genetic Analysis

    7. How are they identified? There are many methods to identify variance RFLP Single strand confirmation polymorphisms. Heteroduplex analysis. Direct DNA Sequencing. Variant detector Arrays.

    8. SSCP In SSCP the DNA fragment spanning the putative SNP is PCR amplified, denatured and run on denaturing PAGE. During gel run the fragments attain secondary structure based on their sequence. Any change in the migration pattern is observed and then sequenced to find the SNPs It is widely used and simple technique It has a variable success rate of 70 – 95%. Its labour intensive and low throughput.

    9. Heteroduplex Analysis This technique relies on the detection of heteroduplex formation of the PCR product of a heterozygote after denaturation and reannealing. The most reliable device for detection is HPLC. It is simple, low cost, and the efficiency is about 95 – 100%. Throughput is app 10minutes per sample using commercially available systems like “transgenomic wave”

    10. Direct DNA Sequencing

    11. VDA It is a new tool for SNP detection It is like microarray The strength between the matched and mismatched oligonucleotides are measured. It has a high-throughput and its sensitivity is that of the Direct DNA sequencing method

    12. Varied Detector Array (DNA Chips)

    13. Recent Technologies for SNP detection Fluorescent Micro array based system (Affymetrix) Fluorescent bead based technologies (Luminex,illumina, Q-dot) Automated ELISA assays (Orchid biocomputer) Pyrosequencing Fluorescence resonance energy transfer-(FRET) based Cleavase assays (third wave technologies) Mass Spectrophotometry detection (Rapigene, Sequenom)

    14. Applications

    15. Other Applications Some of the other applications of SNPs are Health Care Prognosis Tailored medicines

    16. Conclusion High-throughput screening of SNPs is emerging as an important new field New technologies with advantages and disadvantages proliferate. SNP genotyping technologies are maturing, and companies are commercializing them in the form of products. SNPs could potentially help optimize clinical trials through patient stratification.

    17. Thank You

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