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Unraveling Human Genome: SNP and Its Applications

Explore single nucleotide polymorphisms (SNPs) and their significance in gene mapping, disease association, diagnostics, and response prediction. Discover the future potential in gene function identification using SNP data.

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Unraveling Human Genome: SNP and Its Applications

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  1. Introduction to bioinformaticslecture 11SNPby Ms.Shumaila Azam

  2. Human Genome and SNPs • Now that the human genome is (mostly) sequenced, attention turning to the evaluation of variation • Alterations in DNA involving a single base pair are called single nucleotide polymorphisms, or SNPs • Map of ~1.4 million SNPs • It is estimated that ~60,000 SNPs occur within exons;

  3. Goals of SNP Initiatives • Immediate goals: • The hundreds of thousands of SNPs estimated to be present in the human genome • Interest also in other organisms, e.g. potatoes(!) • Establishment of SNP Database(s)

  4. Longer term goals: Areas of SNP Application • Gene discovery and mapping • Diagnostics/risk profiling • Response prediction • Gene function identification

  5. Polymorphism • Technical definition: most common variant (allele) occurs with less than 99% frequency in the population • Also used as a general term for variation • Many types of DNA polymorphisms, including RFLPs, VNTRs, microsatellites • ‘Highly polymorphic’ = many variants

  6. Use of Polymorphism in Gene Mapping • 1980s – RFLP marker maps • 1990s – microsatellite marker maps

  7. Gene Discovery and Mapping • Linkage Analysis • Within-family associations between marker • Linkage Disequilibrium (LD) • Across-family associations

  8. Crossing over and Recombination

  9. Disease-Marker Association • A marker locus is associated with a disease if the distribution of genotypes at the marker locus in disease-affected individuals differs from the distribution in the general population • A specific allele may be positively associated (over-represented in affecteds) or negatively associated (under-represented)

  10. Examples: Alzheimer’s The E4 allele appears to be positively associated with Alzheimer’s disease: Odds Ratio = (58/16)/(33/55) = 6

  11. Linkage Allele D is created Mutation occurs Nearby marker Allele M was nearby D and M subsequently transmitted together

  12. Candidate Polymorphism Testing • Large SNP collections may allow testing for direct, physiologically relevant associations with trait

  13. Diagnostics/Risk Profiling • Identified SNP associations can potentially be used to develop diagnostic tools

  14. Response Prediction • Pharmaceutical companies especially interested in this: • Aim to identify those likely to respond • Predict toxicity reactions in susceptible individuals • Response to any kind of substance; creation of ‘functional foods’

  15. Gene Function Identification • Alternative to other experimental procedures (e.g. knock-outs, which cannot be used in humans) • Studies to compare individuals with and without naturally occurring disease predisposing genetic profiles

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