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Single Nucleotide Polymorphism

Single Nucleotide Polymorphism

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Single Nucleotide Polymorphism

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  1. Single Nucleotide Polymorphism Mining SNP Data

  2. What is a SNP? • Mutation of a single nucleotide (A,C,T,G) • Some can be associated with various phenotypic differences • Drug resistance • Propensity towards disease • Over 5 Million SNP locations identified in the human genome, growing daily

  3. How can SNPs aid research? • Biomarkers • Association Studies • Genotyping • Loss of Heterozygosity • DNA Copy Number

  4. SNP Microarray Chip • Use microarray platform similar to gene expression studies • Hybridization of fluorescently tagged samples to probes which correspond to sequences of interest

  5. Affymetrix Probe Layout • Two alleles, A and B • PerfectMatch (Signal)MisMatch (Background) • Sense (forward)Antisense (reverse) • Shifted Sequences(-2, -1, 0, 1, 2) • Read intensity values

  6. Genotyping • Each probe gives some indication of allele A or B • Aggregate information from all probes for a given SNP • Create classifier for each SNP • Make genotype calls • (AA, BB, AB, AB_A, AB_B, Unknown)

  7. SNPs and Cancer • Tumors frequently exhibit DNA alterations • Loss (0 or 1 copy) • Additions (3 or more copies) • Could be responsible for some cancers • Tumor suppresor genes • Oncogenes

  8. Loss of Heterozygosity (LOH) • Each cell contains two copies of a given chromosome (mother’s and father’s) • Loss of Heterozygosity occurs when there is a change in relative allele signals (AB in normal and AA in tumor, for instance).

  9. DNA Copy Number Changes • Determine regions where additions or losses take place. • Complimentary to LOH studies • LOH can detect “balanced” mutations • Copy number analysis can detect amplifications or losses of homozygous markers

  10. Other Analysis • Association Studies • Haplotypes • Shared LOH regions