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Single Nucleotide Polymorphism Mining SNP Data 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 How can SNPs aid research? • • • • • Biomarkers Association Studies Genotyping Loss of Heterozygosity DNA Copy Number SNP Microarray Chip • Use microarray platform similar to gene expression studies • Hybridization of fluorescently tagged samples to probes which correspond to sequences of interest 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 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) 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 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). 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 Other Analysis • Association Studies • Haplotypes • Shared LOH regions