single nucleotide polymorphism
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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.

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what is a snp
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
How can SNPs aid research?
  • Biomarkers
  • Association Studies
  • Genotyping
  • Loss of Heterozygosity
  • DNA Copy Number
snp microarray chip
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
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
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
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
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
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
Other Analysis
  • Association Studies
  • Haplotypes
  • Shared LOH regions
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