Single nucleotide polymorphism
Download
1 / 10

Single Nucleotide Polymorphism - PowerPoint PPT Presentation


  • 103 Views
  • Uploaded on

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.

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha
Download Presentation

PowerPoint Slideshow about ' Single Nucleotide Polymorphism' - gregory-richard


An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript

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