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2012-03-02 08:25:05

questions on genomics GWAS studies lecture
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  1. What is GWAS?
    • Genome-wide Association Studies
    • Identifying genes that may potentially cause or be associated with a disease state.
  2. GWAS attempts to interrogate the entire ______ using high density ___ ________ without a priori developing an
    • Genome
    • DNA microarrays
  3. T/F: Associations made from GWAS studies, prove causation, allowing involvement of a gene with the
    • False: Does not prove causation
    • allows development of a testable hypothesis concerning the connection of a gene with a disease
  4. T/F: The basic design of GWAS:
    1. SNPs microarrays from non diseased and diseased people
    2. compare the presence/absence of markers
    3. fine tune the relationship of the disease with markers
    4. narrow the gene location to a small region of a chromosome.
  5. ______ ______are sizeable regions of the genome to which little recombination has historically occurred, possibly over generations.
    Haplotype Blocks
  6. T/F: A limited set of haplotypes can define the entire haplotype block.
  7. Most recombination events that are involved in forming Haplotype Blocks are produced by ________ _________.
    Recombination Hotspots
  8. What is used to reduce the number of SNPs from 10 million to ~500,000 when interrogating a genome?
    Linkage disequilibrium, unexpected changes that should or should not be there
  9. One can use SNPs within the haplotype block to find the actual _______ ________ that contributes to a response or pathology.
    Genetic Information
  10. What is a Linkage Disequilibrium Plat?
    • Provides direct visualization of pairwise associations of single nucleotide polymorphisms (SNPs).
    • measures associations between SNPs
  11. What are some potential GWAS outcomes with identification of susceptible variants?
    • 1. Novel biological insights for clinical advances:
    • Therapeutic targets, Biomarkers, and Prevention

    • 2. Improved measures fo individual aetiological processes for Personalized medicine:
    • Diagnostics, Prognostics, and therapeutic optimization
  12. _____ ______ _______ take all interacting systems that impact the development of a disease and "map" them to make the connections.
    Genetic Linkage Diagrams
  13. What are the two GWAS study requirements needed for analyzing the binding sequences from each sample?
    • Suitable population to study
    • High density DNA microarrays containing a wide range of SNP binding oligonucleotides
  14. ___ _____ ___ microarrays have multi-thousand pico-moles sized oligonucleotides fixed to a solid support that measures the binding of the probe using _________, silver or _________-labeled targets.
    • High Density DNA
    • Fluorometric
    • Chemiluminescent-labeled
  15. Name the two suppliers of High Density DNA Microarrays. What are the length of oligonucleotides used by each?
    • Affymetrix- shorter 25-mer probes
    • Agilent- longer 60-mer probes
  16. What is used to couple the oligonucleotides to the support in the fabrication of HDDM? How are the sequential nucleotides linked on?
    • Epoxy-silane, Amino-silane, Lysine etc.
    • DNA Synthesis Chemistry
  17. What is the advantage/disadvantage of shorter probes on a HDDM?
    • Advantage: more accurate complimentation binding
    • Disadvantage: a slight mismatch will not bind
  18. What is the advantage/disadvantage of longer probes on a HDDM?
    • Advantage: stronger signal, more binding, even slight mismatch will still bind
    • Disadvantage: non-specific binding and false positives