GEN #11 GWAS
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What is GWAS?
- Genome-wide Association Studies
- Identifying genes that may potentially cause or be associated with a disease state.
GWAS attempts to interrogate the entire ______ using high density ___ ________ without a priori developing an
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
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.
______ ______are sizeable regions of the genome to which little recombination has historically occurred, possibly over generations.
T/F: A limited set of haplotypes can define the entire haplotype block.
Most recombination events that are involved in forming Haplotype Blocks are produced by ________ _________.
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
One can use SNPs within the haplotype block to find the actual _______ ________ that contributes to a response or pathology.
What is a Linkage Disequilibrium Plat?
- Provides direct visualization of pairwise associations of single nucleotide polymorphisms (SNPs).
- measures associations between SNPs
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
_____ ______ _______ take all interacting systems that impact the development of a disease and "map" them to make the connections.
Genetic Linkage Diagrams
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
___ _____ ___ 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
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
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
What is the advantage/disadvantage of shorter probes on a HDDM?
- Advantage: more accurate complimentation binding
- Disadvantage: a slight mismatch will not bind
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
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