Lecture notes
GWAS AND GENE NETWORK ANALYSIS
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- University College London (UCL)
detailed summary of how a GWAS and gene network analysis are done.
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4- GWAS AND GENE NETWORK ANALYSISSunday, 1 October 2023 14:58
Variants in our genetics
Variants have different frequencies
Major allele reference
Minor alternative - minor allele frequency : to classify the variants
More than 99% of genomes when comparing two individyals are the sam e
Variants account for 0.6% of the difference btw individuals
Majority of the variants are SNPs
Mutation : actually a neutral term, where in medicine it is thought of as disease
Non-pathogenic variants (mutations) - changes in DNA sequence that do not have an effect o
disease
Pathogen (mutations) - impact on disease, rare in the population
Risk variants - may or may not impact disease but increase the risk of disease
Common variants are investigated in GWAS
Genotyping techniques
DNA microarrays
Varaints should be know in advance
DNA is cut into pieces
Pieces that are complementary to the probes will hybridize and remain on chip to emit light
Next gen sequencing (NGS)
GWAS
Used to identify common SNPs that are associated with a certain phenotype
2 populations : 1 phenotype of interest 2 without the phenotype
Association analysis to evaluate if some SNPs are common
Key words
P-value : prob of genotype-phenotype association
Effect size - beta : how strongly genotype-phenotype is associated
Odds ratio (OR): to represent effect size
Power: the ability of the analysis to identify a true association
After genotyping - association
,on
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