GWAS and SNPs Flashcards
What does SNP stand for?
Single nucleotide polymorphism
What are SNPs?
Single base change in a DNA sequence that is commonly biallelic
What does biallelic refer to?
Found in both alleles
What are the two types of SNPs?
Synonymous SNP
Non-synonymous SNP
What is a synonymous SNP?
Sense mutation
Causes a change in the codon for another codon, but it still codes for the same amino acid since DNA is degenerate
What is a non-synonymous SNP?
Missense mutation
Causes a change in the codon for another codon which leads to the expression of a different amino acid
What are the uses of SNPs?
Identification
Genetic mapping
Estimating predisposition to disease
Predicting genetic traits
What does GWAS stand for?
Genome wide association study
What was GWAS?
Analysed DNA sequence variation from across the human genome
What were the goals of GWAS?
Identify genetic risk factors for diseases common in the population
Predict who is at risk
Identify the biological underpinnings of disease susceptibility for new prevention and treatment strategies
Example of gene studied in GWAS
PNPLA3
What did GWAS reveal about the PNPLA3 gene?
A single nucleotide polymorphism in residue 148 lead to increased
- hepatic fat levels
- hepatic inflammation
Genetic determinant of NAFLD
How did the polymorphism in residue 148 cause the change in PNPLA3 gene expression?
Single nucleotide polymorphism caused cytosine to guanine transition
Substituted isoleucine to mehtionine
What is the clinical importance of the PNPLA3 single nucleotide polymorphism?
Acts as a risk factor for the development of cirrhosis
What was used to quantify the amount of mutated protein expressed by PNPLA3 polymorphism individuals?
Taqman PCR
Red VIC dye linked to the wild-type allele
Green FAM dye linked to the allele expressing the mutation
