GWAS

Question 1

Types of genetic variation

Answer 1

SNPs, STRs, VNTRs, CNVc, InDels

Question 2

SNPs

Answer 2

Single-nucleotide polymorphism

Only one nucleotide is affected, most often biallelic. Must be common genetic variant (have >1% allele frequency).

Question 3

GWAS

Answer 3

Genome-wide association study.

Discovery of associations between certain variations (SNPs) in our genome and certain physical traits (phenotype).

Question 4

First ever GWAS

Answer 4

Genetic associations with age-related macular degeneration (AMD).
Result: variant in complement factor H gene is strongly ass with AMD.

Question 5

Affymetrix

Answer 5

Microarray.
RNA > cDNA > cRNA > labeling with biotin > fragmentation > onto array > hybridize to complementary probes on chip > washing > scan

Color/intensity > amount of RNA that has bound

Question 6

Illumina

Answer 6

DNA fragmentation > adapter binding > loading onto flow cell > binding to attached oligos > cluster generation: bridge amplification > primers/nucleotides (fluorescent terminators) are added > imaaging

Question 7

GWAS analysis

Answer 7

GWAS analysis program: PLINK.
Regression analysis is performed for each SNP in association to phenotype.
Determination of p-value.
p-value has to be very low for SNP to be significant (eg 5x10^-8).
Depiction of p-values (as -log10) in Manhattan-plot.
Ideal: region with several SNPs > which gene?

Question 8

Advantages, disadvantages of GWAS

Answer 8

Pro: hypothesis free, easy data acquisition.
Con: Association does not mean causation.
Limits: some data might get lost (rare SNPs), lack of diversity (mostly European), p-value threshold has to be really low to account for multiple testing

Question 9

Genetic factors influencing effect of Metoprolol

Answer 9

Lack of CYP2D6 affects drug metabolism (SNPs identified by GWAS).

Question 10

Stevens-Johnson Syndrome

Answer 10

Adverse reaction (type 4) to drug.
GWAS identified SNPs significantly associated with carbamazepine-induced adverse reactions (T-cell mediated drug hypersensitivity).

Question 11

Sclerosteosis

Answer 11

GWAS was not used.
Skeletal overgrowth of skull inn South Africa, similar disease in Netherlands. Linkage analysis with microsatellite markers > identification of SOST (sclerostin, inhibits bone formation) as causative gene.
Of pharmacological interest to develop osteoporois medication.