L5 Data Handling Flashcards
What does theta mean in parametric linkage analysis
Recombination likelihood between alleles
If theta = 0 what does this mean
There is strong linkage as the recomb likelihood is 0
If it is max of 0.5 what does this mean
Recombination occurred and not linked to the disease locus
What do likelihood ratio tests for parametric linkage test
The null hypothesis that there is no linkage is tested ie the marked locus is far from disease locus
What is the LOD score
Log 10 of the likelihood ratio
If lod = 3 what does this mean
Your alternate hypothesis is 1000 more likely than null hypothesis (ie they are linked)
This is because log10 of 1000 is 3
What is it called when many loci genotyped along a genomic sequence are tested of LOD scores to see where linkage is most likely to the diseased locus
Multipoint analysis
What does the peak of a multipoint analysis show
Which chr/genomic region is linkage the most likely and reject null
(Passed LOD 3 threshold)
How is a HLOD score different
Accounts for heterogeneity ie understands a phenotype is caused by many other genomic loci/ chr / genes
Zlrlod scores are used for complex disorders. Give example of genes found linked to disease locus of crohns
Nod2 and card15
What do association studies test better than LOD scores / linkage analysis
Small variants with small effects on disease phenotype
What do x2 test in association studies generate
A p value of significance
Which test of association can be done on phenotypes that are quantitative like weight or height to test effects of genotypes
Linear regression analysis (on a graph x = genotype and y = the height of samples at each genotype)
Why can’t you do a gwas with a small sample
A small p value when testing millions of snps would cause too many false positives, to stop this larger popn needed
Which types of plots of associations are done on gwas where millions of snps are tested for association
Manhattan plot
