Association Genotypes and Phenotypes Flashcards
what is a phenotype (trait) ?
Physical, social, behavioural, or emotional quality (characteristic) that varies from one individual to another. eg, blue eyes, hates carrots.
what is a dichotomous phenotype?
2 probabilities, eg affected by disease or isnt.
what is a quantitative phenotype?
continuous or categorical (eg: BMI, Blood pressure, height…)
polygenic trait
controlled by more than two genes (also called multifactorial inheritance
monogenic trait
controlled by a single gene mutation (also called Mendelian inheritance or disease caused by preexisting mutant alleles that have been passed down from one generation to the next.)
what is a genotype?
Refers to the genetic makeup of an organism. The gene(or allele) combination an individual organism has.
what are polymorphisms?
Individual genomic variations within a species are called polymorphisms.
Polymorphisms include: SNPs and CNVs. (single nucleotide polymorphisms, copy number variation)
what is an SNP?
Single Nucleotide Polymorphism.
A DNA sequence variation occurring commonly
A single nucleotide (A,G,T,C) in the genome (all of an organisms genetic material) differs between members of a biological species
what is a CNV?
Copy Number Variation
when the number of copies of a particular gene varies from one individual to the next
polygenic inheritance
refers to a single characteristic that is controlled by more than two genes (skin colour is an example)
what are the source of human variation?
Population bottleneck
Selection
Mutation
Admixture
Migration and environment
what is population bottleneck?
bottleneck = a sharp reduction in the size of a population due to environmental events such as famines, earthquakes ..
what is admixture?
Admixture = mix of two previously isolated (genetics isolate populations)Population
what are the basic measure to capture human variation?
- Allele frequencies in populations
- Hardy-Weinberg Principle/Equilibrium
- Genetic Distance (FST)
- Linkage Disequilibrium
- Population Structure and Admixture
- Association Genotype and Phenotype
How are allele frequencies in populations measured?
pA= (2NAA+NAa)/2N
and then pa=1-pA
N= pop sample
genotype = AA, Aa, aa
what is allele frequency?
refers to how common an allele is in a population.
what is the Hardy-Weinberg principle?
a populations allele and genotype frequencies are constant, UNLESS there is some type of evolutionary force acting upon them
what do we assume for the Hardy-Weinberg principle
- no selection
- no mutation
- no migration
- large population
- random mating, no specific choice
deviation from HWE can be due to…
inbreeding,
population stratification,
selection,
gender-dependent allele frequencies,
non-random (assortative) matin
how is HWE tested?
Compare observed to expected genotype counts using Pearson chi-square test of goodness of fit: with 3 genotypes and 1 parameter estimated (p) we have a test with 1 degree of freedom (df).
Inappropriate for rare variants (low genotype counts): use Fisher Exact Test (FET).
what is FST?
FST/Genetic distance between two populations is the value such that the allele frequency difference between the two populations has mean 0 and variance 2FSTp(1 – p), where p is the allele frequency in the ancestral population
what is Linkage Disequilibrium (LD)?
Linkage Disequilibrium (LD) refers to correlations between genotypes of nearby markers
what is population structure?
Population structure: Genetic differences due to geographic ancestry. Use genome-wide data to classify genome-wide ancestry
