Association Genotypes and Phenotypes

Question 1

what is a phenotype (trait) ?

Answer 1

Physical, social, behavioural, or emotional quality (characteristic) that varies from one individual to another. eg, blue eyes, hates carrots.

Question 2

what is a dichotomous phenotype?

Answer 2

2 probabilities, eg affected by disease or isnt.

Question 3

what is a quantitative phenotype?

Answer 3

continuous or categorical (eg: BMI, Blood pressure, height…)

Question 4

polygenic trait

Answer 4

controlled by more than two genes (also called multifactorial inheritance

Question 5

monogenic trait

Answer 5

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.)

Question 6

what is a genotype?

Answer 6

Refers to the genetic makeup of an organism. The gene(or allele) combination an individual organism has.

Question 7

what are polymorphisms?

Answer 7

Individual genomic variations within a species are called polymorphisms.

Polymorphisms include: SNPs and CNVs. (single nucleotide polymorphisms, copy number variation)

Question 8

what is an SNP?

Answer 8

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

Question 9

what is a CNV?

Answer 9

Copy Number Variation

when the number of copies of a particular gene varies from one individual to the next

Question 10

polygenic inheritance

Answer 10

refers to a single characteristic that is controlled by more than two genes (skin colour is an example)

Question 11

what are the source of human variation?

Answer 11

Population bottleneck

Selection

Mutation

Admixture

Migration and environment

Question 12

what is population bottleneck?

Answer 12

bottleneck = a sharp reduction in the size of a population due to environmental events such as famines, earthquakes ..

Question 13

what is admixture?

Answer 13

Admixture = mix of two previously isolated (genetics isolate populations)Population

Question 14

what are the basic measure to capture human variation?

Answer 14

1. Allele frequencies in populations
2. Hardy-Weinberg Principle/Equilibrium
3. Genetic Distance (FST)
4. Linkage Disequilibrium
5. Population Structure and Admixture
6. Association Genotype and Phenotype

Question 15

How are allele frequencies in populations measured?

Answer 15

pA= (2NAA+NAa)/2N​

and then pa=1-pA

N= pop sample
genotype = AA, Aa, aa

Question 16

what is allele frequency?

Answer 16

refers to how common an allele is in a population.

Question 17

what is the Hardy-Weinberg principle?

Answer 17

a populations allele and genotype frequencies are constant, UNLESS there is some type of evolutionary force acting upon them

Question 18

what do we assume for the Hardy-Weinberg principle

Answer 18

1. no selection
2. no mutation
3. no migration
4. large population
5. random mating, no specific choice

Question 19

deviation from HWE can be due to…

Answer 19

inbreeding, ​

population stratification, ​

selection, ​

gender-dependent allele frequencies, ​

non-random (assortative) matin

Question 20

how is HWE tested?

Answer 20

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).​

Question 21

what is FST?

Answer 21

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

Question 22

what is Linkage Disequilibrium (LD)?

Answer 22

Linkage Disequilibrium (LD) refers to correlations between genotypes of nearby markers

Question 23

what is population structure?

Answer 23

Population structure: Genetic differences due to geographic ancestry. Use genome-wide data to classify genome-wide ancestry