Population Genetics Week And Biostats

Question 1

All current non-African emerge from what branch of Africa

Answer 1

East African branch

Question 2

What caused the move out of africa in early evolution ?

Answer 2

Ice Age

Question 3

On a PCA plot, what is the y and x axis

Answer 3

X- maximum value of variability in the data (pc1)
Y- mixed variability (pc2)

Question 4

admixture analysis

Answer 4

1. Admixture is an algorithm for model-based estimation of ancestry in unrelated individual.
2. Basic algorithm is blind to how individuals are labelled, and works on user-specified number of ancestry components
3. Based on that, K, the program estimates the proportion of ancestry for each individual, from each contributing population considered.

Question 5

Function of a PCA plot

Answer 5

You can identify populations stratification
Relationships between individuals and populations

Question 6

Function of Admixture

Answer 6

To determine Ancestries and gene flow that have been driving the population 

Question 7

Define confounding variable

Answer 7

Variable to be present in a group of patients and leads to incorrect conclusions.

Question 8

Non-normal distribution : what is a positively skewed graph and negatively skewed graph.

Answer 8

Positive : skewed to the right
Negative: skewed to the left

Question 9

What is the equation for proportion .

Answer 9

A/A+B always <1

Question 10

What is a research and null hypothesis.

Answer 10

1. Research- what we aim to gather evidence of
2. Null- what we assume is true to begin

Question 11

What are steps to undertaking a hypothesis test

Answer 11

1. Define study question
2. Set null and alternative hypothesis
3. Calculate a test statistic
4. Calculate a p-value
5. Make a decision and interpret your conclusions

Question 12

What are type 1 and type 2 hypothesis error.

Answer 12

Type 1 error- null hypothesis is true but is rejected
Type 2 error- null hypothesis is false (alternative hypothesis is true) but not rejected.

Question 13

What is the hardy-Weinberg equation.

Answer 13

P^2+2pq+q^2
P^2= genotype for homo
2pq= genotype for hetero
Q^2= genotype for hetero

Question 14

Changes to allele frequency is caused by.

Answer 14

1. Evolutionary forces manipulate allele frequencies in a population.
2. Mating pattern
3. Migration
4. Mutation and recombination
5. Selection
6. Genetic drift

Question 15

What is identical by state or descent

Answer 15

1. IBD: Inherit the similar nucleotide sequences from a common ancestor.
2. IBS: two individuals who share similar nucleotide sequences

Question 16

What is the overall chance of homozygosity at a specific allele due to inbreeding. (Equation)

Answer 16

(Fa x q) + (1-Fa)q^2