Population Genomics in Humans

Question 1

What does the 1000 genome project tell us?

Answer 1

The 1000 genome project tells us that we humans share the majority of our variants (>99.5%), suggesting that we can learn the functional impact of that 99.5 % to our phenotypes by population genetics approach

Question 2

significant association

Answer 2

requires >10 individuals with the target genotype, ex. B/B

Question 3

How are GWAS able to discover “associated variants” to a phenotype?

Answer 3

a common variant can be NEAR to rare and severe variants determining individual phenotypes.

Question 4

how many times does each chromosome recombine between diploid copies?

Answer 4

once or twice per generation

Question 5

What would the average length of haplotype between parents and offsprings be?

Answer 5

30-50% of chromosome sizes

Question 6

Why do we see a decrease in haplotype length by the increase in variant frequency?

Answer 6

Rare variants are relatively new and have a relatively short history. Shorter existence of rare variants means less recombination. Therefore, longer haplotype length is expected in rare variants.

Question 7

What is the concept of the the GWAS approach?

Answer 7

At a given population, GWAS examines statistical association between the genotype and phenotype in all possible examinable variant locations or loci.

Question 8

How to examine statistical association between genotypes and phenotypes

Answer 8

A comparison is always made between two groups of samples. The two groups are divided by either

1) categorical phenotypes (frequency per variant/locus will then be analyzed throughout the entire genome) or
2) by genotype (with or without a variant).

Then, either variant frequency (1) or average phenotype (2) is compared between two groups and statistics test whether the two groups are significantly different or not.