19.04.01 Population genetics definitions Flashcards
Definition of allele frequency
- Proportion of an allele (or variant) among all allele copies at a given locus.
- Given as a percentage
- Used to estimate genetic diversity at an individual, population or species level
Definition of association study
- Statistical method for estimating the co-occurrence of genetic alleles with a phenotype
- association = allele occurs more with phenotype than would be expected by chance
Difference between association study and linkage study?
- Linkage requires families with multiple affected individuals, looks at linked microsatellites/SNPs which can be 20 million bp apart and identifies variants of large effects (but normally requires multiple affected families with variants in the same gene to detect)
- Association studies use a series of unrelated case/control studies to get significance, tests over a million SNPs which are in linkage disequilibrium and require a common haplotype.
Epistasis
The effect of one gene being dependent on the presence of one or more ‘modifer’ genes
Fitness
Probability of survival and reproduction in a particular environment
Gene flow
Flow of genetic material between previously separate populations (caused by migration and mating)
Gene pool
Collection of all of the alleles of all of the genes within a freely interbreeding population
Genetic drift
A change in allele freq in a population over time due to chance (not driven by adaptive pressures).
Can result in loss of some alleles, and can have a significant effect when a population suddenly decreases in numbers (i.e. after a natural disaster).
Genetic hitchhiking
When an allele changes freq because another allele which it is in LD with is under selection pressures.
Genetics linkage
Tendency for gens close to each other to be inherited together during meiosis
The greater the distance between the two genes, the greater the chance of recombination between sister chromatids
Genetic screening programmes
- early detection or exclusion of a genetic disease
- detects predisposition or resistance to disease
- determines whether a person carries a variant
Genotype freq
Percentage of people with that genotype
Genome wide association studies (GWAS)
Look for association between genes and phenotypes at a genome wide level. Normally have only detected common genes which have modest effects and only account for some of the the disease susceptibility
Haplotype
Representation of linked alleles in a cluster of related genes
Hardy-Weinberg equilibrium
Freq of alleles remain constant through generations in the absence of evolutionary forces (so no natural selection, no mutations, no genetic drift etc)
Linkage disequilibrium (LD)
Non-random distribution of adjacent alleles into gametes. Some combination of alleles occur more or less often than chance
Minor allele freq
Freq of least common alelle
Mutation rate
Rate of gene changes from WT to mutation. Normally expressed as number of mutations per unit, i.e. number f mutations per cell division
Natural selection
Individuals within a population who are the fittest for the environment they are in, as they have the best combination of alleles.
Odds ratio
The odds of having the disease and the risk allele, compared to only having the disease (and no risk alleles). The higher the OR the greater the effect on phenotype
Penetrance
Proportion of individuals carrying a particular allele and having the associated phenotype
Recombination freq
Proportion of recombinant offspring produced in a genetic cross between two organisms
Relative risk
Probability of having the disease when the patient has the at risk allele in an association study
SNP
Variation in DNA sequence in which a single nucleotide is replaced by another base. Useful marker in linkage studies. Very prevalent - nearly 10 million in genome
