Unit 1

Locus

location in the genome

can mean genomic region, specific nucleotide, or anything in between

Polymorphism

occurrence of two or more alleles at a locus in a population

does not need to be a gene or do anything functional, just needs to differ among people

Allele

any of the variant forms of genetic material at a polymorphism

Genotype

the combination of two alleles for a polymorphism in a person

Phenotype

trait

observable manifestation of a genotype

Homozygous

having two copies of the same allele at a locus

Heterozygous

having copies of two different alleles at a locus

Minor Allele

the less common allele at a biallelic locus

Major Allele

the more/most common allele at a locus

Dominant/Recessive

describes the effect of an allele on a phenotype

Affected

a person who manifests a genetic condition

Carrier

a person who has a risk allele, but not the genetic condition itself

Central Dogma

DNA is transcribed to mRNA, which is translated to protein

DNA holds the information for coding proteins

Gene

unit of inheritance

sequence of nucleotides forming promoter, exons, and introns, that ultimately codes a polypeptide or nucleic acid molecule

Genetic Code

three-nucleotide codons code for specific amino acids

Genetic Sequence

the sequence of nucleotides in a genome or locus

Inheritance

offspring inherit one copy of the genome from each parent

Unilineal Relatives

related through only one parent

examples: cousins, parent/offspring, grandparent/grandchild, avuncular, half-siblings, half-avuncular

Bilineal Relatives

related through both parents

examples: siblings, double cousins, inbreeding loop

Identical-By-Descent (IBD)

two alleles inherited by a common ancestor

two alleles can be in the same person or in different people

common ancestor depends on how far back you look

Autozygous

two alleles inherited from the same ancestor in the same person

identical-by-descent and homozygous

Identical-By-State (IBS)

two of the same allele not inherited by a common ancestor

Coefficient of Kinship

probability that two randomly chosen alleles in two different people are identical-by-descent

average expected percentage identical-by-descent across the entire genome

measure of how closely related two people are

Coefficient of Relationship/Coefficient of Relatedness (r )

usually defined as twice the coefficient of kinship

can be equal to the coefficient of kinship

Coefficient of Inbreeding (F)

the probability of two alleles being identical-by-descent in an individual

in an outbred population, is equal to the kinship coefficient for the person’s parents

Binomial Distribution

start with an experiment that only has two outcomes and do the experiment n independent times

X is the number of successes

p is the probability of success

Multinomial Distribution

similar to binomial distribution but with more than two categories

Normal Distribution/Gaussian Distribution

bell shaped curve of quantitative/continuous rather than discreet outcomes

Student’s t-Distribution

looks like the normal distribution except for slightly wider tails

width of tail is governed by degrees of freedom

degrees of freedom governed by sample size

χ² Distribution

skewed to the right and also has degrees of freedom

used in a lot of statistical tests

Estimation

using some function of the data as the estimate of the parameter

Standard Error (SE)

the accuracy of a parameter estimate

Standard Deviation (SD)

spread of data around the mean

Confidence Interval (CI)

gives a range into which you can be pretty sure the true parameter falls

constructed with standard error

Allele Frequency

percentage of alleles in a population or sample that are of a particular type

Genotype Frequency

percentage of people in a population who have a particular genotype

Mating Type Frequency

percentage of matings in a population who have this combination of genotypes

Hardy-Weinberg Equilibrium (HWE)

describes an ideal relationship between allele frequencies and genotype frequencies

assumptions: diploid organism, sexual reproduction, non-overlapping generations, random mating, large population size, equal allele frequencies in the sexes, no migration, no mutation, and no selection

Diploid Organism

two copes of genetic material

Sexual Reproduction

one copy of genetic material from mom and one from dad

Non-Overlapping Generations

one generation dies as the next one is born

Large Population Size

population is large enough that chance events of meiosis do not cause fluctuation in allele frequencies from generation to generation

Random Mating

genotype at this locus does not matter when choosing a mate

Equal Allele Frequencies in the Sexes

p is the same in males and females

No Migration

no one is coming into the population from outside

No Mutation

no spontaneous changes in alleles from one generation to the next

No Selection

no genotype is more likely than another to lead to successful reproduction

Penetrance

probability of getting a disease given a person has the disease genotype

Phenocopy

having disease without having disease genotype

Recombination Fraction

probability of recombination occurring between two loci

equals the percentage of offspring that are non-parental types

the genetic distance between loci

Linkage

two loci physically occurring together on the same DNA molecule

Linkage Disequilibrium (LD)

the correlation between alleles at different loci

sources: admixture and new mutation

Admixture

mixing/interbreeding of two populations