Unit 1 HuGen

Locus

A specific physical location on a chromosome where a particular gene or genetic marker is situated.

Polymorphism

One gene exists in a multiple different alleles within a population at the same locus.

Polymorphism just needs to _____ among people

differ

Allele

A variant form of a gene that is found at the same place on a chromosome.

Genotype

Combination of 2 alleles for a polymorphism in a person

Phenotype

observable traits that manifest from a genotype

homozygous

Having 2 copies of the same allele at a locus

Heterozygous

Having copies of two different alleles at a locus

Minor allele

shows less frequently at a a biallelic locus

Major allele

shows more frequently at a locus

Dominant/recessive

describes the effect of an allele on a phenotype; related to expression of the phenotype.

2 copies are necessary for the phenotype expression is

recessive

one copy is necessary for a phenotype is

dominant

affected

person who manifests a genetic condition

carrier

person who has a risk allele but not the genetic condition.

Central Dogma

DNA is transcribed to mRNA which is translated to protein

gene

unit of inheritence

gene regulation stuff

This occurs via promoter, transcription factors, enhancers, silencers, DNA methlyation, histone modifications.

Genetic code

3 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 form each parent.

What is unilineal relationship

related through only one parent

Draw a unilneal relationship with cousins

Are parents and offsprings in a Unilineal or bilineal relationship?

Unilineal because the parent being the parent to the offspring is the relationship

What is the relationship between a grandparent and grandchild and why?

Unilineal because the grandparent is the parent of the grandchilds parent so they are related by one parent.

what type of relationship are uncles/aunts and nieces/nephew

avuncular ( aunt/uncle - nephew/niece relationship) and unilineal

what relationship does a great grandparent and great grandchild have? why?

Unilineal because the great grandparent is the father of the grandparent

What relationship does a great-uncle/aunt and great niece/nephew have?

unilineal

Draw a first cousin once removed

Draw 2nd cousin once removed

Draw 1st cousins twice removed

Draw a pedigree where everyone is related through the father.

Draw a pedigree where everyone is related through the mother.

What relationship is considered for half siblings and why? draw it

Unilineal because they have a common parent

What relationship do half avuncular have? draw it

Unilineal because they share a common parent.

What is a bilineal relationship?

Related by both parents

What type of relationship are siblings and why and draw

bilineal because they are related by both parents.

What relationship is double cousins and draw it out.

They are bilineal

Draw an inbreeding loop and say what relationship it is and why

Bilineal relationship because both the offsprings parents are related by their parents; offsprings parents are siblings

Define Identity-by-descent (IBD)

2 or 1 alleles that are inherited from a common ancestor which depends on how far back you look.

For IBD to happen 2 alleles can be in the _____ person or ______ people. If it is in the same person, it is called ________.

same, different, autozygous.

Goal of IBD is to

identify shared DNA segments to determine how closely to individuals are related.

Identity by State (IBS)

to establish a baseline of genetic similarity across populations.

How many cross overs did this genome have?

2

Show a IBD example where the offspring are sharing 1 allele

Show IBD example where 2 alleles are shared and explain

They came from the same common ancestor (parents) so the offspring’s alleles are IBD with each other.

Is this an example of IBD?

No, from this information the A alleles in the offspring are not being shared by a sibling. So we have to see the granoarenrs to determine

Is this an example of IBD?

No because we know that allele A comes from mom from one child and father for the other for each child.

Is this an example of IBD?

No because the A allele comes from 2 different parents for each offspring per the second allele.

Coefficient of Kinship

Probability that 2 randomly chosen alleles in 2 different people are IBD

Symbol for Coefficient of Kinship

a 0 coefficient of kinship means

people are unrelated

a ½ coefficient of kinship mean

people are genetically identical

if the coefficient of kinship is > ½ then and when does this occur

the people are very very closely related, and this occurs during inbreeding

Coefficient of inbreeding (F)

probability of 2 alleles being IBD in the same person

In an outbred population the Coefficient of inbreeing (_) for a person is _____ ___ the coefficient of kinship for the person’s parents.

F , equal, to

Fill out the Coeficient of kinship table for these relationships

What solves the limitation of Coefficient of kinship and how

Cotterman’s K because it distinguishes between unilineal vs bilineal allele sharing

k₀ =

Probabilty( share 0 alleles IBD)

k₁ =

Probability (share 1 allele IBD)

k₂ =

Probability(share 2 alleles IBD)

How to calculate Coefficient of kinship using Cottermans K

= k₁/4 + k₂/2

Cotterman’s K equation for outbred pedigrees only

k₀ + k₁ + k₂ =1

k₂ = 0 except for

Bilineal relatives

what is the first cousins , 1st cousins once removed, and 2nd cousins cottermans k look like.

Fill out the IBD plot at the circles

Why do we care about Binomial and Normal distributions?

The data we collect, the parameters we estimate, and test-statistics incorporate these underlying distributions.

Binomial distribution measures the likelihood of ______ number of _______ in a set number of ______

Specific, successes, trials

Each trial in a binomial experiment hashow many outcomes? And what are they

2, success or failure

Are binomial trials independent or dependent? Explain

Independent because one trial does not effect the other

The distribution of X is binomial (____,____) where____ is the probability of successes and ____ is the number of trials.

n,p,p,n

What is the shape of a Normal distribution? and what kind of outcomes does it measure?

1. Bell shaped curve

2. quantitative continuous

Mean of normal random variable is

μ

Variance of a normal random variable is

Standard deviation symbol

Normal distribution mean and variance notation

When variance in a normal distribution increases it forms a _______ curve where as when variance is decreased it shows a _____ curve.

wider, narrow

Variance vs standard deviation

• Standard deviation measures how spread out numbers are from the mean.

• Variance calculates the average degree to which each number is different from the mean.

Increased mean creates a curve that is skewed to the ____ while, a decreased mean creates a curve that is skewed to the ____.

left, right

t-distribution vs Normal distribution

The normal distribution is used when the standard deviation is known. While the t-distribution is used when the standard deviation is not known.

The t-distribution is like the normal except for _____ tails.

wider

degrees of freedom are

the ability for