Genetics: Lecture 1

Introduction to genetics
Learning Objectives
• Explain why an understanding of genetics is important for our everyday lives.
• Describe the organisation of DNA.
• Explain the difference between genotype and phenotype.
• Identify homozygous and heterozygous genotypes.

Overview of genetics
• Heredity = sameness
• Variation = differences
• Genetics is central to many human affairs
o Pandemics
o Genetically modified food and engineering

Direct-to-consumer genetic tests

• Method of marketing genetic tests to consumers without direct involvement of a
health care provider
• Public health service: not for profit, based on clinical knowledge
• Commercial service – typically not defined by the fundamental responsibility to the
patient
• “23 and me” DNA reports of ancestry
o Data from these can be used for medical research
• Interpretation of these results are crucial
o Could your decision to do a direct-to-consumer test affect your family?
- Paternity
o Are you happy with what the company might do with your data?
- Used to track down criminals
o What is genetic risk?
- Some people have more or less genetic risks and this number can
increase from environmental conditions

Genetic risk for common health conditions

Impacts of genetics in society
• In some cases this is very beneficial to prevent cases of death
• Sports performance: polymorphism identified
• Genetically modified food and plants
• Media example – lady’s cells taken without consent
• Often there is no right or wrong answer – or we are still working out what it might
be, so not one of us can afford to be ignorant of genetic discoveries and the way
they can influence our lives.

Genetic sequencing
• The revolution in genomic technologies, has touched nearly every area of medicine
• In the UK they are sequencing children to understand disorders for diagnosis
• In some cases this leads to life saving treatments
• Covid 19 sequencing - Transmission patterns of different strains
• Benefits of sequencing the virus
o Identifying different strains
o Understanding biology of the different strains (including transmissibility)
o Develop vaccines
o Understanding covid-19 outbreaks globally

Genes, alleles and chromosomes

• DNA is organised into genes
• Genes are packed into chromosomes within the cell’s nucleus
• Chromosomes consist of 2 sister chromatids (each made of double stranded DNA)
• Somatic cells: contain 2 chromosomes, 1 inherited from each parent
• Humans are diploid – two copies of each chromosome
• Genome: 22 pairs autosomes and one pair of sex chromosomes (=23)
• Variation in an individual’s genotype can cause variation in the amino acids and
proteins they encode
• This results in variation of phenotypes
Useful Definitions

Genetics: is the study of heredity and inherited variation.

Gene: a discrete unit of heredity, consisting of a specific DNA or RNA sequence.
Locus: specific physical location of a gene or other DNA sequence on a chromosome. (street
address analogy)
Allele: alternative versions of a gene e.g. P or p. - usually at a specific gene
Homozygous: an organism having a pair of identical alleles for a trait e.g. pp.
Heterozygous: an organism having two different alleles for a trait e.g. Pp.
Genotype: an organism's genetic makeup e.g. PP, Pp or pp. - includes all different alleles
that are in a person’s genome
Phenotype: an organism's expressed traits e.g. purple or white flowers.
Trait: a specific characteristic of an individual (determined by genes, environmental factors
or a combination of both). A given trait is part of an individual’s overall phenotype. Can be
qualitative or quantitative
Germ cells: sex cells (eggs and sperm) that are used by sexually reproducing organisms to
pass on genes from generation to generation.
Somatic cell: any cell of the body except sperm and egg cells.

Phenotype and Genotype

Genotype: Homozygous dominant, homozygous recessive and heterozygous

Phenotype: physical traits/characteristics determined by genotype
Chromosomes

• Centromere: primary constriction where it joins to its sister chromatid, also where
the spindle attaches
• Telomeres: at the ends of the chromosomes and protect them from damage

• Replicating chromosomes have 2 sister chromatids

• Non-replicating has 1 chromatid
• Homologous pair - 1 maternal and 1 paternal
• We count chromosomes whether they are replicating or no
Human karyotype
• Karyotype is the visual representation of a species chromosomes arranged in pairs at
mitotic metaphase when chromosomes are nice and condensed
• Arranged by size
• Used for diagnosis of down syndrome where the is an extra copy of the 21st
chromosome

Exercise Q & A’s

What is direct-to-consumer genetic testing?
• Direct testing of a person’s genome sequence such as techniques used by "23 and
me"
• Commercial genetic testing -> straight to the consumer and typically doesn’t go
through a health care provider
Why is it important to consider your biological family when deciding to have a direct-to-
consumer genetic test?
• Because genetics are inherited and shared between parent and off-spring, giving
your DNA up also gives up some of your relatives (how much depends on their direct
relation)
• Genetically related
What are some limitations of direct-to-consumer genetic testing
• False positives – errors for genes
• False negatives - BRACA 1 gene has lots of variants and not all are tested
• Scientific evidence
• Use of data - fine print, what are they going to do with the data?
Genetics: Lecture 2
The genetic basis of inheritance – mitosis and meiosis
Learning Objectives
1. Differentiate between the process of replication and reproduction.
2. Explain how replication and reproduction relate to the concepts of heredity and variation.
3. List the phases in the cell cycle and describe changes in the amount of DNA in each phase.
4. Compare and contrast the behaviour of chromosomes in mitosis and meiosis.
5. Explain how sexual reproduction in diploid organisms produces genetic variation.

Mitosis
• Reproduction (in mitosis) is when a somatic cell undergoes division and results in the
production of two genetically identical daughter cells.
• In biology this process is based on the reproduction of cells and the cell’s genetic
material.
• Cell division plays several important roles in the life of an organism.
o In unicellular organisms (e.g. bacteria, yeast) it produces an entire individual
(asexual reproduction).
o In multicellular organisms it allows growth and repair.

Mitotic phase
• two stages - mitosis and cytokinesis
• produces 2 daughter cells

Interphase phase
• ~ 90% of the cycle
• intense biochemical activity/growth of cell
• divided into three stages - G1, S, G2
G1 (gap phase 1)
• Cells grows and produces proteins and organelles such as mitochondria
• Chromosomes are unduplicated here.

S phase: (synthesis phase)

• Chromosomes duplicated
• This is essential because there needs to be enough content for the 2 daughter cells
produced.
• Amount of DNA is doubled here

G2 (gap phase 2)
• Cell prepares for division
• By the end of interphase there is still 46 chromosomes but 92 chromatids
• Mitosis is division of genetic material
• Cytokinesis is division of the cytoplasm and chromatid number is 46 chromatids in
each daughter cell

Chromosome distribution during cell division

DNA in cells during mitosis

Mitosis (continued)

Prophase
• Chromosomes start to condense to a compact form for division, centrosomes start
to move away from each other
• Microtubules help with separation
Prometaphase
• Kinetochores form at the centre of chromatids and microtubules attach pulling them
apart, chromosomes start lining up on metaphase plate
• Formation of specialised protein structures called kinetochores
• Chromosomes start to line up
Metaphase
• Centrosomes at opposite poles, chromosomes line up on metaphase plate,
chromosomes start to get pulled apart from kinetochores
• Start to line up on metaphase plate
• Each sister chromatids point to opposite poles
• Start to get pulled apart

Anaphase
• Chromosomes move to either pole as kinetochore microtubules shorten, separates
genetic material
• Shortest phase of the cell cycle
• Sister chromatids start to move (divide)

Telophase
• Cell cleaves dividing chromosomes, nuclear membrane forms around each set of
chromosomes, cytoplasm of parent cell divided between two daughter cells
• Cell cleavage
• Nuclear membrane forms around each of the chromosomes
• Now have the same genetic make-up as parent cell

Chromosome and chromatid number in mitosis

Chromosome number stays the same but the chromatid number changes
Asexual vs Sexual Reproduction

Asexual reproduction
• Does not involve fusion of gametes or change in chromosome number e.g. hydra
• The asexual reproduction of the hydra “chip off the old block” or a clone
• Exact copies using mitosis
• Hydra is a multicellular organism which "buds" an offspring

Meiosis – Overview
• Meiosis takes paired chromosomes and breaks them apart to make gametes.
• It also provides the opportunity for recombination to occur to produce new
outcomes, which is critical for diversity.

Key terms
Life cycle: sequence of stages in an organism's reproductive history - conception to
production of a new offspring.
Gametes: haploid reproductive cell, produced in the gonads (sperm) in males, ovaries (eggs)
in females.
Fertilization: the fusion of two haploid gamete nuclei to form diploid zygote nucleus.
Haploid: a single set of chromosomes (1n).
Diploid: the condition in which each autosome is represented twice (2n).
Meiosis: the two successive nuclear divisions in which a single diploid (2n) cell forms four
haploid (1n) nuclei.
Zygote: fertilised diploid cell formed from 2 haploid cells

Human life cycle

• The only cells that are not produced by mitosis are the gametes.
• Meiosis halves the number of chromosome sets in gametes, resulting in haploid
sperm and egg cells (n = 23).
• Egg and sperm combine during fertilization to restore diploid state (2n = 46).
• Mitosis conserves this diploid state in every somatic cell.
Chromosome numbers in meiosis
Meiosis I: Separation of homologous chromosomes

Prophase 1
• Crossing over occurs, produces recombinant chromosomes.
• 1-3 crossing over events/chromosome
• Crossing over occurs between non-sister chromatids of a homologous pair
• Produces a recombinant chromosome with both paternal and maternal DNA

Metaphase 1
• Chromosomes orientate randomly on the metaphase plate
• One chromosome of each pair faces each pole
• Each chromosome pair has lined up independently of the others

Anaphase 1
• Homologous chromosomes separate and go to each pole guided by the spindle
apparatus
• If something went from at this stage with the number of chromosomes

Telophase 1 and cytokinesis

• Two haploid cells form
• Each chromosome contains two sister chromatids
• One or both chromatids contain regions of non-sister DNA
Meiosis II
• Meiosis I and II: Two cell divisions to result in 4 haploid cells (gametes) that are
genetically distinct from another and from the parent cell
• Prophase II to Telophase II (below)
• Haploid cells produced are genetically distinct

Chromosome and chromatin number in meiosis

Independent assortment
• Sexual reproduction generates variation because of the orientation of pairs of
homologous chromosomes in meiosis.
• At metaphase I of meiosis, homologous pairs align in a random orientation on the
metaphase plate.
• Therefore, each maternal and paternal homologue assorts independently of every
other pair.
• When n = 23 as in humans, 8.4 million different maternal and paternal chromosome
combinations are possible.
Crossing over
• Crossing over occurs during prophase I of meiosis.
• Crossing over is the exchange of genetic material between non-sister chromatids.
• Crossing over produces recombinant chromosomes, that is chromosomes carrying
genes derived from each parent.
• Crossing over shuffles the genes within the chromosomes.
• Crossing over between homologous pairs of chromosomes is obligative.
• In humans 1-3 crossover events occur per chromosome pair.
Random fertilization
• The random nature of fertilization adds to the genetic variation arising from meiosis
any egg and any sperm
• Even without crossing over, in humans each gamete represents ~8 million possible
chromosome combinations.
• The fusion of a single male gamete with a single female gamete will produce a zygote
with any of about 64 trillion (8 million×8 million) diploid combinations *
• The number of possibilities is truly astonishing, each individual is unique.

*This doesn’t account for crossing over

Exercise Q & A’s

Genetics: Lecture 3
Mendelian inheritance: Inheritance patterns are a consequence of gene transmission
Learning Objectives
1. Describe the evidence that supports the chromosome theory of inheritance and
explain how meiosis underlies Mendelian patterns of inheritance.
2. Explain the way traits are determined by the interaction of alleles at the same or
different loci.
3. Draw a model that explains the biochemical basis of complete, incomplete and
co-dominance.
4. Calculate the genetic distance between two genes using recombinant
frequencies.
5. Construct a genetic map of a chromosome using genetic distances.

Particulate inheritance & mendelian genetics

• Patterns of how traits are passed on
• Transmission of traits are particulate

Mendelian laws
• Mendel crossed pea plants with different characteristics (white or purple flowers)
and observed offspring.
• The study of thousands of genetic crosses allowed him to deduce two fundamental
principles of heredity:
• Segregation and independent assortment
• Egg and sperm can only receive one of two alleles

Mendel’s pea experiments

• Allele for yellow seeds is dominant (Y), allele for green seeds is recessive (y)
• Allele for round seeds is dominant (R), allele for wrinkled seeds is recessive (r)
• Independent assortment results in two new phenotypes -green round seeds and
yellow wrinkled seeds
Behaviour of genes & chromosome
• Chromosome theory of inheritance – parallel behaviour of Mendel’s genes and the
behaviour of meiotic chromosomes.
Alleles
• Alternate versions of a gene
• Alleles are a specific locus or a specific location on a gene

Allelic interactions: Complete dominance

• Huntington’s disease is an autosomal dominant late onset fatal neurodegenerative
disorder that affects 1:10,000 individuals.
• You only need one H allele to have the condition
• A dominant disorder
• The Huntington’s disease allele results in the loss of neurons, primarily in the basal
ganglia and affects motor control, mood and cognition.
Allelic interactions: recessive conditions
• Cystic fibrosis is New Zealand's most common lethal genetic disease.
• Heterozygous carriers possible
• You need two cystic fibrosis genes to have CF
• Wildtype gene can function well enough to make up for the non-functional
• The cystic fibrosis allele results in defective or absent chloride transport channels
• Symptoms include mucus build-up and poor absorption of nutrients in the small
intestines
Allelic interactions: Incomplete dominance
• The dominant allele is not fully expressed in heterozygote.
• The heterozygote has an intermediate phenotype.
• Neither allele is fully dominant
• Still particulate inheritance
Allelic interactions: Co-dominance

• A and B alleles code for carbohydrates (called A or B antigens) attached to specific

cell-surface molecules on red blood cells.
• An individual’s blood cells may have carbohydrate A (type A),carbohydrate B (type
B), both (type AB), or neither (type O).
• Full expression of both alleles in the heterozygote. In humans that have the AB blood
group both carbohydrates are present & detected by immunological tests.

Multiple alleles: Human blood groups

• The gene encoding for the ABO blood group is an example of a gene with multiple
alleles
Linked genes and linkage
• The number of genes per genome far exceeds the number of chromosomes.
• Therefore, there must be more than one gene per chromosome.
• Each human chromosome contains hundreds or thousands of genes, except for the Y
chromosome.
• Linked genes are genes located on the same chromosomes and that tend to be
inherited together.
• Linked genes are exceptions to Mendelian inheritance.
• How does linkage between two genes affect inheritance of characters?

Are body colour and wing size linked

• Alleles for body colour are b+ (grey) and b (black), alleles for wing size are vg+
(normal) and vg (vestigial). Nothing is mutant
• Crossed parental flies to produce heterozygotes which were wild-type in
appearance.
• Black body and vestigial wings are recessive.
• Drosophila: + corresponds to the wild-type allele

F1 testcross hypothesis
• If the two genes are completely linked there will be fewer recombinants (b and vg
alleles get inherited together).
• If the two genes are on different chromosomes, there will be equal numbers of the
four offspring (due to independent assortment).

Offspring if b and vg are on different chromosomes

• Independent assortment will result in equal numbers of the four offspring.

Offspring if b and vg are on the same chromosome

• Most offspring will represent the parental genomes
Chromosomal basis for recombination on linked genes

Linkage with some cross over

Recombination of linked genes

Recombinant frequencies
• Assumes that crossing over occurs randomly, then the frequency that crossing over
occurs should be proportional to the distance between two genes.
• Recombination frequency = No. of recombinants / Total number of offspring ́100 / 1
• A 1% recombinant frequency equals 1 map unit or 1 centimorgan.
• You can use the frequency of recombinants to build linear chromosome maps.
• A genetic map is the order that loci occur along a chromosome.

Linkage map

• The observed recombination frequencies between three fruit fly gene pairs are b-cn
9%, cn-vg 9.5%, & b-vg 17%.
• The b-vg recombination frequency is slightly less than the sum of the b-cn and cn-vg
because double crossing over can occur, reducing the recombination frequency.
• As crossing over can occur many times and is not uniform over the length of a
chromosome, map units do not correspond to actual physical distances.
Exercise
GENETICS: Lecture 4
Non-mendelian inheritance
Learning Objectives
• Describe the inheritance patterns of sex-linked traits in Drosophila.
• Outline the chromosomal basis of sex determination in mammals and draw a
simple diagram detailing the major genetic features of the human X and Y
chromosome.
• Explain why dosage compensation and X chromosome inactivation can lead to
mosaic individuals.
• Describe the process of meiotic non-disjunction and give examples of human
disorders that result from alterations in chromosome number.

Sex linked traits

• Many genes for traits are present on X-chromosomes but not Y-chromosomes = sex-
linked inheritance.
o Smaller mainly for sex determination
• Results in a different pattern of inheritance than genes on the autosomes.
o Different number of genes between male and female
• X-linked genes in males are described as hemizygous (only one chromosome pair (or
segment) rather than two).
• Any male receiving an X-linked allele from a mother (even for a recessive condition)
will express the trait.
• Male cannot give x-linked chromosome to son

Morgan’s flies
• Fruit flies have three pairs of autosomes and one pair of sex chromosomes (X & Y)
• White eye - mutation which means flies can no longer convert colourless precursor
into red pigment, and as a result they have poor eyesight
• White eyed = poor eye sight
• All white eyed flies were male (recessive)
Morgan’s first mutant
• The F2generation showed a typical Mendelian 3:1 ratio (red:white), however all
white-eyed flies were males

Non-mendelian inheritance
Red-green Colour Blindness
• X-linked condition
• Red-green colour blindness - characterised by the deficiency in red or green sensitive
cones, so red and green are seen as the same colour.
• The gene for red–green colour blindness is recessive (designated n here) and located
on the X chromosome.

Chromosomal basis of sex

• Although sex has traditionally been described as a pair of binary categories, we now
know those classifications are less distinct.
• We will use sex to classify anatomical and physiological traits (as opposed to gender).
• Provides an understanding of disorders associated with sexual phenotypes.
• Gonadal development provides an excellent model to study organogenesis and its
genetic control.
• Heterogametic sex – produces two kinds of gametes and determines the sex of the
offspring (e.g. XY).
• Homogametic sex – produces one kind of gamete (e.g. XX).

XY sex determination in humans

Chromosomes and sexual phenotype

Aneuploidy of sex chromosomes

• Nondisjunction of sex chromosomes produces a variety of aneuploid conditions.
• Most of these conditions appear to upset the genetic balance less than conditions
involving autosomes.
• This may be because the Y carries very few genes, and/or because extra copies of the
X chromosome are inactivated as Barr bodies.
• Kleinfelder syndrome – XXY
o Extra chromosome is inactivated
o Some breast enlargement and other female characteristics are common
Sex-determining Region Y (SRY gene)
• SRY triggers testicular development and is a transcription factor (DNA binding
protein) called testes determining factor.
• Absence of this gene in the gonads results in the development of ovaries (even in an
XY embryo).
• Pseudo autosomal regions are short regions of homology on the X and Y
chromosome.
• Allows X and Y to pair and behave like homologues during meiosis.

Sex determination and differentiation

• Mutations in the androgen receptor gene result in partial or complete inability of the
cells to respond to androgens (male hormones)

Androgen insensitivity syndrome.

• Androgen insensitivity syndrome results in the partial or complete inability of the cell
to respond to androgens.
• Therefore, a person has physical traits of a female, but the genetic makeup of a
male.
Dosage compensation and X chromosome inactivation
• Mary Lyon, a British geneticist in the 1960’s proposed that in females, each of the
embryonic cells randomly inactivates one of the two X chromosomes.
• This equalises the dosage of X-encoded genes between female and male cells.
• The inactivated X chromosome is called a Barr body.
• Barr bodies are densely stained objects in the nuclei of females.
• Most Barr body genes are not expressed.
• Barr bodies are stable through mitosis but the X is reactivated in the cells that give
rise to ova.

X inactivation
• Example shown in tortoise shell cats
• Females consist of a mosaic of two types of cells: those with the active X derived
from the father & those with the active X derived from the mother.

Inheritance of organelle genes

• Not all eukaryotic genes are located on nuclear chromosomes, some are located in
organelles.
• Mitochondria as well as chloroplasts in plants contain small circular DNA molecules.
• Mitochondria genes in most plants and animals show maternal inheritance.
• Genes on organelles do not show Mendelian inheritance.
• Most mitochondrial genes are involved in the electron transport chain and ATP
synthase.
• The nervous system and muscles are most susceptible to energy deprivation,
therefore most mitochondrial diseases affect these systems.
Mitochondrial DNA
• The disorder mitochondrial myopathy causes weakness, intolerance of exercise &
muscle deterioration.

Meiotic disjunction
• Aneuploidy refers to an abnormal number of chromosomes
• Non disjunction during meiosis - usually occurs at anaphase
Abnormal chromosome number
• Changes in chromosome number can have a major impact on the development and
have had an impact on the evolution of most organisms.
• Aneuploidy – abnormal number of certain chromosomes.
• Trisomic – 1 extra chromosome (3 copies).
• Monosomic – 1 less chromosome (1 copy).
• Nullisomic – lack both chromosomes (0 copies).
• Polyploidy – more than two complete chromosome sets
o e.g. triploid 3n and tetraploid 4n.

Alterations to chromosome structure

Salivary amylase gene

• AMY 1 gene
• Example of positive selection
• More people who have a high starch diet will
have the AMY 1 gene present
• More need to breakdown starch
Human disorders due to chromosome alterations
• Down’s Syndrome
o The karyotype shows trisomy 21, the most common cause. Incidence 1 in
1,100 children & correlates with maternal age.
• Chronic myeloid leukaemia (CML)
o The cancer cells in nearly all CML patients contain a short chromosome 22
and an abnormally long chromosome 9.

Exercise
GENETICS: Lecture 5
Complex traits and polygenic inheritance
Learning Objectives
• Define the terms pleiotropy and epistasis and give examples of each.
• Explain how continuous phenotypic variation can result from the additive effect of
two or more genes.
• Draw a simple diagram that describes the relationship between the phenotype,
genotype, developmental noise and the environment.
• Give examples that demonstrate how the environment can have major effects on
the phenotype.
• Explain the implications that norms of reaction have on our understanding of the
relationship between genotype and phenotype.

Relationship between genotype and phenotype

• Complete, incomplete, co-dominance and multiple alleles result from the effects of a
single gene.
• However, most organisms have thousands of genes, and a number of genes can
contribute to a single trait.
• Furthermore, most eukaryotes are diploid and have two alleles of each gene.
• The phenotype of an individual is determined by interactions between alleles at the
same locus, and in many cases at a number of different loci, as well as by the
environment.

Pleiotropy
• Pleiotropy – a single gene having multiple phenotypic effects.
• The cystic fibrosis allele results in a defective (or the absence of) chloride transport
channels.
Epistasis
• When one gene / locus affects the phenotype of another gene.
• There are three coat colours in Labradors (black, brown and yellow) and these result
from an epistatic interaction between two genes.
• Colour coats in Labradors
o In Labrador retrievers, coat colour is controlled by a single locus (B/b)
o Black (B) coat colour is dominant to brown (b)
o A second gene determines whether or not pigment will be deposited in the
hair.
o The dominant allele (E) results in deposition of either the black or brown
pigment in the hair.
o If the individual is homozygous recessive (ee) no pigment can be deposited
and the Labrador will be yellow.
o The gene for pigment deposition (E/e) is epistatic to the gene for black and
brown pigment (B/b).
o The alleles on these two genes are not linked, yet the gene products interact.
o Although the two genes affect the same characteristic, they follow the law of
independent assortment
o The mating between Labradors with genotype BbEe - not the expected
9:3:3:1 ratio
Continuous phenotypic variation
• In horses coat colour varies along a continuum from light to dark and is an example
of complex trait.

Polygenic inheritance
• Mendel studied traits that could be classified on a either-or basis (discrete) e.g.
purple or white flowers.
• But many traits vary continuously, for example height and skin colour – quantitative
traits.
• Quantitative traits usually indicate polygenic inheritance.
• Polygenic inheritance is the additive effect of two or more genes that determine a
single phenotypic traits.
• That is a number of genes affect / produce a single trait.

Human skin pigmentation

• Human skin pigmentation varies hugely and shows continuous phenotypic variation
from light to dark.
• Skin pigmentation in humans is controlled by many genes.
• There is evidence to suggest at least three genes are involved.
• Let's consider these three genes, with a dark skin allele for each gene (A, B or C) and
being incompletely dominant to the other alleles (a, b or c).
• AABBCC person would have very dark skin while an aabbcc person would have very
light skin.
• Because the alleles have an additive effect AaBbCc and AABbcc would have the same
skin colour because both have three dominant alleles
• A simplified model for polygenic inheritance of skin pigmentation in humans,
environmental factors can help to smooth the curve.
Environmental effects on phenotypes
• Departures from Mendelian inheritance also arise when the phenotype depends on
the environment as well as the genotype.
• In many cases the genotype is not associated with a defined phenotype, but rather a
range of possible phenotypes due to environmental influences.
• The phenotypic range is broadest for polygenic traits.
• We can contrast a reductionist view of single genes / phenotypic traits to that of
emergent properties of the organism as a whole.
• Phenotype is the interaction between alleles and environment
o Environmental effects on the phenotype (a) Hydrangeas grown in basic soil
(b) Hydrangeas of the same genetic variety grown in acidic soil with free
aluminium.

Norms of reaction
• The environmental impact on phenotype.
• The phenotype is the result of the interaction between the genotype and a given
environment.
• The norm of reaction is the phenotypic range of a given genotype in different
environments.
• For some traits, such as the ABO blood group, the norm of reaction has no breadth,
that is a given genotype always results in the same phenotype.
• However, this is not the case for many other traits, norms of reactions are greatest
for polygenic traits.
• Human blood groups
o ABO blood group, the norm of reaction has no breadth
Eyes of drosophila
• A normal eye, the number of facets determine the eye size.
• Changes in temperature result in changes to the size of the eye.
• Three different genotypes: The relative eye size of the wild type, infrabar and
ultrabar genotypes at a high temperature.

Norm of reaction for three genotypes

Developmental noise
• A phenotype is determined by the interaction of a specific genotype and the
environment.
• However, a closer look at some phenotypes shows unexplained variation.
• The number of cells in the left and right eye of a Drosophila are different, despite
being genetically identical and developing in the same environment.
• Random events in development leads to variation in phenotype called
developmental noise.
• In some characteristics, such as eye cells in Drosophila, developmental noise is a
major source of variation in phenotype.
• A wild-type Drosophila raised at 16oC have on average 1000 facets in each eye, but
an individual might have 1017 facets in the left and 982 in the right eye.

Epigenic landscape
 • The epigenetic landscape is a metaphor proposed by Conrad Waddington to explain
phenotypic variation.

Exercise

GENETICS: Lecture 6
Population genetics – part one

Learning Objectives
• Understand the difference between germline and somatic cell mutations.
• Describe the genetic and biochemical basis of Sickle-cell disease.
• Derive the Hardy-Weinberg equation.

Populations vs families
• In a family there is specific genotypes in an off-spring dependent on the parental
genotype
• Genetic structure of a population will be determined by the frequency of the
different Matings within it.
• The frequency of alleles determines the frequency of genotypes in a population.
 • A recessive trait can be common if the frequency of that allele is very high-
heterozygous carriers
• This helps us understand basic evolution.

Mutations and genetic disorders

• A mutation is a change in an organism’s DNA.
• Point mutation, gene duplication and other processes produce new alleles or genes
(genetic variation).
• A new germline mutation immediately changes the gene pool of a population by
creating a new allele.
• Mutations are relatively rare, at least for coding genes, reflecting the high fidelity of
DNA replication.
• Mutations are random, in that they can occur in any gene without regard to the
benefit of that cell.

Somatic and germline mutations

• Somatic mutations are not transmitted to progeny, while germline mutations are
transmitted to some or all progeny.
• *Germline (gametic): affects the entire organism and can be inherited and can affect
population dynamics
• Somatic mutations: tend to have localized effect (e.g. mole) most are harmless but
can lead to cancer for example. Occurs after the first cell division, is not in gamete so
cannot be passed on.
Population genetic variation
• Not all genetic variation results in changes to the phenotype
• Much of the genetic variation in the alcohol dehydrogenase (Adh) gene occurs in
introns and most exon variation does not change the amino acid sequence (neutral).
• Introns typically have the majority of variants because there is more tolerable DNA
• Not all changes in exons results in a change in amino acid translation
• Most variation is neutral and doesn’t change phenotype

Human genetic disorders

• Most mutations are neutral (no phenotypic effect).
• However some mutations effect function, if this has an adverse effect on the
phenotype it is referred to as a genetic disorder / hereditary disease.
• Sickle-cell disease is caused by the substitution of a single amino acid in the
haemoglobin protein of red blood cells (RBC).
• The sickle-cell protein differs from the wild-type by a single amino acid (glutamic acid
➝valine) and causes a change in function.
Sickle cell disease and sickle cell trait
• When the oxygen content of an individual’s blood is low the sickle-cell haemoglobin
protein aggregates into long fibres and changes the shape of the RBC.
• Symptoms include physical weakness, pain, organ damage and even paralysis as
sickle-cells block and clog small blood vessels.
• Sickle-cell disease is the most common inherited disorder among people of African
descent (1/400 African-Americans).
o 1/10 are heterozygous: high carrier rate
• Heterozygotes are usually healthy, but may suffer some symptoms during long
periods of reduced blood oxygen. Some cells can sickle but most are still healthy
o They have both sickled and normal RBCs.
• Individuals with two copies of the sickle-cell allele manifest the disease,
heterozygous individuals show some symptoms and are said to have the sickle-cell
trait.
• Why is it so common?
o Having 1 copy reduced the frequency and severity of malaria attack, the bug
struggles to survive in the sickle cell.
o Heterozygote will have reduced symptoms of malaria
Gene pools
• Population – a group of individuals of the same species that live in the same area and
interbreed.
• Gene pool – is the sum of all the alleles of all genes of all individuals in the
population.
• Hardy-Weinberg equilibrium – allele and genotype frequencies in a population will
remain constant from one generation to the next.
o allele and genotype frequencies are constant
• Hardy-Weinberg equation – allows the calculation of the expected genotype
frequencies given the observed allele frequencies.
o population is evolving

Calculations of allele frequency

• There is 1000 number of alleles because there are 2 alleles which code for that gene
• For homozygous organisms you take the number of individuals with the phenotype
and times by the number of alleles (as seen above)
Selecting alleles at random from a gene pool
• Allele selections are random so we say chance
Hardy-Weinberg equilibrium
Exercise

A. p+q=1 (allele frequencies) and p2+2q+q2=1 (genotype)

B. q=frequency of the recessive allele, q2 is the frequency of the allele due to phenotypes
q2=0.0001
q= 0.01 which is ~1%

C-p+q=1
p=1-0.01
p=0.99 or 99%

D note these are the heterozygous genotypes

2pq= 2 x 0.99 x 0.01
= ~2% of the population are heterozygote
GENETICS: Lecture 7
Population genetics
Learning Objectives
• List the conditions a population must meet be in order to be in Hardy-Weinberg
equilibrium.
• Describe the processes that result in the loss of genetic variation.
• Calculate allele / genotype frequencies using the Hardy-Weinberg equation.

Conditions for Hardy-Weinberg

1. No mutations – the gene pool is modified if mutations change alleles.
2. Mating occurs at random – if individuals mate with a subset of the population,
genotype frequencies change.
3. No selection – differences in survival and reproduction of individuals with different
genotypes can alter allele frequencies.
4. Extremely large population size – the smaller the population, the more likely that
allele frequencies will fluctuate by chance.
5. No gene flow – movement of individuals in and out of a population can alter allele
frequencies

Allele frequency
• What can alter allele frequencies in a population?
• A deviation from any of the H-W conditions is a potential cause of evolution.
o New mutations
o Non-random matin
o Natural selection
o Gene flow
o Genetic drift
▪ Founder effect
▪ Bottleneck effect

Non-random mating
• Non-random mating affects the way alleles combine to form genotypes.
• Outbreeding promotes variability, while inbreeding results in loss of variation.
• Matings between second cousins or closer are more likely to produce homozygous
genotypes for otherwise rare autosomal recessive genes.
• Cystic fibrosis is the most common life threatening genetic disorder affecting New
Zealand children.
• A child resulting from mating between first cousins has a ~7-fold greater risk of being
affected by cystic fibrosis.
• Inbreeding increases the percentage of homozygous individuals in a population.
• Inbreeding does not have a significant affect by itself on allele frequencies in the
gene pool
o beyond altering the frequency of homozygous and heterozygous genotypes
Natural selection
• Individuals in a population exhibit variations in their traits.
• Traits better suited to their environment produce more offspring.
• This can result in alleles being passed to the next generation in proportions that
differ from those in the present generation.
• For example, there is an allele in Drosophila that confers resistance to several
insecticides.
o In laboratory strains this allele has 0% frequency: before 1930s
o In flies collected after 1960, the allele frequency is 37%.
• Traits that enhance survival or reproduction tend to increase in frequency over time.

Genetic drift
• Genetic drift is the change in allele frequencies as a result of chance events.
• The overall effect of drift is a loss of genetic variation.
• Drift has major effects in small populations including in founder and bottlenecked
populations.
• A small wildflower population has a stable size of ten plants. By chance, the
frequency of the CW allele increases, then decreases to zero.
• Genetic drift therefore tends to lose variation, usually the lower frequency allele.
• Founder effect – when a small population branches off from a larger one, by chance
the small population may not have all the alleles present in the larger population.
• Population bottlenecks – occur when a population is drastically reduced in numbers,
consequently chance effects can result in the loss or fixation of alleles.
Founder effect
• A small population branches off from a larger one
• The smaller population may not have all the alleles of the bigger one (just by chance)
• The North American Amish were founded by a small number of European
immigrants in the 1700s. Several genetic diseases that are rare elsewhere are
relatively common in this community.

Population bottleneck
• An event drastically reduces the size of a population (e.g. disease, pandemic, fire,
flood).
• By chance alone, in the surviving population, certain alleles may be overrepresented
or absent altogether.
• By chance, blue marbles are overrepresented in the surviving population & gold
marbles are absent.
Effects of genetic drift
• Genetic drift is significant in small populations.
• Genetic drift can cause allele frequencies to change at random.
• Genetic drift can lead to loss of genetic variation within populations.
• Genetic drift can cause harmful alleles to become fixed.

Gene flow
• Mutation, non-random mating, selection and genetic drift are not the only
phenomena affecting allele frequencies.
• Gene flow is the movement of alleles into or out of a population due to the
movement of individuals or their gametes.
• Because alleles are transferred between populations, gene flow tends to reduce
differences.
• If gene flow is great enough it can result in two populations combining into a single
common gene pool.
• Gene flow tends to homogenise allele frequencies among populations, thus
maintaining variation within populations.
• The introduced CW alleles would modify the original population’s allele frequency in
the next generation.
• Gene flow tends to reduce genetic differences in populations, but you typically gain
genetic variation by the movement of alleles between populations

Applying the Hardy-Wein burg equation

• Hardy-Weinberg equation is often used as a first test to determine whether a
population is evolving.
• It can also be applied to clinical applications – as we did for PKU in the exercise for
lecture 6.
We assumed:
1. No new PKU mutations were introduced into the population.
2. People chose their mates randomly.
3. Ignored any differential survival or reproductive success of PKU genotypes.
4. No effects of genetic drift or gene flow.
o Note: H-W calculations are approximations.

Exercise
GENETICS: Lecture 8
Recombinant DNA technology & DNA techniques

Learning Objectives
1. Define recombinant DNA technology
2. Describe the basic principles and tools involved in cloning a gene
3. Explain the principles that underpin PCR and electrophoresis
4. Draw a simple diagram that illustrates the process of whole genome sequencing
5. Compare and contrast the methods for capillary sequencing vs high-throughput
sequencing

Recombinant DNA technology

• Recombinant DNA – genes or DNA from two different sources are combined in vitro
in the same molecule.
• Why use recombinant DNA technology?
o make many copies of a gene (e.g. to analyse protein products).
o study the function/expression of genes.
• In order to work directly with genes of interests, tools have been developed for
preparing DNA in multiple identical copies (cloning).
• Most methods of cloning use similar methods:
o Plasmid (small circular DNA molecule).
o Bacterial cells (facilitates the replication of the plasmid).

Restriction enzymes
• Restriction enzymes cut DNA at specific sequences, typically 4 – 8 bp in length.
• Restriction enzymes are isolated from bacteria where they protect the bacteria from
intruding DNA e.g. phages.
• There are hundreds of restriction enzymes and most have different recognition
sequences e.g. EcoRI –GAATTC.
• Most restriction sites are symmetrical and most cleave the sugar-phosphate DNA
backbone in a staggered way producing single stranded ends – sticky ends.
o The restriction enzyme EcoRI is a sticky end cutter.
DNA Ligase
• If the insert DNA is cut with the same restriction enzyme as the cloning vector, they
will have complementary sticky ends.
• When the insert DNA and cloning vector are mixed, they can form hydrogen bonds.
• DNA ligase covalently links two pieces of DNA together.
• DNA ligase catalyses the formation of covalent bonds that close the sugar-phosphate
backbone.
• When cloning a gene, the insert DNA is cut with the same restriction enzyme as the
vector and DNA ligase permanently joins the strands together.

Cloning vectors (plasmid)

• A plasmid is a circular autonomous DNA molecule which can replicate inside a host
bacteria cell
Cloning a single gene into a plasmid
Polymerase reaction chain (PCR)
• PCR is a three-step process that produces millions of copies of a targeted region of
DNA.
• PCR relies upon on a heat stable DNA polymerase.
• The polymerase generates the second strand of DNA from a single-stranded
template.
• DNA polymerase can only extend existing double-stranded regions and therefore
requires a primer.
• The number of DNA molecules roughly doubles each cycle (exponential growth).
• Reagents in a PCR reaction:
o DNA of interest
o Heat stable DNA polymerase
o Deoxyribonucleotides (dNTPs)
o Two primers (one for each strand)
Thermal cycling

Gel electrophoresis
• Gel electrophoresis separates macromolecules (DNA or protein) based on their rate
of movement through a gel in an electrical field – molecular sieve.
• The rate of movement depends on size, electrical charge and other physical
properties of the macromolecules.
• DNA separation depends mainly on size (length of fragment) with longer fragments
migrating less and small fragments migrating further along the gel.
• Size markers or a ladder is a set of DNA fragments of known size used for
comparison with samples of unknown length.
Visualising the gel

Capillary DNA sequencing

• Complementary base pairing can also be used to determine the nucleotide sequence
of a DNA molecule.
• The first automated procedure was based on a technique called dideoxy or chain
termination sequencing.
• This method involves using one DNA strand to synthesise a nested set of
complementary fragments.
• Synthesis is terminated randomly by the addition of a fluorescently tagged
dideoxyribonucleotide (ddNTP) rather than a deoxyribonucleotide (dNTP).
• There is a different fluorescent tag for each type of ddNTP (A, C, G, and T).
• Dideoxy or chain termination sequencing involves synthesis of a complementary
strand of DNA to that being sequenced.
The labelled molecules are separated by size and the fluorescent labels detected on each
fragment

Massively parallel sequencing

• In massively parallel sequencing or sequencing by synthesis, DNA fragments are
amplified to make many copies.
• A strand of each fragment is immobilised and the complementary strand
synthesized.
• A chemical technique is used to identify which of the four nucleotides is added (using
fluorescently labelled nucleotides).
• Thousands or hundreds of thousands of fragments ~300 nucleotides long are
sequenced in parallel.
• Up to 10 million (107) sequences are obtained simultaneously.
• New approaches to achieve long read sequencing are currently being developed –
e.g. Nanopore.
• Massively parallel sequencing has revolutionised DNA sequencing by sequencing
multiple strands of DNA simultaneously.

Step one: purify and copy DNA

Step two: Sequence

Step three: read the sequence

Step four: compare to other sequences (reference genome)

Bioinformatics
• Bioinformatics is the application of computational methods to the analysis of large
biological data sets e.g. DNA sequences.
Exercise
GENETICS: Lecture 9
Biotechnology and gene editing
Learning Objectives
• Compare and contrast genetic engineering with traditional biotechnology methods
such as selective breeding
• Explain the concept of personalised medicine and what it might mean for future
generations
• Describe the potential for gene therapy to cure human genetic disorders and how
CRISPR-Cas9 technology might contribute
• Explain the barriers and limitations of current gene therapy methods
• Review the ethical issues associated with recent advances in genetic analysis and
gene therapy

Biotechnology and Genetic Engineering

• Biotechnology is the manipulation of organisms or their component parts to make
useful products.
• Traditional biotechnology such as selective breeding has been used for thousands of
years to exploit naturally occurring mutations / genetic recombinants.
• However, recombinant DNA technology has launched a revolution in biotechnology.
• Genetic engineering is the in vitro alteration of genetic material and the
reintroduction of the altered DNA or RNA into a living organism.
• The key difference of genetic engineering with traditional biotechnology is that
genetic engineering manipulates DNA or RNA in vitro.

Genetic engineering vs selective breeding

• Genetic engineering is not a substitute for traditional methods but is a
complementary technology.
• Genetic engineering
o Precise choice of 1 or a few genes to manipulate (in vitro – outside of body)
o Genes from any species
o Control gene expression (example is a promoter)
• Selective breeding
o New combinations of many genes – usually naturally occurring mutations
o Only genes from related species
o No control of gene expression (natural reproduction reliance)

Traditional biotechnology – selective breeding

• Plant breeders have at their disposal a range of traditional biotechnology methods
• These methods include selective breeding and mutagenesis
• Remember that the rate of mutation is very slow
• Mutagenesis typically involves using either chemicals or radiation to induce
mutations and thereby enhance genetic variation
• Mutations can result in polyploidy due to error in cell divisions
• In agriculture variation in chromosome number has been exploited to create new
plant cultivars.
 o New world cotton is a polyploid that arose spontaneously – this is what
clothes are made from today.
o The common commercially available Cavendish banana is a sterile triploid (3n
= 33).

Cavendish and wild banana

• There are no seeds in the Cavendish banana (sterile triploid)
• Sterile = uneven chromosome number
• Essentially clones of each other
• They cannot divide their chromosomes equally to create a sex cell
• The black specks are the remnants of seeds (inviable gametes)
• Wild banana seeds are very hard and ‘tooth breakers’
• Very little genetic variation so disease is bad!

Genetically engineered food

Round-up ready maize (corn)
• Glyphosate is the active chemical in the herbicide Roundup and it inhibits amino acid
synthesis. The images above show a weed-infested glyphosate-resistance maize plot
before (B) & after (C) Roundup treatment.

Public concerns
• The initial concerns regarding genetically modified plants revolved around safety,
public health and environmental effects.
• More recently arguments in New Zealand involve branding of the country as
'genetically engineered-free' and protecting this image.
• Recent studies indicate that genetically engineering challenges peoples fundamental
beliefs regarding the sanctity of nature.
• The public is concerned that scientists are essentially ‘playing God’.
• When considering such issues it is important to carefully consider the information
and to insist that all sources of information be revealed.
• Care must be taken to read all arguments and base judgements on reliable facts.

Personalised medicine
• Personalised medicine - where each person’s genetic profile can inform them about
diseases and conditions for which they may be at risk.
• Direct-to-consumer testing and food allergies
• Many human genetic disorders can now be diagnosed using DNA sequencing (e.g.
PCR or massively parallel approaches).
• Sequence-specific primers can be used to amplify a DNA fragment, the fragment
characterised / sequenced and the disease-causing mutation identified.
• New human genetic disorders can be detected by whole genome sequencing using
massively parallel DNA methods.
• Massively parallel sequencing is close to delivering the $1000 human genome.
• Eventually, this might lead to the situation where everyone's genome is sequenced
at birth.

Preimplantation genetic diagnosis

• A form of prenatal diagnosis applied to embryos of parents with known carrier status
of a disease (e.g., Huntington’s disease)
• Fertilise egg in vitro
• Embryo culture
• Embryo biopsy
• Cell screening (PCR or FISH)
• Transfer of desired embryo that isn’t disease
Gene editing: CRISPR-Cas9
• This system comes from bacteria
• Cas 9 is a bacterial protein which supports the immune system of bacteria
• CRISPR-Cas9 can make targeted deletions, insertions and single nucleotide changes
in genomes.
• Cas9 protein acts together with a 'guide RNA' made from the CRISPR region of
bacteria.
• Cas9 will cut any DNA that is exactly complementary to the guide RNA.
• We can design guide RNA that targets any sequence in the genome
• Cas9 cuts both strands and triggers a DNA repair system.
• When there is no undamaged DNA for the repair system to use as a template, the
repair system sometimes inserts or removes nucleotides.
• If the cut is directed at a gene the repair often alters the gene so that it no longer
functions – 'knock out'.

How does CRISPR work?

Cas 9 protein Guide RNA

Guide RNA
Complementary
sequence
 Template by
repair enzymes

a) No template is provided, and repair enzymes insert and/or delete random

nucleotides, making the gene non-functional.
b) Repair enzymes use the normal gene as a template to synthesise the correct gene
sequence.

DNA and RNA oligonucleotides

• The use of a complementary sequence to a specific mRNA can inhibit its expression
and then induce a block the transfer of genetic information from DNA to protein.
• Several types categorized by their mechanism of action.
• Antisense oligonucleotides (ASOs) are short strands of DNA or RNA that modify the
production of specific proteins by binding to sequences of RNA made by faulty
genes.
• Commonly used in the laboratory an d many are now in clinical trials to treat human
conditions (e.g. Huntington’s disease).

Therapies targeting DNA and RNA in Huntington’s disease

Potential for gene therapy
• Broadly, gene therapy is a technique that modifies a person’s genes to treat or cure a
disease.
• The aim is to replace a disease-causing gene with a healthy copy or inactivate a
disease-causing gene.

Huntington’s disease
• ASO drug Tominersen (suppresses production of both the mutant and healthy form
of huntingtin).
• Significantly lowered levels of mutant huntingtin in the cerebrospinal fluid, without
serious side effects in early trials.
• 2021:phase III trial was stopped as it failed to show higher efficacy than placebo, and
when given frequently, led to worsened outcomes.
• Could decreases in levels of the normal protein cause problems? Did the ASO reach
the right parts of the brain? Has the disease progressed too far in the trial
participants for the drug to be beneficial?
• 2022: a new Phase 2 trial announced with the drug on a younger group of adult
early-manifest HD patients (lower disease burden).

Potential for gene therapy

• For gene therapy to be permanent, the cells that have the healthy allele must be
cells that multiply throughout the patient's life.
• Prime candidates are bone marrow cells, which include stem cells that give rise to all
the cells of the blood and immune system.
• At present, this treatment is only applicable to a small number of disorders that are
caused by single defective genes.

Technological limitations and ethics

• In May of 2019, Dr Francis Collins announced the results of a gene therapy trial for
sickle-cell disease & suggested that they now have a 'cure' for sickle-cell disease.
Exercise

Ethical issues:
• Benefit vs harm
o Benefit: could it save lives?
o Harm: expressed appropriately?
• Gene thearpy in the germline
• Gene therapy for improvement/enhancement
• Very expsensive
• Priority of treatment
GENETICS: Lecture 10
Comparitive genomics
Learning Objectives
• Detail the relationship between genome size, the number of genes and gene
density
• Assess the role that gene duplications and rearrangements have played in the
structure of the human genome
• Explain how the comparative method is used in genomics and detail some of the
major findings

Genome size & number of genes

• Eukaryote genomes tend to be larger than prokaryotes (bacteria and archaea) and
vary ~5000-fold from the largest to the smallest.
• There is no relationship in eukaryotes between genome size and phenotypic
complexity.
• The number of genes varies considerably between prokaryotes (1,500 - 7,500) and
eukaryotes (5,000 -40,000).
• In eukaryotes the number of genes is often lower than expected given the size of
their genomes.
• The human genome is 10 times larger than C. eleganswith about the same number
of genes (~ 21,000).
Gene density & noncoding DNA
• Eukaryotes generally have larger genomes but fewer genes in a given length of DNA
than prokaryotes.
• Of the genomes sequenced so far, humans and other mammals have the lowest
gene density.
• Most bacterial genomes consist of genes for proteins, tRNA or rRNA, with the
remaining consisting of non-transcribed regulatory regions e.g. promoters.
• In eukaryotes, the vast majority of DNA neither encodes protein nor is transcribed
into RNA of known function.
o Humans have 10,000 times more noncoding DNA than bacteria.
o Some of the noncoding DNA regions in eukaryotes are within genes (introns)
but others are not.

What enables us to get by with no more genes than a worm

• An important reason is alternate splicing of RNA transcripts.
• An estimated 90% of our genes are spliced in at least two different ways (some in
many, many different ways)
• Therefore, the number of proteins encoded for in the human genome far exceeds
the number of genes
• Humans also have small RNAs that can play regulatory roles, contributing to greater
complexity via regulation of the expression of genes

Types of DNA in the human genome

• Because repetitive DNA is difficult to sequence and analyse classification of some
proportions is tentative
Type of human DNA
• DNA sequences that code for proteins or produce tRNA or rRNA make up ~1.5% of
the human genome.
• Most human genes contain coding regions (exons), and intervening sequences that
are not translated (introns).
• The number and size of introns in genes is variable.
• The function of introns is not clear, however many are now known to be transcribed.
• Introns account for ~20% of the human genome, and gene-related regulatory
sequences for ~5% of the human genome
• The remaining unique sequences (15%), are noncoding DNA, located between
functional genes (intergenic regions) e.g. pseudogenes

Transposable & repetitive sequences

• Transposable elements are stretches of DNA that can move from one location to
another in the genome.
• Approximately, 75% of repetitive DNA is made up of transposable elements and
related sequences
• McClintock first proposed the idea of mobile genetic elements after observing
variegation in the colour of corn kernels.

Transposable elements
• Transposable elements are mobile DNA sequences found in the genome of all
organisms.
• In many genomes they are abundant for example they make up ~ 44% of human
DNA.
• Most transposable elements are able to insert into many different locations in the
genome.
• Transposable elements often cause mutations by direct insertion into genes.
• Transposable elements can also promote DNA rearrangements such as chromosome
deletions, inversions and duplications.
Gene duplication
• Gene duplication can result from misaligned recombination during meiosis (unequal
crossing over).
• The repetitive regions of transposable elements provide homologous sites enabling
non-sister chromatids to cross over during meiosis.

Multigene families
• Gene duplication has played an important role in genome evolution.
• Most gene families arise through duplication of an existing gene (via errors in DNA
replication/recombination).
• The exact DNA sequence of the genes within the family may change and different
genes may come to have different functions.
• Several types of proteins are encoded by families of homologous genes spread
throughout the genome.
• Such families may comprise only a few genes or in some cases many hundreds of
genes.
• Some of the genes within the family may become non-functional – pseudogenes.

Human globin genes

• Non-identical human a- and b-globin gene families are organized into clusters that
contain functional and non-functional copies (pseudogenes ψ).
• Allows different forms of each globin subunit to be expressed at different times in
development.
 • Comparison of globin genes indicates these genes evolved from one common
ancestral globin gene that underwent duplication, and then they diverged from each
other in sequence – likely due to mutation.
• Some mutations must have altered function of the protein product in a way that
benefited the organism (e.g. at a particular life stage) without adversely affecting the
protein’s ability to carry oxygen.

Tandem gene families

• Cells need large amounts of some gene products and therefore the genes have
evolved into tandem arrays.
• Often the multigene families consist of identical tandemly repeated DNA sequences.
• The genes for histones are arranged in tandem arrays in some species e.g. sea
urchins and Drosophila.
• Similarly, the ribosomal RNA genes are repeated tandemly hundreds to thousands of
times.
• The many copies of this ribosomal RNA help cells make the millions of ribosomes
needed for active protein synthesis.

Ribosomal RNA (rRNA)

• The primary transcript is cleaved to yield three rRNA molecules which combine with
proteins and other rRNA to form ribosomal subunits.
Primate genomics
• Chimps, gorillas and orangutan have 48 whereas humans have 46 chromosomes.
This difference is due to a translocation and loss of a chromosome in humans.
• Sometime in the last 6 million years, the fusion of two chromosomes led to different
haploid numbers for humans (23) and chimpanzees (24)
• Human chromosome 2 is a large metacentric chromosome that resulted from fusion
of two acrocentric chromosomes of apes.

Chimp and neanderthal genome

• Comparing the human genome with that of the chimp & Neanderthal helps answer
the question – what makes us human?

Mouse FOXP2 gene

• FOXP2 regulates genes involved in vocalisation
• Mice produce whistles to communicate stress, heterozygote knock outs of the
FOXP2 gene show a dramatic reduced and homozygotes, an absence of vocalisation.
• There is evidence, including from a mouse model to suggest that a regulatory gene
FOXP2 turns on genes needed for vocalization in mammals.
• Humans and chimpanzees differ in the expression of the FOXP2 gene.
• These differences might explain why humans but not chimpanzees can speak.
• Furthermore, the DNA sequence of the FOXP2 gene of Neanderthals is identical to
that of humans.
• This sequence similarity might suggest that Neanderthals may have been capable of
speech.
Exercise
GENETICS: Lecture 11
The era of personalised genomics
Learning Objectives
• Compare and contrast whole exome and whole genome sequencing
• Apply your genetics understanding to diagnose a rare neurodevelopmental
disorder
• Explain the ethical principles associated with human genome sequencing

Human genome project

• The Human Genome Project began in 1990.
• In 2001, the Human Genome Project published the first draft sequence of the human
genome, with the “finished version” published in 2003.
• Using massively parallel sequencing, researchers have now sequenced the genome
of countless species.

Moore’s Law

Whole genome sequencing

• Essentially, the whole genome is sequenced (including non-coding regions).
• Enables the detection of structural variants (e.g. copy number variants) as well as
SNVs (single nucleotide variants) and small insertions and deletions (indels).
• Can detect variants in coding and non-coding regions of the nuclear DNA, and
mitochondrial DNA.
Whole exome sequencing
• A massively parallel sequencing technique (using methodology discussed in lecture
8).
• Key difference to whole genome sequencing: there is a capture step to isolate the
exome (~1.5% of the human genome) which is mainly the protein coding regions
(exons).
• The ~180,000 exons (~ 50 million bp) are then sequenced using standard massively
parallel sequencing technology.
• Biologically interpretable (85% of known disease mutations are located in protein
coding regions of the genome).
• Difficult to detect structural variants (e.g. copy number variants).
WES vs WGS

Identifying causative variants

• After alignment to a reference genome, we can identify changes in the DNA
sequence that deviate from the reference.
• An average human genome has 3-5 million variants compared to the reference
human genome.
• Therefore, to identify a causative variant for a condition or disease, we need to
prioritise variants for interpretation.
o Variants that change the amino acid sequence (e.g. Missense, stop-gain,
deletions, insertions).
o Variants that fit the predicted mode of inheritance (e.g. Recessive, dominant,
X-linked).
o Variants with a population frequency that does not exceed the frequency of
the condition.
o Variants in biologically relevant genes for the condition of interest.

Case report
• Profound muscular hypotonia
• Severely bradykinetic
• Epilepsy
• Intellectual disability
• Limited vocalisation
• Abnormal eye movements
• Low neurotransmitter levels

Sequencing and analysis approach

• Whole exome sequencing of both brothers identified ~3,000 shared variants that:
o changed a start or stop codon.
o caused a frameshift in the amino acid sequence.
o caused a non-synonymous amino acid substitution.
• Variants were prioritised if their allele frequency was less than 2% in the population.
• Variants were prioritised if the gene they were in was expressed in the brain.

Causative variant
• Homozygous variant identified in the gene SLC18A2 (solute carrier family 18
(vesicular monoamine), member 2).
• Encodes a transporter of dopamine and serotonin.
• Autosomal recessive mode of inheritance.
• Non-synonymous mutation resulting in amino acid change: CCC > CAC: Proline >
Histidine.
 • Treated with a dopamine agonist in surviving sibling at 14 years of age.
• Improvement in his use of vocal communication and a reduction in abnormal eye
movements.
• Improved communication and social interaction.
• No improvement in his gross motor skills.

Ethical principles
• Genetic results that relate to a human disease or condition are reviewed and
delivered by genetic experts such as clinical geneticists and genetic counsellors.
• Clinical geneticists are medical doctors with advanced training in medical genetics.
• Genetic counsellors have a postgraduate Masters level degree.
• This is important for:
o Appropriate management of a genetic disease.
o Consultation on reproductive implications and options of genetic disorders.
o Genetic testing for those affected by or perceived to be at risk of genetic
disorders in extended families.
Ethical decisions
• Autonomy: facilitating informed decision making by the patient, free of coercion
with protection of their privacy.
• Beneficence: intent of intervention is to do good for the patient involved.
• Non-maleficence: “first, do no harm”.
• Justice: burdens and benefits of care and treatments must be distributed equally
over society.

Huntington’s disease
• Ethical dilemmas emerge out of our increased understanding of genetic disorders,
and the unifying ethical principles are not always absolute.
• Case taken to trial in the UK in 2018:
o Woman suing doctors as they failed to tell her about her father’s diagnosis of
Huntington’s disease before she had her own child.
o She later found out she had inherited the HD gene, and her daughter now
had a 50% chance of having it too.
o The woman said she would have had an abortion had she known about her
father’s condition.
o It was the first case in English law to address a relative’s claim over genetic
responsibility.
GENETICS: Lecture 12
Indigenous perspectives on genetics

Learning Objectives
• Understand the importance of genetic research and technology in the context of
indigenous communities.

Indigenous People
• 370-500 million Indigenous Peoples in the world (~ 5-6% of global population) (UN,
2022)
• 7000+ languages articulating unique knowledge systems
• Kaitiaki: Lands inhabited by Indigenous Peoples contain 80% of the world’s
remaining biodiversity
• Face common problems related to the protection of their rights, marginalization,
discrimination, lack of access to social and health services... and more.

Colonisation
• Indigenous health is widely understood to also be affected by a range of cultural
factors
o racism
o loss of language
o loss of connection to the land
o environmental deprivation
o spiritual, emotional, and mental disconnectedness

Indigenous rights and interests in genomics

• International Agreements
• The Mataatua Declaration (1993) – Cultural and Intellectual property rights of
Indigenous Peoples
• United Nations Declaration of Rights of Indigenous Peoples (UNDRIP) (2007)
• Convention on Biological Diversity (CBD)
• Nagoya Protocol – Access to Genetic Resources and Benefit-Sharing (supplementary
agreement to CBD)

UNDRIP
• United nations declaration on the rights of indigenous peoples
• Adopted by the UN General Assembly on 13 September 2007
• Comprehensive human rights document on the rights of Indigenous Peoples
• 46 Articles that cover freedoms and rights to:
o Self-determination
o Culture and identity
o Education
o Economic development
o Religious customs
o Health and language
UNDRIP and Genetics
• Article 31: Indigenous peoples have the right to maintain, control, protect and
develop their cultural heritage, traditional knowledge and traditional cultural
expressions, including human and genetic resources, seeds, medicines, knowledge of
the properties of fauna and f lora, oral traditions, literatures, designs, sports and
traditional games and visual and performing arts. They also have the right to
maintain, control, protect and develop their intellectual property over such cultural
heritage, traditional knowledge, and traditional cultural expressions.

UNDRIP and Research

• Article 18: Indigenous peoples have the right to participate in decision-making in
matters which would affect their rights, through representatives chosen by
themselves in accordance with their own procedures, as well as to maintain and
develop their own indigenous decision-making institutions.
• Article 19: States shall consult and cooperate in good faith with the indigenous
peoples concerned through their own representative institutions in order to obtain
their free, prior and informed consent before adopting and implementing legislative
or administrative measures that may affect them.

Te Tiriti O Waitangi
• Preamble: Queen to provide a government while securing tribal rangatiratanga
• Article 1: Māori gave the Queen “te kāwanatanga katoa” –complete government
over their land
• Article 2: Māori were guaranteed “te tino rangatiratanga” – the unqualified exercise
of chieftainship over their lands “wenua”, villages “kainga” and all their
property/treasures “taonga katoa”
• Article 3: The Crown gave an assurance that Māori would have the Queen’s
protection and all rights – “tikanga” – accorded to British subjects = Equity.

Wai 262
• One of the largest and most complex claims in the Waitangi Tribunal’s history
• Covers flora, fauna, and artistic expression
• Claimants sought recognition of their tinorangatiratanga over the full breadth of
their taonga as assured within the Treaty, where:
• Iwi and hapū were guaranteed tino rangatiratanga over “ngā taonga katoa”
• Taonga are defined as anything that is of value to Māori

Te tiriti – Genetic and Genomic research

• Te Tiriti o Waitangi – tino rangatiratanga (Article 2) over “taonga katoa”
• Decision-making authority over conservational and proprietary interests in natural
resources
• Rights to participation in and benefit from existing and future technological advances
• Rights to protect, enhance, transmit knowledge and concepts found in Indigenous
flora and fauna
• Right to the environmental wellbeing of taonga
• Genetic material of taonga species Kaitiakitanga
• Wai262 - Ko Aotearoa Tēnei report, Waitangi Tribunal 2011
Summary of data
• Decision-making authority over resources
• Rights to participation in and benefit from existing and future technological advances
• Rights to protect, enhance, transmit knowledge and concepts found in Indigenous
Peoples, flora and fauna
• Right to the environmental wellbeing of taonga
• Taonga includes Health

Genome wide association

• ‘Stark bias’ towards European ancestry noted among genome-wide association
studies (GWAS)
• Indigenous people are underrepresented in GWAS conducted worldwide

Missed Opportunities
• Frequencies of variants associated with drug metabolism (e.g. CYP26D – at least 100
variants) unknown in some populations
 • Missed opportunity to discover new associations with disease traits
• Genomic research can identify new druggable targets and new companion diagnostic
tests
• A lack of reference variant data for Indigenous populations for the interpretation of
gene panels and genome sequencing, which is often used to assist in clinical genomic
variant analysis.
o Garrison, Hudson, Ballantyne et al. (2019)
o What would a gene panel be used for?
▪ Molecular profiling of a cancer patient’s tumour to inform clinical care
▪ Finding the right drug for the right patient

Bias
• Convenience and controlling for variables in GWAS
• Limited access to medical, research centres, or genomic technologies (all needed for
GWAS)
• Some populations choose not to contribute their samples to research for cultural or
historical reasons

Indigenous peoples experiences with genetic research

• Lack of clear communication and transparency
• Lack of community engagement
• Lack of cultural competency
• Lack of informed consent for secondary use
• Not respecting the interests of the communities
• Not addressing the priorities of the communities
• Negative representation of Indigenous populations in publications
• Exploitation of genetic material
• Theft of intellectual property

Te Mata Ira
Tissue and DNA are Taonga and so is the Data

Biobanking and genomics

• The construction of racial or ethnic groupings for genetic comparisons
• The attribution of familial characteristics to larger groupings
• The analysis and interpretation of results and
• An interest in the scientific novelty rather than clinical application
• Genomic data are commonly seen by Indigenous communities as more sensitive
than other types of health data
• Holds information about family and whakapapa (genealogy and ancestry)
• Identity claims affecting rights to land and other Resources

Consequences of poor practices

• Mistrust between researchers and Indigenous communities
• Fatigue from being in studies with no benefit
• Hesitancy to participate in genomic research
• If genomic-guided precision medicine does deliver on it’s promise, then based on
these barriers, inequity gaps will widen.

Enhancing responsiveness
Cancer – Oncology
• 5-10% of all cancers caused by inherited germline mutations= hereditary cancers90-
95% of cancers are caused by somatic mutations= spontaneous cancers