Genetics 11 - Genetic Diversity and Complex Genetic Diseases

Question 1

Composition of antibody or Ig molecule

Answer 1

composed of four chains: an identical pair of longer heavy chains and an identical pair of shorter light chains, which are linked together by disulfide bonds

Question 2

Types of heavy chains

Answer 2

5

termed γ, μ, α, δ, and ε

Question 3

Types of light chains

Answer 3

κ and λ

Question 4

γ

Answer 4

IgG

Question 5

μ

Answer 5

IgM

Question 6

α

Answer 6

IgA

Question 7

δ

Answer 7

IgD

Question 8

ε

Answer 8

IgE

Question 9

What do immature B lymphocytes produce

Answer 9

ONLY IgM

but as they mature, a rearrangement of heavy chain genes called class switching occurs

Question 10

Class switching

Answer 10

Produces the other 4 major classes of immunoglobulins, each of which differs in AA composition, charge, size, CHO content

Each class tends to be localized in certain parts of the body, and each tends to respond to a different type of infection

The two types of light chains can be found in association with any of the five types of heavy chains

Question 11

Relationship between light and heavy chains

Answer 11

2 types of light chains can be found in association with any of 5 types of heavy chains

Question 12

What determines the major class to which an Ig belongs

Answer 12

Heavy chain constant region

Question 13

What part of Ig recognises and binds antigens

Answer 13

Variable regions of the light and heavy chains

Question 15

Production rate of humoral immune system

Answer 15

can generate 100 billion structurally distinct antibodies

Question 16

Why is the 1 gene-1 antibody hypothesis incorrect

Answer 16

because the human genome has only 20,000 to 25,000 protein-coding genes

Question 17

Multiple Germline Immunoglobulin Genes

Answer 17

Molecular genetic studies (cloning and DNA sequencing) have shown that for each heavy and light chain, an individual has more than 80 different V segments located continuously in his or her germline and 6 different J segments

There are at least 30 D segments in the heavy chain region

Question 18

Somatic Recombination - VDJ Recombination

Answer 18

Specific combination of single V and J for light chain and separately, V, D and J for heavy chain

accomplished by deleting the DNA sequences separating the single V, J, and D segments before they are transcribed into mRNA

→ by recombinases (encoded // RAG1 and RAG2 genes) which intitiate 2x strand DNA breaks at specific DNA sequences that flank V and D segments

Question 19

What does mutation of RAG1 and RAG2 genes lead to

Answer 19

severe combined immunodeficiency disease (SCID) as the recombination mechanisms are also involved in generation of T cell receptors (as well as recombinases)

Question 20

When are Ig molecules formed

Answer 20

During B lymphocyte maturation

Question 21

What happens after deletion of all but 1 V, D and J segment

Answer 21

Non-deleted segments are joined by ligases

This cutting-and-pasting process is known as somatic recombination (in contrast to the germline recombination that takes place during meiosis)

unlike most other cells of the body, whose DNA sequences are identical to one another, mature B lymphocytes vary in terms of their rearranged immunoglobulin DNA sequences

Many possible combinations of single V, J and D segments, somatic recombination can generate 100,000-1,000,000 different types of antibody molecules

Question 22

Junctional diversity

Answer 22

As the V, D, and J regions are assembled, slight variations occur in the position at which they are joined, and small numbers of nucleotides may be deleted or inserted at the junctions joining the regions

This creates even more variation in antibody AA sequence

Question 23

binding affinity between B cells and their cell surface receptors (Igs)

What happens upon binding

Answer 23

only a small subset of B cells has cell-surface receptors (immunoglobulins) that can bind to a specific foreign antigen, and their binding affinity is usually low

Once this subset of B cells is stimulated by a foreign antigen, they undergo an affinity maturation process characterized by somatic hypermutation of the V segments of immunoglobulin genes

Question 24

Action of activation-induced deaminase

Answer 24

cytosine bases replaced by uracil

Errorprone DNA polymerases are recruited, and DNA repair processes are modified so that mutations can persist in the DNA sequence

Question 26

consequences of persistence of mutations in DNA sequence

Answer 26

the mutation rate of these gene segments is approximately 10³ per base pair per generation (recall that the mutation rate in the human genome is normally only 10⁸ per base pair per generation)

This causes much additional variation in immunoglobulin-encoding DNA sequences and thus in the antigen-binding properties of the encoded immunoglobulins

Question 27

Effect of somatic hypermutation on Igs

Answer 27

somatic hypermutation produces a subset of immunoglobulins that have high-affinity binding to the foreign antigen, and the B cells that harbor these immunoglobulins are selected to proliferate extensively

The end result is a population of mature plasma cells that secrete antibodies that are highly specific to the invading pathogen

Question 28

Multiple combinations of Heavy and Light Chains

Answer 28

Further diversity is created by the random combination of different heavy and light chains in assembling the immunoglobulin molecule

Each of these mechanisms contributes to antibody diversity

Considering all of them together, it has been estimated that as many as 1011 distinct antibodies can potentially be produced

Question 29

5 mechanisms that produce antibody diversity

Answer 29

1. multiple germline immunoglobulin gene segments
2. somatic recombination of the immunoglobulin gene segments
3. junctional diversity
4. somatic hypermutation
5. potential for multiple combinations of heavy and light chains

Question 30

Similarities & differences between T cell receptors and Igs (B cell receptors)

Answer 30

T-cell receptors must be able to bind to a large variety of peptides derived from invading organisms

Unlike immunoglobulins, however, T-cell receptors are never secreted from the cell, and T-cell activation requires the presentation of foreign peptide along with an MHC molecule

Question 31

Generation of T cell diversity by

Answer 31

Most of the mechanisms involved in generating immunoglobulin diversity—multiple germline gene segments, VDJ somatic recombination, and junctional diversity

Question 32

What occurs with B cell receptor diversity but NOT t cell receptor diversity

Answer 32

somatic hypermutation does not occur in the genes that encode the T-cell receptors

This is thought to help avoid the generation of T cells that would react against the body’s own cells (an autoimmune response)

Question 33

Copy Number Variants

Answer 33

CNVs

deletions and duplications of genomic sequence, ranging in length from a kilobase to multiple megabase pairs

They are known as major contributors to human genetic diversity

CNVs are known to influence both normal and disease variation

Question 34

Molecular cytogenic techniques enabled

Answer 34

detection of submicroscopic deletions that encompass many genes and have typical characteristics of “chromosomal disorders,” even though specific features may be due to haploinsufficiency of specific genes

Question 35

How have bridged and blurred the gap between chromosomal and monogenic conditions

Answer 35

recent advent of array technology allows for the detection of smaller and smaller copy number variants (CNVs)

Question 36

prevalence of CNVs

Answer 36

most individuals (65% to 85% of the population) harbour a CNV of at least 100 kb of DNA

Much larger (exceeding 500 kb) variants occur in 5% to 10% of individuals

at least 1% of the population carries a CNV exceeding 1 Mb

While some of these CNVs are clearly pathogenic, others may represent risk modifiers for common diseases or may be completely benign

Question 37

What do CNVs cause

Severity

Answer 37

CNVs can cause structural chromosome abnormalities via duplication or deletion

The clinical severity largely depends on the size of the respective chromosome segments

Question 38

Smaller CNVs (< 10kb) - class of CNVs

What are they associated with

Answer 38

copy number polymorphisms (CNPs) because they are common in the general population (>1% frequency)

A subset of these CNPs are highly variable with respect to copy number

They often encode proteins involved in drug metabolism and immunity and are associated with susceptibility to complex inflammatory or immune disease such as psoriasis and Chron’s

Question 39

2nd class of CNVs - larger (> 10kb but < 5 Mb)

Prevalence

also known as

How do they occur

how were they discovered

Answer 39

rare in the general population

They ae also known as microdeletions or microduplications, and usually have a much more recent origin within a family, sometimes occurring as a de novo mutation in the gamete

The era of molecular cytogenetics, with newer molecular methods of genomic quantification (e.g., fluorescence in situ hybridization [FISH] and array analysis), led to the molecular characterization of microdeletion and microduplication syndromes (genetic syndromes caused by a deletion that is not visible by light microscopy)

Question 40

Microdeletions/duplications are associated with

Answer 40

susceptibility to neurocognitive diseases including autism spectrum disorders and schizophrenia

Question 41

Examples of microdeletion syndromes

Answer 41

Williams Syndrome (Micro del 7q11.23)

Smith-Magenis Syndrome (Micro del. 17p11.2)

Potocki-Lupski Syndrome (Micro dup. 17p11.2)

Question 42

Occasionally what might a microdeletion cause

Answer 42

Haploinsufficiency of several adjacent genes, of which 2+ are associated to distinct genetic disorders, including TSC2 (causing tuberous sclerosis) and PKD1 (causing autosomal dominant polycystic kidney disease) on chromosome 16p13

Question 43

2 contiguous gene syndromes

Answer 43

tuberous sclerosis - TSC2 on chr 16p13

autosomal dominant polycystic kidney disease - PKD1 on chr 16p13

Question 44

what is the phenotype of monogenic disorders influenced by

Answer 44

exogenous factors - otherwise treatment would not work

Question 45

Phenylketonuria (PKU) - PAH, Chr 12q

what sort of disorder is it

how is it influenced

Answer 45

monogenic disorder

the clinical phenotype is fundamentally influenced by an exogenous factor (i.e., reduced intake of phenylalanine)

While untreated individuals with classic PKU develop a severe intellectual disability, a person with PKU who has been treated with an optimal diet is, clinically, not different from a “healthy” person

In this way PKU is similar to a risk factor for a disorder; however, in the absence of treatment the risk of disease is far larger than with classic multifactorial disorders

Question 46

Genetic disorder

Answer 46

disorder = clinical symptoms of a person, not to his or her genome

Question 47

asymptomatic mutation carrier and reduced penetrance

Answer 47

A carrier for myotonic dystrophy falls ill when the first symptoms occur; before that he or she is an asymptomatic mutation carrier

Some carriers of dominant disease-causing mutations never fall ill (reduced penetrance)

Question 48

What does detection of a mutation imply

Answer 48

especially during predictive testing, may only imply an increased risk or probability for the disorder

Question 49

Multifactorial disorders

examples

Answer 49

= complex disorders

those disorders that do not follow a clear inheritance pattern and whose clinical symptoms are suspected to have been caused by the interplay between several genes (polygenic) and exogenous (environmental) factors

T2D

Coronary artery disease

Inflammatory bowel disease

cancers

Question 50

Polygenic theory

Answer 50

useful framework for considering the inheritance patterns of traits/disorders that rely on the interaction of a large number of genetic factors, each of which makes a small contribution to the overall phenotype

Question 51

2 main concepts of polygenic theory

Answer 51

Heritability – The proportion of the total phenotypic variance that is attributable to genetic variance in a population

Estimates how much of the differences between people in a social group are down to genetic differences between them, and how much is down to differences in their environments (i.e. nature vs nurture)

relates to population > individuals

estimated by comparing the incidence of a condition in relatives of affected people with the incidence of the condition in the general population - relevance of genetic factors to a condition in specific place/time

if a phenotypic trait has a heritability of 0.25, that means that 25% of the variability in that trait in the population is down to genetic differences among the people e.g. PKU - depends on intake of phenylalanine

Question 52

Threshold effect as a principle of polygenic theory

Answer 52

explains how dichotomous characters can be polygenic

susceptibility to a disease is a continuous character that depends on combined effect of many genes

According to this concept, a certain polygenic/complex trait (for example, a congenital malformation) becomes phenotypically evident only once the threshold of genetic predisposition is exceeded; when this happens, the effect is complete (i.e., the all-or-nothing principle)

Question 53

What happens when you’re susceptibility exceeds a threshold

Complex diseases and prevalence in one’s family

Answer 53

you will manifest the disease

relatives will therefore be more likely to also manifest the disease than the general population as they are more likely to share your high risk alleles (probability)

Therefore complex diseases tend to run in families, but this tendency is much weaker than with Mendelian diseases

Question 54

Parents with multiple affected children

Answer 54

Higher risk of future recurrence

Question 55

Close relatives of more severely affected individuals

Answer 55

also at greater risk of manifesting the phenotype. Likewise, closer relatives of the index case are more at risk than more distant relatives

Question 56

gender dependence

Answer 56

In the case of some conditions, the threshold of genetic predisposition seems to differ between males and females

e.g. Hypertrophic Pyloric Stenosis - males have a lower threshold of genetic predisposition and as such are more likely to manifest the clinical phenotype

herefore, if a female is affected it is likely that she was dealt a particularly band genetic “hand” from her parents and the recurrence risk will be higher in her descendants

Question 57

Carter effect

Answer 57

: Multifactorial diseases with a gender-dependent threshold effect have a higher recurrence risk if the index patient is of the less commonly affected sex

Question 58

Incidence of hypertrophic pyloric stenosis

Answer 58

t its incidence is highest in sons of affected women and lowest in daughters of affected men

Question 59

Hypertrophic pyloric stenosis

Answer 59

postnatal hypertrophy of the circular muscle of the pylorus that results in functional obstruction of the pylorus, projectile vomiting, and failure to thrive

Cumulative freq = 1 in 1,000

boys are affected 5x more frequently than girls

In most cases, the disorder is diagnosed in infants between 3 and 12 weeks of life

Sometimes the pylorus can be felt as a cylindrical tumor in the upper right quadrant of the abdomen

Water and salt deficiency can result in a hypochloremic alkalosis

The treatment of choice is pyloromyotomy (i.e., Ramstedt procedure)

Question 60

Why don’t monozygotic/’identical’ twins share 100% of their genes

(originate from same fertilised zygote)

Answer 60

CNVs and somatic mutation of the immune receptor genes

(Nonetheless, MZ twins do share homology at the majority of loci, and by studying differences in MZ twin genomes and relating it to phenotype, we can identify genetic changes implicated in disease onset)

Question 61

Discordance

Answer 61

presence of a given genetic or phenotypic trait in only one member of a pair of MZ twins (called discordance) suggests environment strongly effects such a trait (low heritability)

⇒ end result of many twin studies is an estimate of the heritability of the condition

Answer 62

A classic twin study design compares many pairs of MZ and fraternal (dizygotic - DZ) twins, where one twin in each pair is known to be affected

The frequency that the co-twin in each pair is also affected is investigated, with the assumption being that both MZ and DZ twins share their environment to the same degree

Higher concordance (both display the phenotype) in MZ twins than DZ twins is evidence for genetic factors – i.e. heritability in the trait

Question 63

Linkage

Answer 63

relationship between loci (not alleles)

Question 64

Linkage analysis

Answer 64

looks at physical chunks of the genome of related individuals with the phenotype and associates them with given traits

Principle: if we find a common genetic marker (e.g. microsatellite, SNP), we assume that the gene that causes the disease is somewhere in the same area

Question 65

What is linkage useful for

Answer 65

associating large sections of the genome with highly penetrant disorders/traits shared between relatives, but it is also useful for identifying chromosome sections to target for association analysis in unrelated or more distantly related groups of people

Question 66

Resolution of linkage

Answer 66

Low

we can link a haplotype or section of chromosome to a trait, but cannot zero in on the exact gene without more information

Question 67

Genetic Association Studies

Answer 67

purely statistical phenomenon and not specifically genetic

Association is when one or more genotypes (alleles) within a population co-occur with a particular phenotypic trait more often than would be expected by chance

It is important to stress that association is not causation

Association studies seek to identify particular allele/marker variants that are associated with the phenotype at the population level

Question 68

Principle of genetic association studies

What are they used for

Answer 68

gather some people with a disease (cases) and some people without a disease (controls) and look to see what alleles are present more in cases than controls

Association is used to find common low penetrance alleles associated with a disease

Question 69

causes of association between a genetic variant and a disease may have several causes

Answer 69

1. The variant may directly confer disease susceptibility
2. The variant may be on the same shared ancestral Chr segment as the variant that directly causes disease
3. The variant may be more frequent in the population subgroup in which the disease is also more frequent

Question 70

Positional cloning

Answer 70

process of identifying a disease gene based on its location on a chromosome

Linkage and association are complimentary methods to describe the aetiology of complex traits -

By using linkage analysis we can define large candidate genome regions - Usually by analysis of a genome wide panel of a few hundred markers in affected sibling pairs - Positional cloning can then be used to zero in on the position of interest using high density SNP genotyping

Question 71

dbSNP database

Answer 71

has 10 million SNPs – one for every 300 bp of human DNA

In this way, we can associate short shared segments of a few Kb with a disease phenotype

Next candidate genes in this section are analysed for mutations (candidate gene analysis)

So by knowing only a genes’ location on a chromosome, researchers can identify or “clone” a gene using positional cloning

Question 72

Functional cloning

Answer 72

Cloning a gene required knowledge of the disease pathology

Prior knowledge of what the gene function is was essential in order to make an educated guess

Question 73

Genome Wide Association Studies (GWAS)

Answer 73

GWAS typically test hundreds or thousands of individuals and scans all genes in the genome to look for associations between variants (alleles) and phenotypic traits

No prior knowledge is needed, just a large number of cases and controls

High resolution SNP chips are usually used - 1 for every 3000 bps of human genome

Question 74

Gold standard for linkage/GWAS

Answer 74

replication of linkage/association in different populations

Question 75

What is GWAS used for

Answer 75

calculate individual genome-wide polygenic risk scores (GPSs) for complex polygenic diseases such as coronary artery disease, type 2 diabetes, inflammatory bowel disease and cancer

Sophisticated algorithms were used to integrate pervariant risk scores from hundreds of thousands of individuals into one GPS associated risk, which was found for many individuals to be as good a predictor of disease as some single mutations causing rare Mendelian diseases already routinely considered in clinical settings