1
Q
How many chromosomes are in the human genome?
A
46 Chromosomes
2
Q
What does chromatin consist of?
A
DNA + Protein
3
Q
Describe the packaging of DNA in (a) non-dividing cells and (b) dividing cells
A
(a) Non-dividing cells
- DNA = for transcription therefore losely packaged
- DNA appears to be “strung out”
(b) Dividing cells
* DNA = tightly packaged (for safer transmission to daughter cells)
4
Q
What is the role of the centromere?
A
The centromere holds two (sister) chromatids together and aligns to the mitotic spindles to ensure the correct amount of genetic information enters each daughter cell
5
Q
Outline the roles of the following:
(a) Introns
(b) Exons
(c) Promoters (or enhancers)
A
(a) Introns = non-coding regions, eventually spliced out
(b) Exons = coding regions
(c) Promoters = upstream regulatory sequences
6
Q
Briefly outline the processes of (a) transcription and (b) translation
A
(a) Transcription = DNA –> mRNA
- Proceeds in the 5’ –> 3’ direction
- mRNA processing (5’ cap + 3’ poly(A) tail)
(a) Translation = mRNA –> Proteins
7
Q
What is a UTR?
A
UTR = untransated region - i.e. the DNA is transcribed into RNA but not into proteins. Their role is in gene regulation
8
Q
(a) What is a reading frame?
(b) What is an open reading frame?
A
(a) A reading frame is a way of dividing the sequence of nucleotides into a set of sonsectuive, non-overlapping triplets
(b) An open reading frame is part of a reading frame that has the potential to code for a protein - it is a continuous stretch of DNA with a start and stop codon
9
Q
What is the purpose of (a) mitosis and (b) meiosis?
A
(a) The purpose of mitosis is to duplicate cells - all cells created are identical diploid (2n) cells
(b) The purpose of meiosis is to produce gametes - all cells are difference haploid (n) cells
10
Q
Explain “crossing over” (part of meiosis)
A
- Crossing Over is a process that occurs in meiosis during the first mitotic division
- It is a process which enables diversity due to multiple recombination events - i.e. genetic information is mixed between the daughter cells to produce variablility.
11
Q
Outline the major principles of Mendelian Inheritance
A
Mendelian Inheritence = off-spring inherit one copy of a gene from each parent
It is based on 3 principles:
- Inheritance of each trait is determined by units that are passed onto off-spring unchanged
- An inidividual inherits one unit from each parent, for each trait
- The trait may not necessarily be expressed in that individual but it can still be passed on to future generations
12
Q
Define the following:
(a) Locus
(b) Allele
A
(a) Locus = region of DNA (usually a gene)
(b) An allele = different copies of the same gene region (locus), each gene has to alleles (one from each parent)
13
Q
Define the following terms -
(a) dominant
(b) recessive
A
(a) Dominant = stronger allele, will overpower the other (wild-type) allele.
(b) Recessive = weaker allele, the second allele (wild-type) can over-come the disease
14
Q
Describe the following pattern of genetic disease:
**Autosomal Dominant **
A
- Copy is found in one of the parents - 50% of off-spring will be affected
- If present, will cause disease
- Example = achondroplasia
- Gain of function mutation (rare) in FGF-R2 (represses ossification of chondrocytes therefore causes short limbs)
- Presents as dwarfism
15
Q
Describe the following pattern of genetic disease:
Autosomal Recessive
A
- One copy = carrier
- Both copies must be present to cause disease (i.e. both parents must be carriers)
- Probabilities if both parents are carriers
- 50% carriers
- 25% unaffected
- 25% disease
- Cystic Fibrosis
- Lack of function mutation in CFTR protein
16
Q
Describe the following pattern of genetic disease:
Sex-Linked (X-linked, recessive)
A
- Females are carriers, males are affected
- No male-male transmission of disease
- If mother is a carrier
- 50% disease in sons
- 50% carriers in daughters
- If father is a carrier
- 100% carriers in daughters
- All sons unaffected
17
Q
Describe the following pattern of genetic disease:
Mitochondrial Disease
A
- Mitochondria have their own DNA = mDNA
- Mitochondrial inheritance is from the mother only
- If diseased, males & females can be equally affected (but an affected male will not pass it on to their offspring)
- Diseases are known as “non-mendelian” (as only one copy is inherited)
- Transmission is unpredictable (i.e. the presence of a mitochondrial disease in a female does not give classifcal probabilities for affected children)
18
Q
Outline the concept of Co-Dominant Inheritance
A
- Co-dominant = both alleles are expressed
- Example = AB Blood Group
- Normally, only one antigen is expressed (i.e. coded for) giving A, B or O blood groups
- There can be co-expression of A and B antigens giving AB blood group
- This is possible as A and B are both dominant over O but co-dominant with each other (i.e. both will be expressed if present but O will never be expressed if A and/or B are present)
19
Q
Define the following DNA variants:
(a) Polymorphism
(b) DNA sequence variants
A
(a) Polymorphism = a variant in a population with fq. more than 1% (a mutation is a variant in a population with fq. of less than 1%)
(b) DNA seq. variants = any change from the reference sequence
20
Q
(a) How does a mutation occur?
(b) What normally stops mutations from occuring?
(c) What is the consequence of a mutation?
A
(a) A mutation occurs when there is an error in replication
(b) Proof-reading mechanisms - these are in place to ensure that DNA is copied correctly and to fix any mismatches
(c) The consequene of mutations = permanent alteration of the DNA, this can be disease-causing (i.e. pathological mutation) or benign
21
Q
What are the four major effects of altering the DNA sequence?
A
- Alter protein-coding seuqence (exons)
- Alter intron regions (i.e. non-coding)
- Alter intergenic regions (i.e. between coding)
- Alter UTRs
22
Q
What are the three types of mutations?
A
- Missense Mutations = amino acid substitution for another amino acid
- Nonsense Mutartions = amino acid substituion for a stop codon
- Indels = insertions & deletions (either in or out of frame) of amino acids
23
Q
Outline the principle of missense mutations
A
- Missense mutations = amino acid substitution for another amino acid
- These can either be pathological (disease-causing) or benign (i.e. tolerated with no ill-effet to the individual)
- Pathological example = achondroplasia
24
Q
Outline the principle of nonsense mutations
A
- Nonsense mutations = amino acid substitution for a stop codon
- These can be in-frame or out of frame
- Nonsense mutations are a common cause of genetic disease as they result in truncated proteins (i.e. loss of function mutations)
- The most common consequence of a nonsense mutation is nonsense-mediated decay (i.e. no protein is produced)
25
Outline the principle of **indels**
* An indel is either an insertion or deletion of amino acids
* They can either be in-frame or our of frame
* In-frame Deletions
* Deletion of an amino acid within the triplet
* These can either be pathological or benign
* Pathological Example = CF (there is a protein but it is dysfunctional)
* In-frame deletions can result in the complete lack of protein - example = muscular dystrophies
* Out of Frame Deletions
* Mutations in the splice site are common pathological mutations
* Outcomes are difficult to predict because there are multiple potential sites
* General consequences of such deletions
* Exon skip
* Intron retention
* Small deletion
26
Define **penetrance**
Penetrance = principle gene(s) causing a condition
27
# Define the following patterns of inheritance, give an example for each:
(a) Variable penetrance
(b) Phenocopies
(c) Epistasis
(d) Imprinting
(a) Variable penetrance
* Altered gene does not have the same effect in everyone
* *Retinitis pigmentosa* (late-onset blindness)
(b) Phenocopies
* Mutations in various genes
* *Cardiomyopathy*
(c) Epistasis
* Different clinical disease features depending on mutations present in other genes
* *Haemophilia*
(d) Imprinting
* Disease may differ accodring to which parent has transmitted the diseased allele
* *Prader-Willi Syndrome*
28
Define **non-penetrance**
Non-penetrance is the state in which a genetic trait, although inappropriately present, fails to manifest in the phenotype
(i.e. you have the gene but you don't have the disease)
29
Outline how imprinting is possible
* Imprinting occurs due to normal gene regulation - i.e. you preferentially express either the maternal or paternal allele for each gene
* If the diseased allele is prefernetially expressed than the disease will manifest
* Example = Prada-Willi Syndrome
* Disease state only if paternal allele is preferentially expressed
30
What is the difference between screening and testing?
* Screening = routine examination of healthy people in order to prevent later illness
* Testing = investigation of a clinical problem
31
What is a **linkage assay**?
* Linkage = tendency of genes that are spacially related (i.e. proximal) to be inherited together during meiosis
* Linkage assay = tracking and analysing the inheritance of alleles throughout families to discern relative positions of genes within the genome
32
(a) Define congenital abnormality
(b) Give an example of a congenital abnormality
(c) What is the incident of congenital abnormalities in live births?
(d) What is the genetic contribution to congenital abnormalities?
(a) A congenital abnormality (aka birth defect) is a anomaly that presents at the time of birth
(b) Cleft palate
(c) Incident = 1 in 50 (common)
(d) Genetics contributes to around 40% of all congenital abnormalities
33
# Define the following classification of congenital abnormality:
**Malformation**
* Malformation is a _primary_ structural defect
* Usually involves a single organ showing multifactorial inheritence (i.e. polygenic + environmental)
* Example = cleft palate
34
# Define the following classification of congenital abnormality:
**Disruption**
* Disruption is a _secondary_ structural defect
* Caused by ischaemia, infection or trauma - there is no genetic inheritance
* Certain genetic factors can pre-dispose
* Example = digital amputation by amniotic band
35
# Define the following classification of congenital abnormality:
**Deformation**
* Deformation is _structural distortion_ usually caused by abnormal mechanical forces
* Usually occurs in late pregnancy
* Good prognsis as the underlying structures are normal
* Example = club foot
36
# Define the following classification of congenital abnormality:
**Syndrome**
* A syndrome is a consistent pattern of abnormalties with a _specific underlying cause_
* Often has an underlying genetic basis
* Example = Down's Syndrome
37
# Define the following classification of congenital abnormality:
**Sequence**
* A sequence is a chaing of evetns leading to a _primary factor_ which causes _multiple abnormalities_
* The primary factor can have a genetic component
* Example = Potter's sequence
38
# Define the following classification of congenital abnormality:
**Dysplasia**
* Dysplasia is the _abnormal organisation_ of cells into tissues
* Example = thanatophoric dysplasia (i.e. short flat bones)
39
# Define the following classification of congenital abnormality:
**Association**
* Association = _unexplained_ (but not random) occurance of abnormalities (i.e. cause is unknown)
* Example = VATER association
40
# Define the following type of chromosome abnormality:
**Numerical**
* A numerical abnormality = **aneuploidy** (loss or gain)
* Loss of a chromosome = **monosomy**
* Gives a reduction of 50% of all expressed gene products
* Poorly tolerated (i.e. no compensation) - almost always fatal
* Gain of a chromosome = **trisomy** and **tetrasomy**
* Trisomy = gain of one chromosome (3 in total)
* Tetrasomy = gain of two (4 in total)
* Better tolerated than loss - clinical manefestations but not fatal
41
# Define the following type of chromosome abnormality:
**Structural**
* Structural changes are mutations
* Invovles - translcations, indels, inversions etc.
* **Translocations = partial aneuploidy **
* Material is exchanged between different chromosomes during meiosis
* Balanced = no overall change therefore no presentation (i.e. a swap between two)
* Unbalanced = overall gain or loss in a sequence causing severe disease or death
42
# Define the following type of chromosome abnormality:
**Mosaicism**
Mosaicism = differnet cell lines mixing to form an organism
43
Outline the clinical features of Down's Syndrome
* Newborn = severe hypotonia, sleepy, excess nuchal skin
* Craniofacial = macroglossia, small ears, epicanthic folds
* Limbs = short stature, gaps between first and second toes, single plamar crease
* Cardiac = atrial and ventral septal defects
* Neurological = cognitive defects
44
What is the most common cause of Down's Syndrome
**Trisomy 21**
* 3 copies of chromosome 21
* 95% of all cases (of which, 90% = maternal)
45
What are alternative causes of Down's Syndrome (i.e. other than trisomy)
**Translocations**
* Robertsone Translocation (breakage of specific chromosomes)
* 4% of cases
* Commonly de novo
**Mosaicism**
* Mitotic non-disjunction
* 1% of cases
46
Which gene determines gender?
SRY gene
Presence = male, Absence = female
47
At what age is sex determined?
6 weeks gestation -
SRY gene is activated 6 weeks after conception on the Y chromosome to give male attributes
48
What are SRY Translocations?
* SRY Translocations cause the foetus to be genetically one gender but phenotypically another
* Loss from Y = genetically male, phenotypically female
* SRY gene has been lost from Y chromosome
* Default female development
* Will be infertile
* Addition to X = genetically feamle, phenotypically male
* SRY gene added to an X chromosome
* Stimulates male development
* Will be infertile
49
Outline the following Sex Chromosome Aneuploidy
## Footnote
**Turner's Syndrome**
* Affects females
* Either loss of X or Y
* No obvious problems at birth
* If genetically female, oestrogen replacement can reverse most effects
50
Outline the following Sex Chromosome Aneuploidy
## Footnote
**Polysomy (males and females)**
**Polysomy in Females**
* XXX
* Usually no obvious defects - normal fertility
**Polysomy in Males **
* XXY (known as klinefelter's)
* Variable physical manefestations
* Infertile
51
Briefly outline the role of genetics in cancer
* Cancer is a genetic disease
* It is driven by an accumulation of genetic canges that lead to alterned tranctiption and/or abberant gene transcripts
* These changes ause cancer because the resulting protein is mutated which has downstream effects on signal transduction
* The most commonly affected pathways are cell cycle and proiferation control, apoptosis control and adhesion
52
What is the difference between sporadic and germline cancers?
* Sporadic cancers are non-inherited, they are caused by acquired changes in somatic tissue - 99% of all cases
* Germline cancers are inherited, they are caused by inherited mutations in germline tissue - 1% of all cases (but higher risk of development if present)
53
What are proto-oncogenes
* Oncogenes (and proto-oncogenes) are invovled in **_growth and proliferation_**
* They favour the **_halt of the cell cycle_**
* Examples - growth factors, transcription factors, TKs
54
What is the difference between a proto-oncogene and an oncogene?
A proto-oncogene is a normal gene that has various functions within the cell.
An oncogene is a mutated proto-oncogene causing unregulated cell division
55
What are tumour suppressor genes (TSGs)
* TSGs have a variety of functions, including:
* **_Regulating cell division_**
* **_DNA damage checkpoints _**
* **_Apoptosis_**
* **_DNA repair_**
* They favour controlled **_proliferation_**
56
What is a point mutation?
A point mutation is a cancer-causing mutation as it has carcinogenic effects on the protein - it can either be silent (no effect), abrnomal protien (aa change) or truncated protein (stop codon insertion)
57
How would a point mutation in TSGs cause cancer?
Any alteration in the repication of TSGs will produce abberant proteins therfore there will be **_uncontrolled cell proliferation_**
58
Describe the "two-hit model"
* Most TSGs require damage to both alleles to confer a carcinogenic effect
* Most commonly, the first hit occurs as a point mutation in the germline and a second hit in somatic cells
* These two hits = TSG inactivation
59
Define haploinsuffiency
If only one hit is required (i.e. damage to a single allele) = haploinsufficiency
60
What types of mutations can cause TSG inactivation?
* Mutation in coding region
* Genomic deltion (or whole chromosome loss)
* Mutation in promoter
61
What types of mutations can cause proto-oncogene activation?
* Mutation in promoter
* Mutation in coding region
* Genomic amplifaction (or whole chromosome gain)
* Gene fusion
62
Concerning breast cancer:
## Footnote
(a) What are BRCA1/2?
(b) What do mutations to BRCA1/2 result in?
(c) Apply the "two-hit model" to BRCA1/2
(d) What percentage of breast cancers involve BRCA1/2 mutations?
(e) What is the risk of develpoing breast cancer if BRCA1/2 mutation is present?
(a) BRCA1/2 are TSGs - when mutated they cause an inherited predisposition to breast (and ovarian) cancer
(b) A mutation will cause a truncated (and non-functional) protein
(c) Hit 1 = inherited germ line mutation in BRCA1/2 genes. Hit 2 = somatic mutation in breast (and ovarian) tissues
(d) Up to 4%
(e) 60% (by the age of 90)
63
Concerning colorectal cancer:
## Footnote
(a) What is APC?
(b) What is FAP?
(c) What proportion of colorectal cancers does FAP contribute to?
(d) Explain the inheritance of APC mutation
(e) What are the risks of developing cancer with APC mutation?
(a) APC = adenomatous polposis coli = TSG (normal function = control of cell division)
(b) FAP = familial adenomatous polposis - characterised by the growth of mulitple intestinal polyps, one or more of which is likely to become cancerous
(c) 1%
(d) Mutated APC = autosomal dominant
(e) virtually 100% lifetime risk of colorectal cancer
64
Concerining colorectal cancer:
## Footnote
(a) What is HNPCC (aka Lynch Syndrome)?
(b) Which TSGs are mutated in HNPCC?
(c) Explain the inheritance of mutations in HNPCC
(d) What are the risks of developing cancer with affected TSGs?
(a) HNPCC = hereditary non-polyposis colorectal cancer
(b) MHL1 & MSH2
(c) Autosomal Dominant
(d) 80% lifetime risk
65
Define cytogenic change
A cytochenic change is a visible change in chromosome structure or number
Most cancers consists of cytogenic changes in addition to molecular mutations
66
AML (acute myeloid leukaemia)
* What is AML?
* Explain the pathogenesis AML
* Cytogenic change
* Protein affected
* AML = abnormal accumulation of immature granulocytes
* Characterisd by **chromosomal translocation** causing fusion = **_fusion protein_**
* Proteins = RARa (retinoic acid receptor a)
* Regulator of DNA transcription
* Mutation = blocking transcription
67
CML (chronic myeloid leukaemia)
* What is CML?
* Ouline the progress of CML
* Which chromosome is affected and how?
* CML = chronic myeloproliferative disorder
* Progress = triphasic (chronic, accelerated, terminal/acute)
* Philadelphia Chromosome
* TK
* Translocation alters the chromosome
* Increases myeloid precursor production
68
What is a pharmacogenomic test?
A test that is used to identify which pateints are most liely to respond to a treatment based on the presence (or absence) of a particular somatic mutation
69
Define obesity
Obesity = BMI \> 30 kg/m2
Morbid Obesity = BMI \> 40 kg/m2
70
Outline the purpose of Genome-Wide Association Studies (GWAS) & its results
* GWAS = identify common variants to help identfy specific genes that contribute to obesity
* Found that obeisty is _polygenic_ (i.e. not a single gene invlved)
71
What is a copy number variant?
Copy number variants are a form of structural variation causing alterations in DNA and abberant function
72
What are the three major types of obesity?
Common obesity
Syndromic obesity
Monogenic obesity
73
What is an "obesogenic environment"?
Describe the role of genetics in response to the obesogenic environment
* Obesogenic envrionment = an env. in the Western World that tends to "make" adults obese
* Genetics helps determine an individuals response to the environment
* Not everyone will become obese even though they are exposed to the same enviornmental influences
* 70% of a child's obesity can be explained by genetics
74
Explain the envrionmental influenes in common obesity
* Environmental = behaviours - this includes feeding and activity
* Behaviours
* High calorie diet
* Lack of physical activity
* Stress
75
Explain the genetic influenes in common obesity
* Genetics affect physiology
* BMR - low BMR = higher propensity to gain weight
* Active energy expenditure
* Genetics (in part) affect behaviour
* Appetite
* Physical activity
76
What is the major influential factor in syndromic obesity?
Genetics
77
Name and outline two major syndromic obesity disorders
**Prader-Willi Syndrome**
* Most common syndromic obesity
* Involves 7 genes on chromosome 15
* Signs & Symptoms
* Floppy at birth
* Hypogonadism
* Short Stature
* Lack of appetite control (permentantly feels starving)
* Severe obesity
**WAGR Syndrome**
* Caused by BDNF mutation
* Signs & Symptoms
* Wilms tumour (kidney)
* Genitourinary anomalies
* Mental retardation
78
What major signalling pathway is affected in monogenic obesity?
Appetite regulation
79
Given an example of a dominant mutation in monogenic obesity
**MC4R**
* Most common single gene form of obesity
* Caused by a deletion
* Present in up to 6% of all childhood obesity cases
80
Given an example of a recessive mutation in monogenic obesity
**Leptin**
* Most commonly - Ob/Ob humans - i.e. do not produce any leptin
* Can also invovle lack or receptor (LEPR)
* Causes increased hunger (i.e. lack of appetite regulation) resulting in obesity
* Co-morbidities
* Poor growth
* Immune problems
* Lack of puberty --\> infertility
81
Outline the ethics of genetic testing
* Right to know
* Data protection
* Genetic privacy
* Equality of access
82
Otuline the principle of the following genetic tests:
(a) Tests for Monogenic Diseases
(b) Tests for Complex Diseases
**Monogenic Diseases**
* Can provide carrier status information
* Can predict risk in late-onset disease
* Includes genetic councelling
**Complex Diseases**
* Limited clinical utility
* Can cause undue alarm or false reassurance
83
Give three applications of whole genome sequencing
* Catalogue genetic variations within a population
* Idetify genetic changes in cancer cells
* Identify novel gene mutations in monogenic disease
84
Outline pre-implantation genetic diagnosis (PGD) tests and how they work
* PGD tests are genetic tests carried out on IVF embryos
* PGDs are an alternative to prenatal testing
* Usually, these are perormed to ensure that only embryos free from particular genetic conditions are implanted
* They are most commonly performed on families with high risks of having children with serious genetic conditions
85
What are the two types of PGDs
* FISH - fluorescent in situ hydridisation = detect chromosomal conditions (eg: Down's Syndrome)
* PCR & DNA sequencing = detect mutations in single genes
86
Outline the ethical issues of PGD
* Invovles discarding unused/affected embryos
* Disbility rights argument
* Slippery slope argument
* Eugenics
87
What PGDs are currently allowed in the UK?
The following PGDs are allowed in the UK:
* Tests for severe early onset diseases (eg: Tay Sachs)
* Tests for severe late onset diseases (eg: Huntington's)
* Tests for diseases with incomplete penetrance (eg: Breast cancer)
MCD
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