Week 10 Flashcards
Where do most disease causing mutations fall?
They fall within a spectrum ranging from rare alleles with major effects to common alleles with small effects
What are Mendelian loci disease?
Very low frequency but is highly penetrant eg CFTR- Cystic fibrosis
What are goldilocks loci disease?
Low frequency with moderate effect eg NOD2-Chron’s disease
What are infinitesimal loci disease?
Common alleles with small effects eg PPARG- Type 2 diabetes
What are RAME disease?
Very low frequency with variable penetrance eg NRG3- Schizophrenia
What are CD-CV disease?
Common alleles with moderate effect eg CFH2- Macular degeneration
What are the 5 types of human single gene disorders?
X-linked recessive traits
X-linked dominant traits
Y-linked traits
Autosomal dominant traits
Autosomal recessive traits
What are the key feature of X-linked recessive traits?
Primarily affects males, females acts mainly as carriers eg colour blindness, muscular dystrophy and haemophilia
What are the key feature of X-linked dominant traits?
Affected males produce affected daughters but not sons
Female heterozygotes transmit trait to half of her children (males and females)
Seen in Hypophoshpatemia- low P levels in blood and skeletal deformitites
What are the key feature of Y-linked traits?
Traits passed from father to son (very rare)
What are the key feature of autosomal recessive traits?
Two defective alleles required, males and females equally effected eg sickle cell anaemia and cystic fibrosis
What are the key feature of autosomal dominant traits?
Affects males and females equally, only one defective allele required eg Huntington’s disease
What can be used to determine the inheritance of diseases?
Human pedigrees
What is compound heterozygote?
They have two different recessive alles but they both code for a similar effect so they are more likely to be expressing the gene than a heterzygote which doesnt have these mutations
What causes sickle cell anaemia?
A mutation in the gene encoding the beta chain of human haemoglobin.
What is the mutation causing sickle cell anaemia?
A substitution in the genetic code from GAG to GTG. This changes the amino acid from glutamic aicd to valine
What is the consequence of having sickle cell anaemia?
The haemoglobin becomes sticky and hard which causes vaso-occlusion (becoming stuck in capilaries), this causes poor blood flow and pain. People tire easily and are susceptible to heart failure, requiring constant medical treatment (transfusions)
What happens to the haemoglobin with sickle cell anaemia?
Sickle cell anaemia the Hb in RBCs forms long linear crystals under low O2 concerntrations leading to sickle cell shape, they then breka up easily during circulation
What happens with heterozygous sickle cell anaemia?
They have Hb^A/Hb^S which means some cells are normal and some have sickle cell shape meaning they have more milder symptoms
What is the advantage of being heterozygous for sickle cell anaemia?
They have more resistance to malarial parasite plasmodium falciparum. This is an example of Heterozygous advantage
How frequenct is the mutation for sickle cell anaemia in African Americans?
Heterozygous carriers are 1 in 12 meaning 1 in 500 births have dual allele sickle cell anaemia
How can you detect the prescence of sickle cell anaemia?
The SNP mutation in the Hb^S allele can be detected by CAPS (Cleaved Amplified Polymorphic Sequence)
How does CAPS work?
Both alleles have the same primers so DNA region can be amplified
Add in the restriction enzyme MstII which its restirction site is CCTGAGG meaning wildtype allele has the appropriate sequence so will cut
These DNA sections can then undego a gel electrophoresis
What are the results for the gel electrophoresis of identifing sickle cell anaemia?
Homozygous sickle cell- 1 band at 500 bp
Wildtype- 2 bands at 300bp and 200bp
Heterozygous- 3 bands at 500bp, 300bp and 200bp
What is the inheritance of cystic fibrosis?
Autosomal recessive condition
Common genetic disorder in Europeans affecting 1/~2500 births
What happens with people with cystic fibrosis?
Mucus build up in the lungs and pancreas result im breathing and digestive problems
What is the overview of the cystic fibrosis gene?
The CFTR gene is responsible for the disease is located on chromosome 7
Spread over a distance of 250 kbp
~1000 different recessive loss of function mutations have been described in the CFTR gene across the 24 exons
What health problems are caused by cystic fibrosis?
Frequent lung infections
Sinus problems
Salty sweat
Trouble breathing
Abnormal pancreas function
Trouble digestive food
What does CFTR code for?
CFTR codes for a chloride ion transporter on the epithelia of the lung and other tissues. This helps create sweat, digestive juices and mucus
What is the Hardy-Weinberg law?
A mathematical model for the genetic structure of populations developed independantly by Godfrey Hardy (mathematician) and Wilhelm Weinberg (Physician)
What is the formula for the Hardy-Weinberg law?
p^2 + 2pq + q^2 = 1
p= frequency of allele A
q= frequency of allele a
Using Hardy-Weinburg law how many people are carriers for cystic fibrosis?
1 in 2500 = 0.0004 = q^2 therefore q= 0.02
p = 1 - q p = 1 - 0.02 = 0.98
Heterozygous = 2pq
2 x 0.98 x 0.02 = 0.04 = 4%
1 in 25 people have a defective allele
Where is the CFTR gene expressed?
Analysis of CFTR mRNA expression shows that it is expressed in the lungs and pancreas
What is the most common mutation leading to cystic fribrosis?
c.70% is the deltaF508 mutation. This single amino acid (phenylalanine) deletion results in the protein being mis-folded in the Golgi
What percentage of people with cystic fibrosis are homozygous for the deltaF508?
Approximately 50% of individuals, the Orkambi treatment is effective in these individuals
What are the other 50% of individuals with deltaF508?
They are compound heterozygous for which there are six different classes each characterised by distinct CF seversity
How many disorder of metabolism are there?
Approximately 200 known disorders or inborn errors of metabolism
Who pioneered studies on inborn errors of metabolism?
Archibald Garrod
What idea did Archibald Garrod develop?
Developed the concept of metaboliv pathways proceeding in steps which in turn led to the idea of one gene = one enzyme
What did he suggest could be the cause of inborn errors of metabolism?
The segregation of recessive mutations
How did Archibald Garrod study his hypothesis?
He studied four different enzyme defects that are responsible for abnormal urine colour eg PKU
What did Archibald Garrod notice about the relationship with people with mutations?
These conditions ran in families often where parents are related
Consistent with a recessive mutation according to the newly discovered laws of Mendal
What happens if a mutation occurs in a biochemical block?
It disrupts amno-acid metabolism
What is alkaptonuria?
A mutation preventing the forming of a functional Homogentisic acid oxidase. This prevents the converting of Homogentisic acid into maleylacetoacetic
How frequent is alkaptonuria?
Benign disorder (affects 1 in 250,000)
What are the symptoms of alkaptonuria?
Brown discolouration of baby’s nappy due to massive urinary excretion of homogentisic acid (alkapton is the oxidised form)
In later life- onchronosis (a form of arthritis from cartilage damage which is caused by polymers of phenols accumulating in cartilage matrix)
What are the key features of phenylketonuria?
Deficiency in enzyme, phenyalanine hydroxylase, needed for phenyalanine to tyrosine (genetic block in metabolic pathway)
Affects ~1 in 10,000 births
What are the symptoms of phenylketonuria?
Children exhibit intellectual disability abd convulsions due to accumularion of phenylalanine
Lack of tyrosine leads to decrease in melanin pigment
What is the treatment for phenylketouria?
Careful diet with restricted phenylalanine to prevent intellectual disability (tyrosine supplementation is also required)
Once brain development is completed dietary restrictions can be relaxed
What are most metabolic disorders?
They are autosomal recessive or x-linked recessive
Can metabolic/cellular disorders be autosomal dominant?
Very few are autosomal dominant unless they are ‘late’ onset
What is haploinsuffciency?
The single WT allele can’t produce sufficient protein to confer a normal phenotype
What is the theory for X-linked dominant traits?
Affected males produce affected daughters but not sons
Female heterozygotes transmit to half of her children (male and females)
Generally, clinical expression is more severe in hemizygous males than heterozygous females
What is the relality for X-linked dominant traits?
Depending on the condition, expression in hemizygous males can result in lethality
Severity in heterozygous females is variable due to random X-inactivation
What are examples of X-linked dominant traits?
Rett syndrome and Aicardi syndrome
What is the overview of Rett syndrome?
Males with pathogenic MECP2 mutations usually die within the first two years from severe encephalopathy.
<1% are due to transmission, most cases arise due to spontaneous mutations.
MECP2 binds to methylated promoters to repress transcription
What is the overview Aicardi syndrome symptoms?
Affects neurodevelopment and optic atrophy
What causes X-Linked haemophilia A?
Haemophilia A is due to a mutation in a gene that encodes a blood clotting component (Factor VIII)
What is a famous example X-Linked haemophilia A?
European royal families
Queen Victoria was a carrier this lead to both Russian and Prussian royal families to have haemophilia
What is the overview of Lesch-Nyhan syndrome frequency?
X-linked recessive mutation
Affects 1 in 380,000 births- up to 1/3 are spontaneous mutations
What are the symptoms of Lesch-Nyhan syndrome?
Increased levels of phosphoribosylpyrophosphate leading to increased purine synthesis by the de novo pathway resulting in uric acid production
Affects CNS leading to uncontrolled movement, self-harming, motor impairment, intellectual disability and impaired kidney function
What is the treatment for Lesch-Nyhan syndrome?
Drugs that lower uric acid such as Allopurinol have potential as a satisfactory treatment for the effects on the CNS (stops the conversion of oxypurines to uric acid)
What is the biochemistry of Lesch-Nyhan syndrome?
Disorder of purine metabolism
Mutation in the HPRT gene loss of function for hypoxanthineguanine phosphoribosyltransferase
Cell products should be broken down into Guanine or Hypoxanthine and then be recycled by HPRT back to GMP or IMP.
As this cant happen uric acid builds up
What are examples of dominant autosomal genetic disorders?
Huntington’s disease
Achondroplasia (FDFR3 gain of function)
Neurofibromatosis (pheripheral nerves grow into tumours affects - 1 in 4500)
What are the key features of autosomal dominant traits?
Requires just one copy of the affected gene- vertical transmission pattern
High frequencies of spontaneous mutation associated with increased paternal age
What are the key features of anchondroplasia?
A form of dwarfism - mutation in FGFR3
Approximately 80% of cases are spontaneous
Homozygous individuals for mutation die at an early age due to more severe symptoms
Technically semi-dominant= 2 copies gives more extreme phenotype than 1 copy
How can varience in repeat sequence of MS loci occur?
Variation in repeat number at microsatalite loci can result from strand slippage during DNA replication
Can also occur due to unequal crossing over at meiosis
What can result in repeat number expansion or contraction?
Mutations can change repeat number
What usually repairs errors in expansion or contraction?
MMR (mismatch repair system) but not always
What is the overview of Mendelian loci?
Major effect
Primarily due to single gene mutation
Relatively rare
High degree of penetrance (proportion of disease genotypes expressing symptoms)
What is the overview of Rare alleles of major effect (RARE)?
A rare (de novo) mutation event present in one or a few individuals or when an effect is potentially large but not completely penetrant
What is the overview of Common Disease-Common Varient (CD-CV)?
Diseases such as diabetes and coronary heart disease caused by large numbers of genes with common variants, each with a small effect
Moderate effects overall
c.5% population affected
What is the overview of infinitesimal model?
100s or possibly thousands of genes contribute to a particular disease phenotype
Each one contributes a very small effect (too small to quantify)
Small effect overall
What common diseases dont fit the problem of single nuclear gene?
Diabetes
Cancers
Cardiovascular diseases and coronary artery disease
Mental health
Neurodegenerative disorders
Why is studying the diseases that arent from single nuclear gene mutation important?
These diseases have the highest mortality rates in developed countries
Most people are likely to develop one or more of these diseases
It help reduce economic stress on health services
What factors impact multifactorial diseases?
Genetic factors interacting with:
One another
The envrionment
What is the spectrum of human diseases?
Those that are largely environmental
Thises that are entirely genetic (primarily single gene disorders)
What are examples of congenital malformations causing multifactorial diseases?
Cleft lip/ palate
Neural tube defects eg spina bifida - genetic and/or lack of folic acid (vitamin B) in diet
What are examples of congenital malformations causing multifactorial diseases?
Asthma
Crohn’s disease
Diabetes
Parkinson’s disease
Cancer
What is the familial inheritance of multifactorial diseases?
Around 2-4% and is explained by the Liability Threshold model
What is continuous variation of multifactorial traits?
Are influenced by a large number of genetic and environmental factors
Seen in height and intelligence
What are discontinuous variation of multifactorial traits?
Affected or not
Seen in diabetes
What is liability with respect to multifactorial diseases?
Term to collectively describe all the genetic and envrionmental factors that contribute to the development of a multifactorial disease. Usually shown as a standard distrubution
What is threshold level with respect to multifactorial diseases?
The point at which an individual accumlates a certain liability and will be affected by the disorder
What is the relationship between severity of incidence and risk to relatives?
Risk to relatives increases with seversity of incidence
Severe cleft palate risk to offspring is 6%
Mild cleft palate risk to offspring is 2%
What is the relationship between family distance and risk to relatives?
Risk to relatives decreases as family distance increases
Spina bifia- direct offspring 6% nephews/nieces 2% and cousins <0.5%
How does number of family cases increase risk?
More familial cases means higher risk
How does condition affected by sex impact risk?
Then relatives of affected indiviuals of that sex will be at higher risk
How can you work out the risk of first degree relatives?
The risk is the square root of the population incidence
eg cleft palate incidence is 1:10000 (0.001) so siblings/offspring will be 0.03 or 3%
What causes cancer cells?
Successive somatic mutations confer the properties of cancer to a clone of cells
Many cancers require 6-10 mutations, these accumulate over time
What is the concordance of most cancers amogst first degree relatives?
Concordance of most cancers is low
Cancers arise spontaneously (somatic mutations)
What are the exception in the concordanceof most cancers?
Some cancers do appear in families
Inheritance of some mutations predisposes a person to cancer because they have to accumulate fewer mutations
What can increase out chance of cancer?
Mutagens in our environement
What is the relationship between exposure to mutagens and cancer prevalence?
It is common for there to be a lag between exposure to a mutagen and increased cancer prevalence is common
What is the relationship between smoking and lung cancer over time?
Men began smoking frequently in the 1920s and women much later this led to a rise in lung cancer cases
Public health campaigns have led to a decrease in smoking and lung cancer in recent years
Not all lung cancer is caused by smoking, so incidence will not reach 0
What are proto-oncogenes?
Proto-oncogenes often encode proteins needed for cell cycle progression (accelerators). These are the non-mutant allele is referred to as a proto-oncogene
How does proto-oncogene become an oncogene?
A gain-of-function mutation results in increased proliferation
What is the overview of Ras gene?
Usually active when bound to a growth factor receptor. Oncogenic point mutation makes a constitutively active protein that activates cell division
What is the overview of c-Abl gene?
Chromsomal translocation fuses the c-abl and bcr genes (BCR-ABL1). Hybrid protein encodes a continuously active tyrosine kinase
What is the overview of Her2-?
Found in 20% of all breast cancer cells is an over-expressed growth factor receptor
What are the function of tumour suppressor genes?
Encodes fro proteins that slow down the cell cycle (brakes)
How can tumour suppressor genes lead to cancer?
Loss-of-function mutations in both gene copies results in increased proliferation
How can inheritence of mutant tumour supressing genes impact predisposition to cancer?
Tumour suppessor genes indentified through genetic analysis of families with inherited predisposition to cancer
What is the inheritance of tumour supressing genes?
Mutant alleles act reccesively and cause increased cell proliferation
One normal allele sufficient for normal cell proliferation in heterozygotes
Wildtype allele in somatic cells of heterozygotes can be lost or mutated –> abnormal cell proliferation
What are many tumour suppressor gene products also involved in?
Many tumour supressor gene products are involved in DNA repair
What happens if a cell receives too much DNA damage?
It leads apoptosis
What is a challenge for effective drug treatment with tumour supressor mutations?
There is no target protein which means there is no effective way to target that issue
What is the function of p53?
Detect single stranded breaks and signal for p21. Then p21 will either repair DNA or trigger apoptosis
What happens if p53 is non-functional?
p53 cant induce p21 so DNA still replicated with DNA damage
What are critical mutation events that preceded by clonal expansion?
Loss of Apc -> Hyperplastic epithelium
Activation of K-Ras -> Intermediate adenoma
Loss of Smad4 and other tumour supressors -> Late adenoma
Loss of p53 -> carcinoma
Other unknown alterations -> invasion and metastasis
What is the characteritic of DNA at the carinoma stage?
The proliferating cells contain all the genetic errors that have accumulated
When gene screening what genes where seen as important of colorectal cancer?
Identified the genes K-Ras and p53 as important
What was the first heredity colorectal cancer snyndrome study?
The first hereditary colorectal cancer syndrome identified was Familial adenomatous polyposis coli (FAP) - APC gene involved (Adenomatous polyosis coli) an autosomal dominant mutation
When do Polyps appear?
In early adult life amd if not removed one or more will certainly become malignant
What is the time span between polyps to diagnosis of cancer?
It is approximately 12 years
What is the function of APC (Adenomatous polycosis coli)?
APC regulates beta-catenin a protein that plays a crucial role in cell communication, signalling, gorwth and cell death
What is the overview of people with colorectal cancer?
Most patients do not have the hereditary conditon but 80% of their cancers have inactivated/lost both copies of their APC gene
20% of cases due to mutations in the MUTYH gene which functions in DNA repair
What are the approaches to determining genetic susceptibility to common diseases?
Population/migration studies
Family studies
Twin studies
Adoption studies
Polymorphism association studies
Biochemical studies
Animal models
What is quantitive trait loci?
The susceptibility loci and polygenes
How have quantitive trait loci increased in success?
Due to the Human genome and HapMap projects, SNP genotyping techonology, and increasing the use of NGS DNA sequencing technologies
What is genetic mapping or linkage analyis based on?
The genetic distances that are measured in centimorgans (cM)
What does a genetic distance of 1cM mean?
The distance between two gene that show 1% recombination, that is in 1% of meiosis the genes will not be co-inherited and its equivalent to approx. 1 Mb in humans
What is the advatge of genetic mapping?
Very useful for mapping single gene disorders
What is the basic methodology involving genetic mapping?
It involves study of the segregation of the disease in large families with polymorphic markers from each chromosome
Eventually a DNA marker is identified which co-segregates with the disease more often than expected by chance ie disease and loci are linked
When was genetic mapping been used to help identify gene causing disease?
Mapping the Htt gene in humans. One allele of the ‘G8’ Marker co-segregates with the disease phenotype - localised to Chr.4
What are the problems with using genetic mapping with multifacotrial disorders?
Challenging mathmatically to develop strategies for dectecting linkage for polygenes which each gene only having a small contribution
Many show a variable age of onset so status of unaffetced family members is uncertain
Most families which have or had multifactorial diseases only have one or two living affected members
Some multifactorial disorders such as coronary heart disease and schizophrenia are etiologicallu heterogeneous, with different genetic and envrionmental mechanisms involved in different substypes which are ahrd to distinguish at the phenotypic level. This also makes analysis of linkage results very difficult
What are quantitative trait loci (QTLs)?
They are genes that contribute to complex traits like some human diseases
What does mapping QTLs depend on?
Producing inidividuals with different genetic compositions
What is direct QTL mapping?
Requires crosses between individuals that differ in the phenotype of interest- not possible in humans
What is association mapping?
Takes advantae of the history of random breeding population, good for human studies
What are SNPs?
A single nucleotide polymorphis represents a variation of one base in the DNA (each one is a consequence of a single mutational event). They are dimorphic point mutations
What is the frequency of SNPs?
They occur at the frequency of 1x10^9
The total number in the human population is 10^8
How closely related are two unrelated individuals and how are they told apart?
99.9% indentical
They are distinguished by 6x10^6
Each individual has many single nucleotide polymorphisms that together create a unique DNA arrangement for that individual ie distinct haplotype
What are the consequences of SNPs in exons?
If SNPs occur in coding regions, with or without consequence on the sequence of amino-acids and might influence the structure of the protein
What are the consequences of SNPs in non-coding sequences?
Many occur in non-coding sequences but if close to a disease gene may act as a suitable DNA marker that is associated with that gene
Why are family pedigrees not useful for complex traits?
Number of cases are too small
How have geneticists combated the small sample size of family pedigrees?
Genome-wide association study (GWAS) of whole populations
What is haplotype?
A specific combination of two or more closely linked DNA markers on a chromosome
What happens if a disease mutation occurs in the haplotype of closely linked SNPs?
This can be passed from generation to generation along with SNPs
What is the method for GWAS?
Collect DNA samples from individuals expressing the disease
Choose and equal number of samples of people not exhibiting the trait
Perform genome-wide SNP analysis
Indentify haplotypes at a higher frequency in the disease samples to indentify genes involved
Mutation can be surrounded by haplotype markers which are often ingherited together due to linkage disequilibrium. So SNP near it will more lilely to be inherited
What is used to show a significant different between control and disease group?
A chi square test
What is a Manhattan plot?
-log10 p value (from chi squared) is plotted
Rare peaks indicate a significant association
