Principles

Question 1

Multifactorial Diseases

Answer 1

Multifactorial (complex) diseases are non- Mendelian disorders that occur in families more frequently than permitted by chance alone, but show no clear classical pattern of inheritance (genetic and enviro factors)
-no clear single gene identified
Among the most common diseases encountered in medical practice and include:
1. common adult onset disorders:
coronary artery disease autoimmune disorders Parkinson’s disease hypertension Alzheimer’s disease schizophrenia
diabetes (type 1 and type 2)
2. birth defects (e.g. congenital heart disease, spina bifida, cleft lip +/- cleft palate)

Question 2

Genetic Factors in Disease

Answer 2

Cystic Fibrosis:
Autosomal recessive disorder
Mutation in CFTR gene
Thick mucous secretions
Recurrent chest infections Lung damage
-Bronchiectatic lung (widely dilated BV clogged up with mucoid secretions/consolidation)
-Monogenic, single gene disorder

Question 3

Environmental Factors in Disease

Answer 3

Asbestosis:

• predominantly environmental in its origin
• Work related exposure to asbestos fibres (demolishen industry, or early engineering or plumbing industry, where asbestis in cladding of fibres)
• are carcinocenic
• Lung and pleural fibrosis
• Mesothelioma (rare tumour but directly related to the carginogenic effects of asbestis

Question 4

Multifactorial disease Inheritance

Answer 4

Now recognition of the inheritance of gene(s) (genetic factors) which predispose towards disease, or modify the course of the disease process e.g. Crohn’s disease
Crohn’s disease =Inflammatory Bowel Disease = Genetic susceptibility + Infectious disease + Immune response
-when susceptibility genes are placed in appropriate environmental exposures (microbial, dietary or mixture) results in abnormal information –> Crohn’s disease
-Some genetic predisposing genes can be polymorphisms in immune response genes in gut transport proteins within bacterial recognition genes
-Polymorphisms: mild variations/single base changes. On its own wont cause disease:
-but when sufficient number together, in the correct environment events = development of disease

Question 5

Multifactorial disease graph **

Answer 5

Genetics/Environment

1. Monogenic diseases (CF)
2. Combination of hereditary predisposition and environmental factors
   - majority seen in clinical practice
   - asthma, diabetes, hypertension etc
   - interaction of genetic landscape and enviro
3. Environmental factors (e.g. injuries, nutrition) (almost entirely enviro disorders)

Question 6

Pathology of Multifactorial inheritance

Answer 6

Inheritance of common alleles that have small to moderate effects
Genes that have greater phenotypic impact when combined than they do separately (POLYGENIC traits)
Impact of MODIFIER genes (genes not susceptibility but modify (melanoma))
Chrons disease predisposition genetic risk factors would be modifying genes - body’s immune response to different gut bacteria
Interactions among genes and epigenetic factors (acquired and developmental) - recognise changes in gene packaging in chromosome (methylation) resulting in up or down regulation of specific genes expression
Interactions between genes and environmental factors

Question 7

Epigenetic factors

Answer 7

(acquired and developmental) - recognise changes in gene packaging in chromosome (methylation) resulting in up or down regulation of specific genes expression
Have epigenetic modifier drugs in clinical trial/practice for cancer area

Question 8

Pathology of multifactorial inheritance

Answer 8

High risk of early Heart Disease
-ONLY in overlap
-Needs both Environment AND genetic predisposition
Coronary artery disease:
Genetic risk Factors: Low –Clotting g –High Cholesterol g – BP g – Heart Failure g – unknown g –> High
- clotting: makes blood more hyper coaguable
Environmental Risk Factors: High

Question 9

Modifier Genes

Answer 9

Not associated with the disease origin, but once disease susceptibility is present or the disease has developed, these genes modify the severity of disease phenotype

e. g. the melanocortin-1 receptor gene is a modifier gene for melanoma
- influence pigmentation
- changes in a/acid sequence within melanocortin-1 receptor
- alters the severity of the melanoma (size, depth, invasion into nerves/BV)

Question 10

Threshold Model for Polygenic Trait

Answer 10

Assumes that all individuals have a susceptibility to develop the trait (due to genetic and environmental factors) but a threshold must be reached before it is expressed
The normal distribution curve (bell curve) for individuals from families who have demonstrated a trait is farther to the right along the risk axis
As more individuals are reported in the family, the curve shifts even more to the right
-polygeneic disease= accumulation of at risk genes
-threshold/liability threshold= influenced by number of at risk/susceptibility genes

Question 11

Identification of Multifactorial Threshold Trait

Answer 11

• Disorders can be common (but can also be rare) (asthma, diabetes vs congenital cleft palate)
• Disorder runs in families, but no distinctive pattern of inheritance (alerts to genetic predisposition. but inheritance pattern doesnt fit into clear Mendalian inheritance patterns)
• Concordance rate in monozygotic twins (20-40%) is greater than in dizygotic twins
• Frequency of disease in 2nd degree relatives much lower than 1st degree, but declines less rapidly for more distant relatives (due to having multiple susceptibility genes, declines less rapidly, seen in more distant relatives)
• Recurrence risk is proportional to number of family members already affected (allelle burden, or number of genes involved)
• Recurrence risk is proportional to the severity of the condition in the proband (reflects concentration of adverse alleles) eg cleft palate (unilateral (single) cleft palate = 2% risk in subsequent siblings) (bilateral cp = increased 6-7% risk = due to number of different alleles/bad risk alleles more present)

Question 12

Linkage analysis

Answer 12

Linkage analysis looks for co- transmission of disease with polymorphisms of possible linked genetic markers
When a disease affects 1st degree relatives (siblings, parent, child), genetic analysis can be performed to determine whether a genetic locus can be linked to the phenotype
This was how causative genes were identified in single gene disorders

Question 13

Linkage analysis and Multifactorial Diseases

Answer 13

Multifactorial diseases can also be analysed for linkage but it is more challenging because of causation generally by a combination of genetic polymorphisms

• resulting in subtle changes in gene interactions/gene expression levels
• any single allele may not always be associated w disease phenotype
• has been less applicable/easy

Question 14

Genome-Wide Association Studies (GWAS)

Answer 14

Examine many common genetic variants in different individuals to see if any variant is associated with a trait
GWAS typically focus on associations between single nucleotide polymorphisms (SNPs; occur every 100-300 bp) and multifactorial diseases
-SNPs are variation that we all have. inherited. mainly in non-coding region.
-look for association between SNPs and disease
Variable results

Question 15

Genome-Wide Association Studies (GWAS) Graph

Answer 15

Rare, High risk (Mendelian) variants
Rare, Low-risk variants, hard to identify genetically
Low frequency variants with intermediate effects
Common variants of modest effect - require interaction with other gene and enviro factors

Question 16

Craig Venter

Answer 16

Established Celera Genomics – sequenced human genome (‘completed’ 2001)
—Sequenced own genome 2007 4.1 million gene variations
3.2 milllion SNPs 1.0 million indels
Sequenced own genome 2007
(Polymorphisms )Contains sequences associated with: (clinical phenotypes- wont cuase but predisposed so that if in conjunction with other genetic and enviro factors may increase risk of developing these conditions)
-Wet ear wax
-Anti-social behaviour
-Alzheimer’s disease (APOE)
-Cardiovascular disease
Genome sequencing will have a huge impact on clinical medicine

Question 17

Genomic Sequencing Availbility

Answer 17

US$174 for international customers
Buy kit online, saliva sample that is to be sent back
-get result back in few weeks
-look at SNPs (not disease prediction)
-Provide information on ancestry and disease risk
May become part of testing/clinical discussion re its meaning

Question 18

Opportunities Following Gene Identification (Improved understanding of disease pathology and diagnosis)

Answer 18

Improved understanding of disease pathology and diagnosis:
• Advance understanding of disease pathophysiology
• Reclassification of disease based on knowledge of genetic basis
• Ability to examine gene-environment interactions

Question 19

Cilantro/Coriender

Answer 19

AA genotype coriander has soapy taste

Question 20

Opportunities Following Gene Identification (Advances in patient management)

Answer 20

Advances in patient management:
(better targetted advice re diet, exercise, lifestyle)
• Provision of tools for risk prediction (molecular assays to monitor/diagnose disease)
• Disease preventive strategies; e.g. environmental modification
• Develop biological assays to monitor disease progression; possibly pre- symptomatic at molecular level prior to physiological changes
• Identification of new drug targets; for traditional drugs or development of novel therapies

Question 21

Personalised Medicine

Answer 21

Refers to the utilisation of individual genetic information and DNA-based technologies to make decisions aimed at maintaining health, preventing disease or improving outcomes of disease
-BRAF mutation in Melanoma, treat with BRAF protein inhibitor

Question 22

Precision Medicine

Answer 22

-Refinement of PErsonlised Med, take all info
Involves the creation of a dynamic infrastructure where patients’ health information (including genetics, blood test results, responses to medications and reactions to therapies) would be accessible to scientists – and where discoveries made in the laboratory could inform patient care
-funded to now become a platform to help make more informed patient care decisions

Question 23

Personalised / Precision Medicine: Examples

Answer 23

1. Prevention: identify those at greatest risk of disease from ‘adverse lifestyle’
   e.g. smoking, high alcohol intake, obesity, sun exposure
   -more targetted approach
2. Screening: identify high risk individuals for prioritised screening e.g. earlier
   age, more frequent, greater sensitivity
3. Diagnosis: pre-symptomatic diagnosis; DNA-based tests that provide diagnosis before other (often invasive) studies
   -Selfery cancer DNA: cancer cells also shed DNA into plasma- early presymptomatic test
4. Prognosis: identify disease process that may be aggressive and require alternative therapeutic approach
5. Drug efficacy: identify patients who will receive greatest benefit from a particular drug (avoiding ‘try and see’ approach)
6. Drug tolerance: identify patients likely to experience drug side-effects, who would benefit from either a lower dose of the drug or an alternative agent

Question 24

Alzheimer’s Disease
Larry is a 54 year old man whom you have been treating for mild hypertension for the past 4 years. His health is otherwise good, though he also has mild hypercholesterolaemia, for which he was recently started on statin therapy to protect him from atherosclerosis by lowering his cholesterol.
At a routine follow-up visit he asks about testing for Alzheimer’s disease. His mother had been diagnosed as having presenile dementia several years ago, and recently died of this disorder.
There is no other family history of which Larry is aware.

Answer 24

Is Larry at high risk of developing Alzheimer’s disease based on this family history?
• Neurodegenerative disorder that presents with memory loss and behavioural changes
• Defective cleavage of amyloid-β precursor protein (APP) causing β-amyloid plaques and
neurofibrillary tangles in the brain, with progressive loss of neurones

Question 25

Alzheimer’s Disease

Answer 25

• Neurodegenerative disorder that presents with memory loss and behavioural changes
-accumulation of amyloid plaques (abnormal protein deposited, resulted in loss of neurons)
=memory loss and behavioural changes of dementia
• Defective cleavage of amyloid-β precursor protein (APP) causing β-amyloid plaques and
neurofibrillary tangles in the brain, with progressive loss of neurones
• ~2% of cases inherited as autosomal dominant (early onset), but most multifactorial
• In families without AD transmission, empirical lifetime risk of 20% (which is doubled in 1st degree relatives). Affects 40-50% of Caucasians in their 90s
• At least 7 susceptibility loci/alleles; presenilin 1 & 2, APP (chromosome 21), ApoE

Question 26

Is Larry at high risk of developing Alzheimer’s disease based on this family history?

Answer 26

• Larry is told that there is no genetic testing that would be recommended at this time
• He has no symptoms of Alzheimer’s disease and his physical examination is normal
• Not entirely satisfied, Larry does his own internet research and finds a lab that offers ApoE testing

Question 27

What is the relationship of ApoE to Alzheimer’s disease?

Answer 27

Apolipoprotein E (ApoE) locus known to be associated with late-onset familial and sporadic Alzheimer’s disease
Polymorphic locus with 3 alleles: ε2, ε3, ε4 Involved in clearance of cleaved amyloid
protein
ε4 allele associated with increased risk of Alzheimer’s disease (not a cause but susceptibility gene)
“Larry calls the office the next day to ask if he can be tested for ApoE.
You explain that this testing is not recommended as a screen for Alzheimer’s disease” (as only susceptibility gene, does predict a development, and isnt an intervention we can do becuase of it)

Question 28

How would you evaluate ApoE testing in terms of clinical accuracy, clinical validity and clinical utility?

Answer 28

Testing for the ε4 allele is highly accurate (DNA test), but has limited clinical validity and utility - inadeuate studies. dont have intervention/therapy to change risk of carrier
Relative risk greatest for those homozygous for ε4 allele, but also increased in heterozygotes
Nothing to offer to carriers to modify risk Test not recommended on routine basis
“Returning to the internet, Larry finds a lab that will accept a saliva sample without a physician’s referral
The internet advertisement notes that the lab is ‘CLIA’ (Clinical Laboratory Improvement Amendments; US regulatory standards ) certified
He contacts the lab, which provides a kit in the mail
He follows instructions for the saliva sample, which is sent off”

Question 29

Are there specific concerns about saliva as a source of material for testing that would be different from blood?

Answer 29

Saliva is a convenient source of epithelial cells for DNA analysis
Small quantity of cells obtained but sufficient for targeted mutation testing (and apoE allele testing)
Insufficient DNA for large number of tests and no RNA available
“A month later, Larry gets a report in the mail saying that his ApoE genotype is ε2/ε4 (heterozygous for at risk allelle)
He now calls your office again to ask what this means
Is he going to get Alzheimer’s disease?”

Question 30

How are you going to counsel Larry?

Answer 30

Larry has one ε4 allele, which does increase his risk of Alzheimer’s disease
-homo: 10x increase
-heter: less than 10x but still increase
ApoE is a predispositional test, and is not diagnostic, so there is still only a low risk that he will develop the disorder
No preventive treatment, nor any special care plan based on outcome of test