Final (cumulative) Flashcards
(258 cards)
1
Q
What are the factors that disrupt HWE?
A
- assortative mating
- drift
- migration
- selection
- lethal alleles
- heterozygote advantage
2
Q
What are the four categories of non-random mating?
A
- stratification
- assortative mating
- consanguineous mating
- inbreeding
3
Q
What is stratification?
A
Breeding populations are effectively separate since they tend to breed within the population (ex. SCA carrier frequency is higher in African Americans than the general US population, they tend to reproduce within the African American minority)
4
Q
What is assortative mating?
A
Choosing a mate based on their possession of a particular trait. People tend to mate with people who resemble themselves
5
Q
Consanguinity vs. inbreeding
A
Consanguinity means the mating pair is related by descent from a common ancestor, while inbreeding means that the mating pair is related by descent from a recent common ancestor
6
Q
What do consanguinity and inbreeding allow uncommon alleles to do?
A
Allows them to become homozygous by increasing the frequency with which carriers mate
7
Q
What are Hutterites?
A
A genetic isolate in which the average degree of relatedness is ~2nd cousins. Normally rare autosomal recessive alleles are common
8
Q
What is genetic drift?
A
Random fluctuations of allele frequencies from generation to generation that take place in small, isolated populations such as islands or socioreligious groups. Chance occurrences have significant effects on disease allele frequency
9
Q
What is the founder effect?
A
A type of genetic drift in which a population starts with a small number of individuals or undergoes a drastic reduction in population
10
Q
What is an example of a disease caused by the founder effect in French Canadians?
A
Leigh disease
11
Q
What is gene flow/migration?
A
The slow diffusion of genes across a barrier, merging allele frequencies so that differences between populations decrease
12
Q
What is the primary force that leads to evolutionary divergence and the formation of new species?
A
Natural selection
13
Q
True/False? Natural selection acts on the individual
A
False. Acts on the genetic diversity in populations
14
Q
Why do new alleles have little impact on the allele frequency of the population?
A
- could be neutral
- most are carried by heterozygotes
- selection advantage may be low
15
Q
What are lethal alleles? Provide an example
A
Alleles that cause the individual to die before reproducing; DMD
16
Q
Why does DMD occur so frequently if the affected individuals die before reproducing?
A
The mutation rate in the gene is relatively high (mutational hotspot), so deleterious mutations occur frequently
17
Q
How is the frequency of the DMD allele balanced?
A
Balanced between alleles introduced by mutation and those removed by deaths (stays at a relatively stable freq)
18
Q
What is heterozygote advantage? Provide two examples
A
Heterozygotes have an increased fitness, so the frequency of genetic disorders is greater. SCA (resistance to malaria) and Tay-Sachs (resistance to tuberculosis)
19
Q
What parasite causes malaria?
A
Plasmodium
20
Q
What are the requirements necessary for the χ2 test?
A
- observed allele frequencies
- observed genotype frequencies
21
Q
What is the χ2 formula?
A
χ2 = ∑(Oi – Ei)^2/Ei
22
Q
What is the critical value? How do you use it?
A
The value where α = 0.05; once calculated, you compare your χ2 value to the critical value for the correct df. If above the critical value, then your results are significant. If below, then they are not
23
Q
What does it mean if your χ2 value is significant?
A
It means that the difference between your observed and expected values is statistically significant, suggesting that the population is likely not in HWE
24
Q
What does it mean if your χ2 value is not significant?
A
It means that the difference between your observed and expected values is not statistically significant, suggesting that the population is likely in HWE
25
What is a disease model?
An animal, tissue, or cells that display some or all pathological features of the actual disease in a controlled, experimental setting
26
What is the objective of a disease model?
To understand the disease, devise a management strategy, and find a cure
27
What are the validity criteria for animal models?
1. Face
2. Construct
3. Predictive
28
Describe the face validity criteria for an animal model
Similar symptoms are observable in both the animal model and the patient (the disease presents the same way in both)
29
Describe the construct validity criteria for an animal model
The molecular and cellular mechanisms of the disease are similar (develops the same way in both, effects the same systems in the same way)
30
Describe the predictive validity criteria for an animal model
The animal's response to a pharmaceutical or behavioural testing is similar to humans (treatment is effective in both)
31
What are the common disease models used today?
- 2D cell culture
- *C. elegans*
- *D. melanogaster*
- *D. rerio*
- *M. musculus*
- patient-derived xenograft
- human organoids
32
What are 2D cell cultures good for? What're they bad for?
Good for:
- ease of maintenance
- duration of experiments (short repro cycle)
- genetic manipulation
- genome-wide screening
- relative cost
Bad/partially suitable for:
- ease of establishing system
- recapitulation of developmental biology (starts with the disease)
- physiological complexity (single cells, not a whole body system)
33
What are *C. elegans* and *D. melanogaster* good for? What're they bad for?
Good for everything except recapitulation of human physiology because they're living systems, just not humans (obviously)
34
What is *D. rerio* good for? What is it bad for?
Good for:
- recapitulation of developmental biology
- duration of experiments
- genetic manipulation
- genome-wide screening
- physiological complexity
- recapitulation of human physiology (a bit more complex than worms and flies)
Bad for:
- ease of establishing system
- ease of maintenance
- relative cost
35
What is *M. musculus* good for? What is it bad for?
Good for:
- recapitulation of developmental biology
- duration of experiments
- physiological complexity
- recapitulation of human physiology (a bit more complex than worms and flies)
Bad for:
- ease of establishing system
- ease of maintenance
- genetic manipulation
- genome-wide screening
- relative cost
36
What are patient-derived xenografts (PDXs) good for? What're they bad for?
Good for:
- duration of experiments
- physiological complexity
- recapitulation of human physiology
Bad for:
- recapitulation of developmental biology
- genetic manipulation
- genome-wide screening
- relative cost
37
What are human organoids good for? What're they bad for?
Good for everything except physiological complexity, as they resemble one organ of the entire body and lack interactions with other systems
38
Why do human organoids have a high experimental pliability but low physiological relevance?
You're able to do a lot with them, but they cannot properly show physiological complexity
39
What is an advantage of using a zebrafish model over a 2D cell culture model?
Zebrafish (*D. rerio*), have physiological complexity and may recapitulate developmental biology and human physiology
40
How is the physiological relevance increased in human organoid models?
- directed organoid morphogenesis
- vascularization of the organoid
- create organ systems so they may interact with each other
41
Describe directed organoid morphogenesis
Controlling where stem cells grow to facilitate different structures to form, such as the lumen and crypts in an intestinal organoid
42
Why are directed organoids good for studying?
Good for modelling parasitic infections of organs, as they form the main body of the organ and last for about a month
43
True/False? Directed organoid morphogenesis does not result in stem cell differentiation, it only controls the shape of the organoid
False. Differentiated cells may arise due to the different structures formed (crypts in the intestinal organoid)
44
What is the intestinal monolayer model? What is it used for?
It is an intestinal organoid that has been unfolded into a singular layer. It allows for the study of the regulation of stem cell differentiation, proliferation, and maintenance
45
What are the ways in which vascularization of organoids can be achieved?
- manipulating cell differentiation via transcription factors
- manipulation of physical environment
- orthotopic transplantation
46
Explain how directed differentiation allows for vascularization
Inducing the expression of certain transcription factors in the organoid allows for vascularization to occur
47
Explain how the manipulation of the physical environment allows for vascularization in kidney organoids
Because kidneys require high pressure to filter blood through the bowman's capsule, the application of high pressure actually caused kidney organoid differentiation to form a bowman's capsule and vascularization without needing to induce transcription factors directly
48
Explain how orthotopic transplantation allows for the vascularization of cerebral organoids
The transplantation of the organoid into the organ it resembles within a living system induces vascularization of the organoid. This was seen in mice, where a human cerebral organoid was transplanted into their brains, then functional vascular structures were detected using dyes injected into the bloodstream
49
What is an organ system?
An organ system is basically a network of multiple different organisms connected through a shared media that resembles the human system, which increases its physiological relevance
50
What are patient-derived xenografts?
The transfer of human tissue to a mouse model. Often cancer cells injected below the skin of mice to allow for growth of a subcutaneous tumor
51
What is an orthotopic xenograft?
The transfer of human cancer to the same organ in mice as the organ from which is came from in the human patient (not always feasible, so PDX is used more commonly)
52
Explain how patient-derived xenografts are used to model disease
The diseased tissue (and organoids) are injected into the host (mouse) to validate them for use as a model for bladder cancers for study of possible treatment options
53
Describe how orthotopic xenografts work in determining metastasizing colorectal cancer genes
They use CRISPR Cas9 to screen for tumorigenic genes commonly found to be mutated in colorectal cancer. They create a pool of potential target genes and test them one-by-one by creating organoids from them and transplanting them. The mice that exhibit a worse phenotype then tell us that the organoid they were injected with is responsible for metastasis
54
How are PDXs used to study colorectal cancer?
The xenografts are used to determine which drugs are toxic to the cancerous cells
55
What are the steps in choosing a disease model?
1. Research objectives
2. Study physiological context, tissue type, disease
3. Choose the model that most sufficiently mimics the disease (validity criteria)
4. Ensure genetic interventions are easy to introduce
5. Choose a model that enables you to have options about genetic tools
6. Quantifiable results
7. Results should match the cost of the study
8. Continuous supply of biological material for replicates
9. Ethical approval
56
What is genetic counselling?
The process of helping people understand and adapt to the medical, psychological, and familial implications of genetic contributions to disease
57
What information should be provided to a genetic counselling patient?
- medical diagnosis and its implications in terms of prognosis and treatment
- mode of inheritance of disorder and the risk of developing/transmitting it
- option of genetic testing including pros, cons, limitations, and potential results
- options available for dealing with the risks
58
What are the six steps covered in a genetic counselling session?
- contracting
- information gathering
- establishing/verifying diagnosis
- risk assessment
- information giving
- psychosocial counselling
59
What is contracting?
The counsellor seeks to gain what the patient's understanding of the situation is
60
What is information gathering?
Gathering a history of genetic diseases within family that may or may not be linked to the purpose of the counselling
61
What is risk assessment?
The risk of inheriting or passing on the genetic disease
62
What are the chances for a positive first trimester screen for trisomy 21? Negative?
Positive is when the FTS reported risk is greater than 1/300. Negative is below 1/300
63
Why may the risk assessment step be covered before the information gathering step?
It reduces the anxiety of the patient and increases the chance the patient will reveal genetic history information that they may not have otherwise thought to share
64
What is one way to reduce anxiety of a patient during risk assessment?
- tell them the facts
- word it in a way that they are able to quantify the risk in a way that makes sense to them by using numbers (2% chance baby has Down Syndrome, 98% it doesn't)
- explain what it means to get a positive FTS
65
In order to offer testing to a pregnant patient that says her sister has CF, what must be done?
Her sister must be contacted and asked to sign a release of information (ROI) so that her medical records may be accessed. This allows us to confirm her diagnosis and determine the genetic mutation in order to offer testing to determine if our patient is a carrier (may pass CF onto child)
66
What are the advantages and disadvantages of CVS and amniocentesis?
Both are 100% accurate, but have a risk of causing miscarriage. Amniocentesis must be used if the fetus is above a certain age
67
What are the advantages and disadvantages of NIPS?
It is a maternal blood test, so there's no risk of miscarriage, but it's more expensive and less accurate
68
For a woman who had a positive FST test for her pregnancy, what are the options available to her that a genetic counsellor would discuss?
- prenatal diagnosis with CVS, amniocentesis, NIPS, or an ultrasound
- discuss pregnancy termination
69
What are ethics?
Moral principles that govern a person's or group's behaviour
70
What are the four ethical principles?
1. Autonomy
2. Beneficence
3. Non-maleficence
4. Justice
71
What are the codes of ethics?
NSGC and ASHG
72
What is autonomy?
The patient has the right to choose or refuse treatment/testing by making an informed decision by themselves based on information and values
73
What is beneficence?
The practitioner should act in the best interest of the patient
74
What is non-maleficence?
It is the job of the practitioner to do no harm to the patient
75
What is justice?
Fair, equitable, and appropriate treatment of persons
76
What is the most important ethical principle when considering the testing of minors?
Autonomy
77
Consider a 6 year old girl. Her mom is a carrier for Fragile X syndrome and her brother is affected. The girl shows no symptoms, but the mother wants to get a carrier test for her daughter. Do you do it?
In this case, carrier testing is not permitted, as it would jeopardize the little girl's autonomy. Fragile X syndrome is a disease that will not affect her childhood, as she'd be a carrier. The decision will be up to her when she's able to understand the situation, as it may have reproductive risks when she's older. It may also impact her wellbeing and insurance if she's unable to have kids for this reason later on
78
Consider a mother who is a carrier for Fragile X syndrome. Her son has the disease and her daughter doesn't, but she is pregnant with another child. Do you test the child for the disease?
In this case, the fetus can be tested because we do not know its sex (disease is X-linked) and we don't know if the child will present symptoms when born. Test using CVS. If the fetus is a boy, the parents will have the option to terminate the pregnancy. If the fetus is a girl, they are unable to do carrier testing because the child will be asymptomatic until adulthood, so she can make the decision for herself
79
Consider a mother with Huntington's Disease. She has an unaffected son and daughter. She wants her unborn child tested for the disease. Do you test it?
Because Huntington's is autosomal dominant and has 100% penetrance, it is possible to test the child for Huntington's, despite the fact that the disease is adult onset. The autonomy of the child may be jeopardized, however, because the disease is lethal, the pregnancy may be terminated if it's found that the child does have the disease
80
Consider a mother with a BRCA1 mutation. She has an unaffected son and daughter and wants her unborn child tested. Do you go through with it?
In this case, testing should not be done. This is because BRCA1 is autosomal dominant, except it has incomplete penetrance and treatment is available. So, the autonomy of the child is prioritized in this case, since the disease is non-life threatening
81
What is the general rule for genetic testing of minors for adult-onset conditions?
In most cases, autonomy is preserved. In the odd case where the child has not been born and the disease is lethal later on in life, then testing is possible, as termination may be recommended
82
What is the genetic non-discrimination act (GDA)?
It protects individuals from the use of genetic test results in areas outside of medical care and research, such as insurance and employment
83
A family comes in with a child that is positive for CF. The mother and father undergo genetic testing and find that the mother is a carrier and the dad is not. What are the possible reasons for this, and which should you rule out first?
- lab error
- non-paternity
- de novo mutation (rare)
You should always blame the lab first and ensure the results are accurate as you do not want to create any family turmoil if non-paternity was not the case
84
When should non-paternity be covered and why?
Should be covered in pre-test counselling so it gives the parents a chance to come forward (sperm donor was used instead of infidelity) before test results come in as non-paternity as to reduce family turmoil
85
A male patient comes in that presents developmental delay, dysmorphic features, and seizures. He has a normal microarray and targeted molecular sequencing. Exome sequencing is ordered and a mutation is identified in the BRCA 1 gene. What do you do?
The symptoms the patient presents are not congruent with the BRCA1 mutation found via exome sequencing. The proper thing to do is to not tell the patient unless they consent to be informed about any other disease-causing mutations that are not the main reason they are getting genetic testing
86
What are incidental findings?
Results that are not apparently relevant to the diagnostic indication for which sequencing was ordered, but might still be important in childhood
87
What are secondary findings?
Purposely analyzed as part of the test, but unrelated to the primary testing indication. 78 genes associated with adult onset diseases are routinely tested for, as treatment is available, but consent must be given to disclose this information to the patient
88
Provide an example of a secondary finding
BRCA1 (mostly cancers are tested)
89
Consider a family in which the maternal grandmother has a mutation in BRCA1 and was diagnosed at age 47. She had an affected and unaffected daughter. The affected daughter passed away at 45. The unaffected daughter (who does not want to know her status) had a daughter who was also unaffected but wants to know if she is genetically predisposed to BRCA1. Why is this a conflict and what can be done?
Testing of the unaffected granddaughter will reveal the mother's status, yet the mother does not want to know if she is genetically predisposed. We will still test the granddaughter, as that's what she wants, but it is between them to figure it out. There are benefits for the mom if she knows, as this information is valuable, but it violates her autonomy and may cause psychological harm and relationship strain between her and her daughter
90
What is Peto's Paradox?
The cancer risk in large, long-lived organisms is much lower than the risk in small, short-lived organisms
91
What are the stages of cancer development?
1. Neoplasia (new growth)
2. Hyperplasia (too much growth)
3. Dysplasia (incorrect growth)
4. a) Benign (localized growth)
4. b) Malignant (uncontrolled growth)
5. Metastasis (distant growth)
92
Where is metastasis most common?
High blood flow areas that have many capillaries (brain, lungs, and liver are most common)
93
What are the basic capabilities of an invasive tumour cell?
- growth without external signals
- insensitivity to anti-growth signals
- indefinite replication
- apoptosis aversion
- vascularization
- invasion of tissues and establishment of new tumour sites
94
Describe clonal evolution of tumour growth
The acquisition of multiple oncogenic hits in cells that diverged from a common ancestor. This means that as a tumor develops, it will consist of cells that have only undergone one hit, others that have undergone two hits, etc
95
True/False? Tumours are homogenous, meaning they are made of the same cell that has undergone every oncogenic hit during clonal evolution
False. They are heterogenous, so they consist of multiple cells, from the same ancestor, that have undergone different hits
96
How many independent variants are required for a normal epithelial cell to become metastatic?
6 hits total accumulated within the same cell
97
Why is the lifetime risk for cancer in humans (33-50%) so much higher than expected?
Environmental factors increase the prevalence of cancer
98
What are the 5 environmental factors that increase cancer risk?
- radiation
- chemicals
- diet
- lifestyle
- viral
99
What are some examples of cancers caused by radiation? How are they caused?
UV exposure = melanoma
IR exposure = leukemia
X-rays = lung cancer
100
What are some examples of cancers caused by chemicals? How are they caused?
Asbestos = lung cancer
Smoke soot = scrotal cancer
101
What are some examples of cancers caused by viruses? How are they caused?
Hepatitis = liver cancer
EBV = Burkitt's lymphoma
HPV = cervical cancer
HIV = lymphoma and Kaposi sarcoma
102
What are some examples of cancers caused by diet? How are they caused?
Nitrate preservatives = liver cancer
Alcohol = liver cancer
Low fibre = colon cancer
103
What are some examples of cancers caused by lifestyle? How are they caused?
Smoking = lung cancer
Prostitution = cervical cancer
Nuns = breast, ovarian, and uterine cancer
104
What is retinoblastoma? What percentage is inherited (germline)?
Cancer of the retina caused by an oncogenic hit in the RB1 gene; 40%
105
If there is retinoblastoma in one or both eyes, where the patient has a family history of retinoblastoma, what is the probability that the variant was inherited?
100% in all cases (unilateral, multifocal, unifocal, bilateral)
106
If there is unilateral multifocal retinoblastoma in a patient where it is not in the family history, what is the probability that the variant was inherited?
15-90%
107
If there is unilateral unifocal retinoblastoma in a patient where it is not in the family history, what is the probability that the variant was inherited?
15%
108
If there is bilateral retinoblastoma in a patient where it is not in the family history, what is the probability that the variant was inherited?
90%, as both eyes being affected by independent events is very rare
109
What is the penetrance of RB1?
>99%, so if you have the variant, you will likely develop the phenotype
110
Describe Knudson's Two Hit Hypothesis
You are more likely to develop cancer if one of your chromosomes already has an oncogenic hit (inherited), as you only need to undergo one more hit to develop cancer. It is much less common to have a sporadic disease, in which both chromosomes develop hits independently
111
What is the most common second hit in tumours? What are the ways this can occur?
Loss of heterozygosity (LOH)
- mitotic nondisjunction and duplication of the remaining chromosome that has already developed a hit
- sub-chromosomal deletion of the relevant gene
- unbalanced reciprocal translocation of normal chromosome
- somatic recombination
112
What are the signs of an inherited (Mendelian) cancer?
- multiple primary tumours
- bilateral in paired organs
- early onset
- AD
- same or linked forms of cancer in two or more close relatives
113
What are the signs of a sporadic cancer?
- single tumor
- unilateral in paired organs
- later onset
114
How many hits must be acquired to produce a cancer phenotype in Mendelian cancer? Sporadic cancer?
1; 2
115
What kinds of gene variants cause cancer?
Tumour suppressors and oncogenes
116
What is the function of tumour suppressors?
Keep the behaviour of cells under control by:
- slowing or stopping cell cycle progression
- maintain integrity of genome
- induce apoptosis
117
What are the two roles of tumour suppressors? Explain their function, where they appear in the cell cycle, and what dominance they have
Caretaker: fix DNA damage as it accumulates in the genome; G2; AD, AR
Gatekeeper: prevent cell cycle from getting out of control, promote apoptosis; S; AD
118
What is Li-Fraumeni syndrome?
Cancer caused by germline LOF in TP53. TP53 activates transcription of genes involved in growth suppression in response to DNA damage. AD inheritance and increased penetrance in women due to more mammary tissue
119
What is an obligate carrier?
Someone who carries a germline cancer variant but does not show the phenotype (non-penetrant)
120
What is FAP?
Variants in the APC gene cause polyps to form in the colon (LOF in tumour suppressor). 100% penetrance and AD inheritance
121
What is the relative prevalence of breast cancer caused by familial, Mendelian, and sporadic inheritance?
Sporadic > familial > Mendelian (most commonly caused by independent events)
122
What is familial breast cancer?
Multifactorial, caused by many environmental and genetic factors
123
What is the dominance pattern in BRCA1/2 variants?
AD
124
BRCA1/2 is a (tumour suppressor/oncogene)
Tumor suppressor (repairs dsDNA breaks)
125
If we can't prevent cancer, why look for BRCA1/2 variants?
For the patient: therapy choice (radiation vs. surgery), adjunct therapy, prophylaxis, future surveillance
For the family: prophylactic surgical and lifestyle options (removal of tissue at risk), surveillance frequency and type
126
What is constitutional aneuploidy?
The increased risk (predisposition) of cancer associated with a chromosomal disorder
127
What do constitutional chromosome instability syndromes result from? What tumour suppressor class do these belong to?
Complete LOF variants in DNA repair genes (AR); caretakers
128
What is xeroderma pigmentosum?
Sun sensitivity and high risk of skin cancer due to biallelic (AR) variants in one of six genes that repair DNA damage from UV (NER, GGR, TCR)
129
What is ataxia telangiectasia?
Lymphoid malignancies caused by biallelic (AR) variants in the ATM gene (cell cycle control during DSB repair). Makes them sensitive to ionizing radiation (IR)
130
What is bloom syndrome?
Sun sensitivity due to biallelic variants (AR) in the BLM gene (DSBR). Increased rate of sister chromatid exchange and gaps/breaks on karyotype
131
How are Mendelian cancer syndromes related?
They all arise from mutations in the DNA repair pathways or the cell cycle regulation pathways, which are interconnected
132
In relation to Peto's Paradox, why don't large organisms like elephants get cancer despite having a long life and trillions of cells?
They have multiple copies of tumor suppressor genes (like TP53), so LOF mutations require multiple hits to cause cancer
133
What is a proto-oncogene?
A normal gene involved in some aspect of cell proliferation. May become activated (SNV or other mechanism) to become an oncogene
134
What is an oncogene?
A dominantly acting gene responsible for tumour development after a proto-oncogene has accumulated a GOF mutation
135
What functions do proto-oncogenes usually have? Provide a couple of examples
When activated, they allow cell proliferation. Things like growth factors, or their receptors, TFs, telomerase, anti-apoptotic genes
136
What are the four ways in which proto-oncogenes can be activated?
- activating variant
- gene amplification
- translocation into active chromatin
- rearrangement creating a novel fusion protein
137
Describe how the RET receptor may undergo an activating mutation. What type of mutation is this (germline/somatic)?
Cysteine residues are encoded into the receptor, which link together and form disulfide bridges between each subunit of the receptor, causing constitutive activation; germline
138
What is a driver variant? Provide an example
A driver is a variant that undergoes positive selection during tumourigenesis and drives tumour formation; somatic activating variants in BRAF
139
What is NMYC?
A transcription factor that regularly promotes tumour progression due to extra copy numbers. Usually, the copy number correlates with cancer stage. Amplified NMYC genes may be found on extrachromosomal structures that only contain copies of this gene, which increases the copy number drastically
140
What is Burkitt Lymphoma?
A B-cell leukemia that has the MYC gene rearranged into the immunoglobulin loci, so it is under control of the promoter at this region. This promoter is highly expressed in the lymph nodes, where this cancer develops
141
What are the types of variants seen in Burkitt Lymphoma?
- endemic variant: found in locations endemic with malaria
- sporadic: found in locations where malaria is not endemic
- immunosuppression-related: seen in HIV patients
142
What is Chronic Myeloid Leukemia (CML)?
A rearrangement of the BCR and ABL1 genes to create a fusion, which replaces ALB1 tyrosine kinase under control of the BCR and exhibits constitutive activation of the growth cascade
143
How may fusion proteins be targeted? Provide an example
Creating a drug that targets specific locations unique to the fusion itself. Imatinib causes steric hindrance in ALB1 kinase so ATP cannot bind and thus the fusion is not activated
144
What is a possible treatment for breast cancer?
- Herceptin, which prevents receptor dimerization
- Olaparib, which inhibits ssDNA repair enzyme PARP, causing DSB
145
How does Olaparib work?
It inhibits PARP, a ssDNA repair enzyme, causing a dsDNA break. Cells that lack DSBR (cancer cells) die and cells that have DSBR via homologous recombination repair (HRR) survive
146
Define precision medicine
Emerging approach for disease treatment and prevention that takes into account individual variability in genes, environment, and lifestyle for each person. While some advances in precision med have been made, the practice is not currently in use for most diseases
147
Define personalized medicine
Genomics and medical information and technology and patient empowerment
148
Define stratified medicine
Matching therapies with specific patient population characteristics using clinical biomarkers (individual's reaction to drugs due to their personal characteristics)
149
Describe why a breastfeeding mother taking painkillers has the potential to kill her baby with a painkiller overdose. What gene is responsible?
The mother must've been an ultra-rapid metabolizer (has more than 2 functional alleles) of the pain killer, causing most of it to be converted into the active form. The baby was exposed to extremely high levels of the active drug, causing it to overdose; CYP2D6
150
What is pharmacogenomics?
The study of how someone's combination of genotypes predicts how they respond to drug treatment
151
What are the parameters for pharmacogenetics?
Genotypes that mediate drug toxicity and effectiveness
152
How common is pharmacogenomics testing done for drugs?
Not very common at all, as healthcare officials do not want to pay for the tests. Very bad considering some drugs have the potential to MELT PEOPLES SKIN OFF
153
What must be known about a cancer in order to treat it? How is this identified?
What kind of cancer it is. Identified by comparing cancer genotype to healthy cell genotype to figure out the type of variant. In other words, we must know the molecular mechanism of the cancer to properly treat it
154
What might make genetic variants difficult to predict?
If they are multifactorial, usually this makes it harder to predict the variants and their effects on the patient
155
What are the five therapies for lysosomal storage disease?
- transplant of the lysosomal enzyme into bone marrow (enzyme is produced by macrophages)
- enzyme replacement therapy (tagged with mannose-6P for recognition by cell)
- chaperone therapy (correctly folds misfolded lysosomal enzyme)
- gene therapy (add a functional copy into the genome
- substrate reduction therapy (reduce need for lysosomes)
156
Why are so many therapies needed to treat lysosomal storage disease?
There's a specific therapy for each specific variant
157
How does the treatment of spinal muscular atrophy (SMA) vary between patients?
Type of disease depends on age of onset
158
What is the cause for SMA and how can it be treated?
Cause: exon 7 is skipped due to variant in the intron, causes frameshift in SMN2
Treatment: oligonucleotide binds to intronic splice silencer, leading to inclusion of exon 7 (converts SMN2 (10% functional) into SMN1 (normal function))
159
Compare SMN1 and SMN2
SMN2 is a pseudogene of SMN1, it has 10% residual function and SMN1 is completely functional
160
Clinical severity for SMA is correlated to:
SMN2 copy number (more means better function, as each has 10% function of SMN1). Having one copy of SMN1 gives a normal phenotype
161
Why is SMA now included in newborn screening? How does treatment work?
It may be cured if detected before onset of symptoms, however treatment is expensive ($2.1mil). Replaces dysfunctional copies with functional ones
162
How may SMA treatment be limited?
Require a basal amount of SMN activity (4 copies), cure is expensive, and non-curative treatment only delays the onset of symptoms
163
Example of targeted therapy for one individual
N-of-1 therapies (Milasen) - Batten disease
164
How was Mila's disease treated?
Basically turned her into a carrier instead of a homozygote, but it still ultimately killed her
165
What is Batten disease?
A lysosomal storage disease affecting the CNS and retina
166
Which types of diseases are rare and which are common?
Rare: chromosomal and Mendelian/monogenic disorders
Common: polygenic and multifactorial disorders
167
What is a monogenic disorder?
A single gene disorder in which the pathogenic variant in a single gene is sufficient to cause the trait, may be dominant or recessive
168
What is a polygenic disorder?
Multiple variants at the same time are required to cause the pathogenic trait
169
What is a multifactorial disorder?
A complex disorder in which variants in multiple genes and environmental factors are needed to cause the pathogenic trait
170
What percentage of the population has a genetic disorder by age 5? Lifetime prevalence? What type of genetic disorder makes the greatest contribution?
5%; 67%; multifactorial diseases
171
How do genes work together? What does this mean?
- appropriate expression of genes
- pathways
- functional complexes
- chaperones
This means that they rely on each other for proper function
172
What are some examples of environmental factors that contribute to disorders?
- glucose levels (insulin)
- hormones (sex hormones characterize biological sex)
- temperature (rabbit coat colour)
- teratogens (chemicals that impact fetal development)
- viral exposure (severity of symptoms depends on genetic makeup)
173
What is the Waddington hypothesis?
Genetic makeup and environmental exposure can both have an impact on the phenotype along a continuum
174
Why are the causes of multifactorial diseases difficult to understand?
Because there is an interaction between the alleles and the environment of a person that determine their phenotype, so linking these factors together can be tricky
175
What is albinism?
A genetically heterogenous condition characterized by little to no melanin production caused by a mutation in a single gene
176
As you add different genes and environmental conditions into effect, what trend emerges?
A bell curve of all of the possible phenotypes related to the genotypes, smoothed out by environmental conditions
177
Polygenic inheritance reflects the ___________ effects of a large number of alleles
Additive
178
What is a quantitative multifactorial disease? Name the associated model
A phenotype that lies on a continuum caused by the accumulation of quantitative trait loci (QTL); Basic model/Quantitative Trait model
179
What is a qualitative multifactorial disease? Name the associated model
A phenotype that relies on penetrance and not expressivity (discrete - you have it or you don't) caused by the accumulation of risk factors beyond a certain threshold; Threshold model
180
Describe the quantitative trait model
A measurable entity that varies continuously. Outside the "normal" range, multifactorial disorders can be described. The genetic component is the accumulation of quantitative trait loci
181
What are some multifactorial diseases associated with the height continuum?
Short stature and hypercholesterolemia on short end, hypertension (high blood pressure) and obesity on tall end
182
Quantitative traits show regression to the __________. What does this mean?
Mean; people on one end of the continuum tend to have offspring with a mean closer to the population mean than them
183
Why do quantitative traits show regression to the mean?
Because it is unlikely that parents will pass on all of their extreme alleles, and some of the other alleles will be passed on instead (tall parents don't pass on all of their tall alleles). However, their offspring will still have a larger proportion of those extreme alleles, so they will still be on one end of the continuum
184
What is the Threshold model? What is the threshold?
A model that allows for the explanation of common birth defects and adult-onset disorders that don't follow the predictable pattern of monogenic disorders. Describes phenotypes as binary/discrete: either present or absent depending on if the minimum number of risk factors (threshold) has been accumulated
185
What are the inheritance patterns for single gene disorders? What does this imply about predicting risk?
Either Mendelian inheritance or non-Mendelian inheritance, so predicting risk is easy because we know how these variants are inherited
186
What are the complications associated with diagnosing single gene disorders?
- incomplete penetrance
- phenocopies
- genetic heterogeneity
- variable expressivity
187
What are phenocopies?
Non-genetic factors causing similar phenotypes to single gene and multifactorial disorders
188
What are the complications associated with diagnosing multifactorial diseases?
- risk factors and genotypes are unknown
- variable environmental effects
- risks are specific for each disease and vary from population to population
- risks are derived from direct observation of families with an affected individual
189
Provide an example of a multifactorial disease that varies in populations and between sexes
Pyloric stenosis is more common in males and more common in Belfast vs. London
190
Describe how multifactorial risk depends on the degree of relatedness
The more related you are to the affected individual, the more risk you have of developing that disease (first-degree relatives)
191
Compare the drop-off of risk of inheriting a multifactorial disease vs. a single gene disorder as the degree of relation decreases. Why?
The risk of inheriting a single gene disorder halves for every generation, while it changes variably for multifactorial diseases, usually a steep drop in risk from a first degree to a second degree relative because so many factors must be inherited in order to have the disease
192
First degree relatives are:
Parents, siblings, and children
193
Second degree relatives are:
Grandparents, uncles/aunts, nieces/nephews, grandchildren
194
The more individuals in the family that are affected by multifactorial disorders, the more _____________
Liability/risk factors
195
Why is pyloric stenosis more common in males?
They require less risk factors to develop the disease (lower **threshold** than females)
196
Why is the risk of a female proband having affected children higher than a male if males more commonly have pyloric stenosis?
Female probands require the accumulation of more risk factors (higher threshold), so more risk factors are passed onto their children
197
Explain how risk depends on the severity of the disease in the proband
Severity positively correlates with risk factor accumulation, so more severe = more risk factors accumulated = more risk factors being passed down to children
198
What may a shared phenotype within families be caused by?
- shared genes
- common environment
199
How is the debate of nature vs. nurture of multifactorial diseases tested?
Twin and adoption studies
200
What is the assumption made by twin studies?
In the environment is constant, differences in twins are due to differences between % alleles shared
201
Differences between monozygous twins can be attributed to:
The environment
202
What is concordance?
Both twins have the same trait
203
What is discordance?
One twin has the trait, and the other does not
204
When are phenotypic differences attributed to genetics in twin studies?
When MZ twins are more concordant than DZ twins for a specific trait
205
When are phenotypic differences attributed to the environment in twin studies?
When MZ and DZ twins both have low concordance
206
What is heritability?
The percentage of population variation in a trait due to genes
207
Fully genetic traits have what heritability?
100%
208
Fully environmental traits have what heritability?
0%
209
h =
relatives that share the trait/# expected to share if trait was 100% genetic
210
Which conditions have the highest risk to relatives?
Highest heritability
211
What are adoption studies?
The comparison of a child's phenotype to biological parents and siblings vs. adopted parents and siblings
212
If an adopted child is more similar to their biological parents, then:
Genetic contribution
213
If an adopted child is more similar to their adopted parents, then:
Environmental contribution
214
What are the complications with twin studies? Explain why they complicate things
- shared environment between MZ and DZ twins may not be equally similar (MZ twins treated more similarly - role of genes is inflated)
- not all MZ twins share the same prenatal environment (role of genes is deflated)
- MZ twins do not have identical genomes and their similarity decreases with time (somatic and epigenetic changes - role of genes is deflated)
215
What are the complications with adoption studies? Explain why they complicate things
- prenatal environment may have long lasting effects on the child (role of genes is inflated)
- adoption doesn't always occur at birth and the child may have a shared environment for a time (role of genes is inflated)
216
Different pathogenic alleles of the CFTR gene correlate with pancreatic insufficiency, but not pulmonary disease. Why?
These alleles alone are not enough to cause pulmonary disease. That's just how they work because it does not correlate with allelic heterogeneity
217
How may modifier genes cause pulmonary disease?
In a person with an existing CFTR variant, they may also accumulate modifier genes that increase the severity of the disease so that pulmonary disease results
218
Which modifier genes are implicated in the severity of pulmonary disease in an individual with CF?
MBL2: normally functions to phagocytose pathogens, so LOF variant increases severity
TGFB1: normally regulates CFTR gene expression, so LOF variant increases severity
219
What five factors increase the risk of inheriting a multifactorial disorder?
- high heritability
- close relationship to proband
- multiple affected family members
- severity in proband
- proband is the rarely affected sex
220
Which questions do we need to answer in order to find and identify multifactorial disorders?
- which genes contribute?
- which alleles contribute?
- are there protective alleles?
- genetic heterogeneity
- must consider different risk factors in each population
221
What are the challenges of finding genetic risk factors
- locus heterogeneity
- interaction of multiple genes
- incomplete penetrance
- age-development onset
- phenocopies
222
Describe how linkage analysis is used to determine genetic risk factors
LOD scores are calculated amongst family members to determine genetic markers that segregate with the disease
223
What is the assumption made by linkage analysis?
The disorder has Mendelian inheritance
224
What are the limitations of linkage analysis?
Inherited (Mendelian) forms don't always exist, locus heterogeneity and phenocopies lower LOD score
225
Describe how sib pair analysis is used to determine genetic risk factors
Siblings are genotyped for their marker alleles around the risk factor to determine which marker allele the disease is associated with
226
What assumptions does affected sib pair analysis make?
Two affected siblings will share marker alleles in the region containing the risk factor
227
How is power increased in sib pair analysis?
Comparing siblings with extreme phenotypes
228
What are the advantages and disadvantages of sib pair analysis?
Advantages: no assumption about mode of inheritance, no effect of reduced penetrance, no effect of age of onset
Disadvantages: large sample size required
229
Describe how association studies are used to determine genetic risk factors
A risk frequency comparison is made between the patient population and control population so that the probability of identifying a risk factor is proportional to its contribution to the disease and its frequency in the population (power) using a Chi-square test
230
What is a disadvantage of association studies?
Large population sized are required, and even larger ones are needed for diseases with small effects on phenotype
231
Describe how the odds ratio for disease association is used to determine genetic risk factors. Why is it not a top strategy?
SNPs in/near biologically plausible candidate genes are used (candidate gene approach) to generate an OR (for MF disorders, 1.1-1.5), but this is a low success approach as results are often not reproducible
232
Describe how genome wide associate studies (GWAS) is used to determine genetic risk factors
An SNP array is constructed with high throughput genotyping to identify variants with small effects on disease
233
What are the pros and cons of GWAS being hypothesis-free?
Pro: biological pathway doesn't need to be known
Con: does not always provide insight into biology, requires statistical methods to identify association, cannot identify the causal variant, can produce different results in different populations
234
How is confidence in GWAS increased?
If the genes in the same disease-associated pathway are found or replicated in another study and p-value is decreased to 5x10^-8 to reduce risk of false positives
235
The SNPs found in GWAS are rarely functional. What assumption must we make about the causal variant?
Causal variant is in linkage disequilibrium with the identified variant either in the coding or non-coding regions
236
What is the major limit to GWAS?
You can identify the region of the chromosome associated with disease, but the causal variant must be looked into further
237
How is GWAS supplemented so the causal variant can be identified?
- RNAseq for expression quantitative trait loci (eQTLs)
- epigenetics for methylation signatures common between cases and not controls
- whole-genome sequencing can detect all types of variation (copy number, indels), not just SNPs and non-coding variants that regulate gene expression, allows for N=1 studies
238
Describe how animal studies are used to identify genetic risk factors
Animal matings are manipulated to control genetic backgrounds and environment. Used to identify potential disease-causing strains and compared to other strains. Commonly used to test safety and efficacy of potential treatments
239
Correlation is a (direct/indirect) relationship
Indirect
240
Causation is a (direct/indirect) relationship
Direct
241
Most congenital malformations are considered:
Multifactorial
242
What may be some genetic causes of congenital disorders?
- monogenic syndromes or chromosomal disorders (trisomy 13, 18, 21)
- single gene disorders (HOX, PAX, TBX)
243
What may be some environmental causes of congenital disorders?
- thalidomide (phocomelia)
- retinoic acid (heart, ear, CNS defects)
- maternal rubella infection (congenital heart defects)
244
What is the congenital anomalies surveillance system (CASS)?
A registry on structural congenital anomalies used to establish prevalence rates and trends watched over time. Used for planning and policy decisions and evaluating prevention strategies
245
What are two examples of policy decisions that emerged as a result of the CASS?
Response to Zika and folic acid fortification to decrease neural tube defect risk
246
What is the leading cause of death worldwide?
Cardiovascular disease (specifically, coronary artery disease CAD)
247
What causes CAD? What are the risk factors that contribute?
Atherosclerosis (narrowing of the coronary arteries resulting from the formation of lipid-laden lesions); obesity, smoking, high blood pressure, high cholesterol, positive family history
248
What are the genes associated with CAD?
- heterozygous pathogenic variants in LDLR (AD, 1/500) causes familial hypercholesterolemia (FH) (lipid metabolism and transport)
- elevated LDL cholesterol (lipid metabolism)
- inflammation genes
249
What are the treatments of FH?
- dietary reduction of cholesterol
- drugs that bind cholesterol in circulation (excreted)
- drugs that reduce cholesterol synthesis
250
Describe how the candidate gene approach may be used to characterize CAD
The identification of genes that are associated with symptoms of CAD such as lipid metabolism/transport and inflammatory response can be targeted, as combinations of these variants and environmental risks are responsible for multifactorial CAD
251
What are the single gene disorders of cardiomyopathy?
Single gene disorders such as hypertonic cardiomyopathy, dilated cardiomyopathy, and long QT syndrome
252
What is the key takeaway of characterizing multifactorial diseases using the candidate gene approach?
Inherited forms of the conditions have provided valuable insight into mechanisms of disease and thus potential targets for treatment
253
What is a polygenic risk score?
The probability of developing disease due to family history, lifestyle, and exposures
254
Why are ancestry tests not good for diagnosing the risk of multifactorial disorders?
They do not take into consideration the lifestyle of the individual, only the genetics, so they either tend to inflate or deflate the risk of developing a certain disease
255
What information do direct-to consumer tests provide?
- disease risk stratification
- carrier status for autosomal recessive disorders
- drug response
- nutrition
256
Inherited forms of multifactorial disorders most commonly have a(n) (earlier/later) age of onset
Earlier
257
Diseases most likely to cluster in families tend to be:
More severe
258
Compare the genetic and environmental contributions to a multifactorial disorder
Environmental > genetic
