Week 7 - Cormier Flashcards
1
Q
Why are single-gene traits often called Mendelian?
A
They appear in roughly fixed proportions.
~ 4000 human diseases have Mendelian patterns of inheritance
2
Q
What is a segment of DNA at a specific location called?
A
locus
3
Q
What is the sequence of DNA that contains a particular locus?
A
Gene
4
Q
What are alternative variants of a gene called?
A
Alleles
5
Q
What do variant alleles show?
A
Polymorphism
6
Q
What are variant alleles referred to as?
A
polymorphic alleles
or
polymorphisms
7
Q
What do some polymorphisms affect?
A
disease susceptibility
(vs. wildtype)
8
Q
What does wild-type allele mean?
A
the single prevailing allel present in the majority of individuals
9
Q
What do mutations refer to?
A
New genetic changes in a family and/or to disease-causing mutant alleles.
10
Q
What does genotype refer to?
A
An entire set of alleles in a genome or the set of alleles at a specific locus.
11
Q
What does phenotype refer to?
A
The observable expression of a genotype as a morphological, clinical, cellular or biochemical trait.
12
Q
What does homozygous mean?
A
An individual’s two alleles are functionally identical at a specific locus.
(something you can measure, not just different sequence)
13
Q
What does heterozygous mean?
A
The two alleles are functionally different at a specific locus.
(something you can measure, not just different sequence)
14
Q
What does the term “kindred” refer to in a pedigree?
A
The extended family depicted in the pedigree.
15
Q
What is the proband in a pedigree?
A
The first affected person who is brought to clinical attention.
-all other family members are analyzed in relation to the proband
(there can be multiple probands)
16
Q
What does the term consanguineous mean?
A
Couples who have one or more ancestors in common.
17
Q
What does fitness mean or refer to?
A
A genetics term that refers to the measure of the impact of a condition or genotype on reproduction and is defined by the number of offspring of affected individuals who survive to reproductive age, compared with an appropriate control group.
18
Q
What are the four basic patterns of single-gene inheritance?
A
- Autosomal dominant
- Autosomal recessive
- X-linked dominant
- X-linked recessive
19
Q
A
20
Q
What two factors affect pedigree patterns?
A
- Penetrance
- Expressivity
21
Q
What is penetrance? Reduced penetrance?
A
The probability that a mutant gene will have any phenotypic expression.
Reduced penetrance: when the percentage of individuals demonstrating some disease phenotype is less than 100% the mutant gene.
22
Q
What is expressivity? Variable expressivity?
A
The severity of expression of the phenotype among individuals with the same disease causing genotype.
Variable expressivity: when the severity of the disease differs in people who have the smae genotype.
23
Q
What is neurofibromatosis (NF1) an example of?
A
Variable expressivity
(due to different mutations in the NF1 gene)
also autosomal dominant disease
24
Q
What is allelic heterogeneity?
A
Many loci contain multiple mutant alleles in a population.
(different mutations in same gene)
ex. CFTR & PKU
25
What is locus heterogeneity?
Many disease phenotypes can be caused by mutations in distinctly **different** genes.
(different genes with mutations causing common/similar phenotypes)
ex. Retinitis pigmentosa
26
What is phenotypic heterogeneity?
Different mutations in the **same** gene cause completely different diseases.
ex. Hirschsprung disease
27
What does sex influenced mean?
One sex has a significantly high frequency of developing an autosomal recessive disorder.
ex. Hemochromatosis
28
What does sex-limited mean?
Some autosomal dominant disorder can show a sex ratio that differs from 1:1, and in some cases the trait is seen only in one sex.
ex. Male-limited precocious puberty
(difficult to distinguish from x-linked disorders becaus the trait is transmitted through unaffected carrier females)
29
What are common characteristics of autosomal dominant inheritance?
* trait appears in **every** generation
* each affected person has an affected parent
* offspring of an affected parent have a 50% risk of inheriting the trait
* males/females are equally likely to transmit the trait to children of either sex
* exceptions when sex-limted/sex-influenced
30
How are X-linked dominant and recessive patterns distinguished?
By the phenotype of heterozygous females:
if the trait is consistently expressed in carriers then it is dominant
(if not, then it is recessive)
31
What are common characteristics of X-linked recessive disorders?
* Much high incidence in males than females
* heterozygote females are usually unaffected
* some may show phenotype depending on pattern of X-inactivation
* Mutant allele is transmitted from an affected male through all of his daughters
* any of his daughter's sons have a 50% chance of inheriting it
* Mutant allele is NOT transmitted directly from father to son
32
What are common characteristics of X-linked dominant inheritance?
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* Affected males with normal mates have no affected sons but all affected daughters
* Both male and female offspring of affected females have 50% chance of inheriting the trait
* Heterozygous affected females develop a milder phenotype than heterozygous males
* often male lethality
* Pattern of inheritance from an affected female is indistinguishable from autosomal dominance
33
What are common characteristics of autosomal recessive diseases?
* Occurs only in mutant homozygotes or compound heterozygotes
* affected individuals have two mutant and no normal alleles
* Unaffected heterozygote parentss are called carriers
* Skips generations
34
What are some of the factors that can complicate pedigree patterns?
* Reduced penetrance
* Reduced expressivity
* Genotypes that may not survive to birth
* Lacking family histories
* False paternity
* Occurence of new mutations
* Small families
* Genetic heterogeneity (allelic, locus, phenotypic)
* Other genes and environmental factors that affect expression
35
What is mutational mosaicism?
* A mutation occuring during cell proliferation (such as early development) that leads to only a proportion of cells carrying the mutation.
* can occur in germline or somatic cells
* ex. X-inactivation
36
What is the effect of maternal inheritance of disorders caused by mutations in the mitochondrial genome?
* Mitochondrial disorders can demonstrate a **wide range of severity**
* segregation of mitochondria during cellular replication is random
* A mutation in mitochondrial DNA may or may not be transmitted to a daughter cell
* The number of mutant mitochondrial in daughter cells vary from one cell to the next
* zygotes inherit their mitochondria only from the egg
37
All disease have what common component?
All disease have a genetic component.
| (according to Dr. Cormier)
38
What kind of medical era are we entering (according to Dr. Cormier)?
Era of **individualized** medicine.
Promise of an era of **regenerative** medicine.
39
What affects disease susceptibility?
host genetic makeup
40
What are the five types of genetic polymorphisms?
1. insertions
2. deletion
3. tandem repeat
4. single nucleotide polymorphisms
5. restriction fragment length polymorphisms
41
What is Restriction Fragment Length Polymorphism?
* allelic variant that abolishes or generates a _restriction endonuclease recognition site_ or changes the size of an RFLP
42
What is restriction fragment lenth polymorphism (RFLP) used for?
* use to distinguish between 2 chromosomes
* usually just a biomarker & not a cause of a dysfunctional gene
* analyzed by Southern blotting or PCR
43
What is variable number of tandem repeats (VNTR)?
* location in a genome where a short nucleotide sequence is organized as a tandem repeat
a. k.a. simple sequence length polymorphisms (SSLPs)
44
What are variable number of tandem repeats (VNTR) or simple sequence length polymorphisms (SSLPs) used for?
* personal or parental identification
* often polymorphic in size between chromosomes & individuals
* analyzed mainly by PCR
45
What are single nucleotide polymorphisms (SNPs)?
* DNA sequence variation occurring commonly within a population (e.g. 1%) in which a single nucleotide — A, T, C or G — in the genome (or other shared sequence) differs between members of a biological species or paired chromosomes
* may or may not affect protein structure
46
What are single nucleotide polymorphisms (SNPs) used for?
* Most common polymorphism
* polymorphic biomarkers
* disease-association
* useful in gene mapping & pharmacogenetics
47
What are SNP chips used for?
* detect thousands of SNPs
* prediction that there will be chips that can detect susceptibility to a wide range of diseases
* especially complex genetic diseases such as cancer, type 2 diabetes, cardiovascular
48
What are haplotypes?
* haploid genotypes
* can be any combination of alleles, loci, or markers on the same chromosome
* commonly refers to groups of nearby alleles or markers on a chromosome that are inherited together
49
What are halotype blocks?
large set of SNPs that are co-segregating in the human population
50
How does haplotype mapping and genotype wide association studies identify genetic factors associated with disease susceptibility?
* they have been constructed form the sequencing of hundreds of human genomas from all major human populations
* permits the association of phenotypic traits with the presence of specific haplotypes and haplotype blocks within and between populations
* i.e. the haplotypes show linkage disequilibrium
* used to trace ancestry of individuals and populations as well
51
What are the genetic events leading to Angelman's syndrome?
* Example of genomic imprinting
* Caused by deletion or inactivation of genes on the maternally inherited chromosome 15 while the paternal copy, which may be of normal sequence, is imprinted and therefore silenced.
52
What are the genetic events leading to Prader-Willi syndrome?
* seven genes (or some subset thereof) on chromosome 15 (q 11–13) are deleted or unexpressed (chromosome 15q partial deletion) on the paternal chromosome
* particular region of chromosome 15 involved is subject to parent of origin imprinting, meaning that for a number of genes in this region only one copy of the gene is expressed while the other is silenced through imprinting
53
What is epigenetics again?
* Non-mutational (no change in sequence) phenomenon that can affect gene expression and its inheritance
* mechanisms include 5-cytosine methylation, histone modifications, etc.
* examples:
* x-inactivation
* imprinting
54
What is imprinting again?
Differential expression of a gene allele depending on parental origin.
55
What is the purpose of imprinting?
To control gene dosage.
Only one allele is expressed as the other allele is imprinted and silenced.
56
When is an imprint created?
In the parental germ cells (egg or sperm).
-different genes are either paternally or maternally imprinted.
57
How is an imprint created or what is the mechanism of silencing?
Mechanism of gene silencing is 5-cytosine DNA methylation leading to chromatin condensation.
58
What is the prevalence of imprinted genes?
At least nine chroms have imprinted regions.
Greater than 100 imprinted human genes.
59
What does dysregulation of imprinting cause?
Dysregulation of imprinting is common in human disease.
Often occurring in childhood, and arise due to aberrant gene dosage.
Examples: Prader-Willi and Angelman Syndrome,
IGF2, and cancer
60
What parent is chroms 15 derived from in PWS? What parent imprints?
* Prader-Willi gene is _maternally imprinted_. When a deletion or other mutation occurs in the expressed allele no PW gene product is made and the result is Prader-Willi Syndrome.
* PWS region has five paternal-only expressed unique copy genes that encode polypeptides and a family of six paternal-only snoRNA genes.
* paternally derived chroms 15
* When this deletion occurs on the chromosome 15 that came from the father, the child will have Prader-Willi syndrome
61
What parent is chroms 15 derived from in Angelman Syndrome? What parent imprints?
* AS is a classic example of genomic imprinting in that it is caused by deletion or inactivation of genes on the maternally inherited chromosome 15 while the paternal copy, which may be of normal sequence, is imprinted and therefore silenced.
* AS gene is paternally imprinted. When a deletion or other mutation occurs in the expressed allele no AS gene product is made and the result is AS.
62
What are the three types of imprinting errors that can affect PWS and AS?
* failure to **erase** the methylation mark in the paternal germ line
* failure to **establish** methylation after oogenesis and fertilization
* failure to **maintain** the methylation after fertilization
63
What is clinical cytogenetics?
Study of chromosomes, their structure and their inheritance, as applied to medical genetics.
64
What are some clinical indicators for chromosomal testing?
1. developmental problems
2. still births & neonatal deaths
3. fertility problems
4. family history of chromosomal defects
5. cancer
6. pregnancy in women of advanced age
65
What are the methods for prenatal diagnosis in order?
* 1st = Non-invasive tests
* Ultrasound
* Radiography
* MRI
* Maternal serum screening
* 2nd = Invasive tests
* Amniocentesis (test amniotic fluid)
* Cordocentesis (test fetal blood from the umbilical cord)
* Chorionic villus sampling (tissue biopsy from vilous area of the chorion)
66
How does a physician go about testing for Cystic Fibrosis in a family member from a cystic fibrosis family?
1. Pedigree analysis
2. Determine if the exact CFTR mutation is known (DNA sample → PCR/Dot-blotting)
3. If unknown mutation: try to identify polymorphic disease-linked markers (VNTR/RFLP)
4. If no markers, unknown mutation test for CF gene (delta508F)
5. If negative, advise of risk based on pedigree
67
What does heritability depend on?
POPULATION!
68
What does genetic variance depend on?
_Segregation_ in a population of alleles that influence the trait, the allele frequencies, effect sizes of the variants and mode of gene actions.
69
What does the "ratio of variances" mean?
Proportion of total variance in a population for a particular measurement, taken at a particular age or time, that is attributable to variation in total genetic value.
70
What can allelic variation in a population lead to?
Different disease susceptibilities
(e.g. alpha1-antitrypsin deficiency has 5 major alleles that differ in the amount of effective protein)
71
Define ecogenetics.
Genetic variation in susceptibility to environmental agents.
72
What two things vary by ethnicity?
* frequency of polymorphic alleles
* frequency of disease-linked alleles
\*\*No population is "wild type": all individuals and all populations carry resistance and susceptibility alleles for different diseases.
73
Describe sickle cell disease in terms of the evolutionary pressure to maintain disease causing alleles in a population.
* People who are heterozygous for sickle cell anemia are resistant to malaria
* **heterozygous advantage**
* mutated allele is maintained in a population because when heterozygous it **increased reproductive fitness**
74
What is the heterozygous advantage?
A presumed increased resistance in heterozygotes which could account for the maintenance of various genetic disorders in certain populations.
Examples:
* Sickle cell - tropical Africa
* Cystic fibrosis - Western Europe (plague? TB?)
75
Is the Hardy-Weinberg Law is used to calculate a population's allelic frequency or genotypic frequency?
Genotypic frequency
76
What do each of the letters represent in the Hardy-Weinberg Law (p2 + 2pq + q2)?
p2 = probability of the AA genotype
2pq = probability of the heterozygotes
q2 = probability of aa genotype
(remember: p+q = 1)
77
What happens in gain of function mutations?
Increased gene dosage or increased protein function.
ex. Down's sndrome is probably due to increased gene dosage
ex. Achrondroplasia is due to single AA change that results in overactivation of fibroblast growth factor receptor
78
What is an example of a disease classed by novel functional protein change?
Sickle Cell Anemia
Sickle hemoglobin chains aggregate when deoxygenated, leading to deformation of red blood cells.
79
What are some examples in loss-of-function mutations?
* beta thalassemias
* PKU
* cancer (p53)
80
What types of changes in protein function are associated with "single gene mutation" diseases?
* loss of activity (loss of function)
* increased activity (gain of function)
* novel activity
* change in spatial or temporal activity
81
Identify the inheritance pattern, genetic defects and molecular causes underlying I-Cell Disease.
* Autosomal recessive
* lysosomal storage disease
* defect in protein trafficking
* acid hydrolases are not properly modified with mannose-6-phoshates and get sent out of the cell instead of to the lysosome
82
Identify the inheritance pattern, genetic defects and molecular causes underlying Tay Sachs.
* Autosomal recessive
* x100 more prevalent among Ashkenazi Jews
* mutation in hexA gene
* build up of GM2 ganglioside sphingolipids in brain
83
Identify the inheritance pattern, genetic defects and molecular causes underlying Cystic Fibrosis.
* Autosomal recessive
* defect in CFTR gene causes dysfunctional ion transport
* required to regulate the components of sweat, digestive fluids, and mucus
84
Identify the inheritance pattern, genetic defects and molecular causes underlying PKU.
* Autosomal Recessive
* mutation in PAH gene causing enzyme defect
* accumulation of **phenylalanine** in body fluids which can damage CNS
* occurs in one tissue (**liver**/kidney), but the phenotype manifests in the **brain**
85
Identify the inheritance pattern, genetic defects and molecular causes underlying Hypercholesterolemia.
* Autosomal Dominant
* defect/deficiency in low-density lipoprotein receptor (LDLR)
* responsible for binding and internalization of LDL & cholesterol
* LDLR deficiency in liver causes cardiovascular disease
86
Identify the inheritance pattern, genetic defects and molecular causes underlying alpha-1-antitrypsin.
* Polymorphism - 5 major alleles that differ in the amount of effective protein (ZZ- worse)
* defect in co-factor metabolism/effective protein
* major serum protein that inhibits proteolytic enzymes
* major target is leukocyte elastase, which can damage lung connective tissue if not down-regulated
87
Identify the inheritance pattern, genetic defects and molecular causes underlying Duchennes Muscular Dystrophy.
* X-linked recessive
* caused by mutation in the dystrophin gene
* codes for protein that:
* maintains muscle integrity
* links actin skeleton to ECM
* maintains synaptic junctions in brain
* 1/3 of DMD cases arise from new mutations due to size of gene and high mutation rates in sperm
88
Describe linkage equilibrium versus disequilibrium.
* Linkage equilibrium
* When the frequency of the marker alleles and the disease alleles correspond
* Linkage disequilibrium
* when the frequencies vary
* can indicate that the specific allele marker is very close to the disease gene
* when 2 genetic loci (across the population as a whole) are found teogether on the smae haplotype more often than expected
89
Describe the clonal evolution hypothesis.
Genetic and epigenetic changes occur over time in individual cancer cells and that if such changes confer a selective advantage, they will allow individual clones of cells to outcompete other cells & expand.
(Darwinian neoplasia)
90
Describe the stem cell hypothesis.
Growth and progression of many cancers are driven by small subpopulations of cancer stem cells.
Survival is a quality of a stem cell.
(allows resistance to certain cancer treatments even after de-bulking, so targeting treatments to kill cancer stem cells is the best plan to effectively treat cancer)
91
Describe the two hit hypothesis.
* Either develop two random mutations spontaneously that cause loss of all function of tumor supressor gene
* Or inherit one mutant gene and develop one spontaneous mutation
* loss of second allele = loss-of-heterozygosity
* inherited tumor suppressor mutations are considered dominant at the level of the organism, but recessive at the level of the cell
92
What is an example of how gene expression profiling of cancers can identify patient subpopulations with differential survival and responses to therapy.
* Large B-cell lymphoma
* most common form of non-Hodgkins lymphoma
* clinically heterogenous: 40% of patient respond to available chemotherapy, remaining 60% do not respond and die rapidly
* DLBCL = two distint cancers, each with different genetic expression profiles
* discovered by microarray analysis
93
Why is there is a need for better targeted cancer therapies?
* Majority of monogenetic diseases are refractory to current therapies
* complex genetic diseases
* environmental and genetic components of the etiology are poorly understood
94
Effectiveness of therapies increases as . . .
as more information is known about the disease, disease gene, and its biochemical mechanisms.
95
What does the progress in gene and stem cell therapy mark?
A new era of regenerative medicine!
96
Describe some current treatment strategies for genetic diseases.
1. dietary modification
2. environmental factor avoidance
3. modification of gene expression
4. protein replacement therapy
5. bone marrow transplants
97
What steps was the Gaucher Disease treatment success based on?
1. Knowledge of the gene, protein, and its function
2. Knowledge about the disease pathogenesis
3. Knowledge about the target macrophage biology
98
What is *ex vivo* gene transfer?
Transfer of a gene outside the body or a stem cell, followed by introduction of it into the body.
99
What is an advantage of *ex vivo* gene transfer?
Advantage: does not require an efficient means to enter a cell since a rare engineered cell can be selected for it in cell culture
100
What is a disadvantage of *ex vivo* gene transfer?
difficult & time consuming
101
What is *in vivo* gene transfer?
Direct injection into the body using a vector (viral/non-viral).
102
What is the advantage of *in vivo* gene transfer?
Quick & easy.
103
What is the disadvantage of *in vivo* gene transfer?
Many including:
- targeting proper cells
- immune responses
- safety
104
What are the limitations and advantages of using Retrovirus as a vector?
* Enveloped
* Limitations:
* only transduces dividing cells
* induce oncogenesis (cause cancer)
* Advantages:
* persistent gene expression
105
What are the limitations and advantages of using Lentivirus as a vector?
* Enveloped
* Limitations:
* cause cancer (induce oncogenesis)
* Advantages:
* persistent gene transfer
106
What are the limitations and advantages of using HSV-1 as a viral vector?
* Enveloped
* Limitations:
* Episomal form → gets degraded → causes inflamation
* Advantages:
* larger packaging capacity
107
What are the limitations and advantages of using AAV as a vector?
* Most commonly used vector!
* Non-enveloped
* Limitations:
* small packaging capacity
* Advantages:
* Non-inflammatory
* non-pathogenic
108
What are the limitations and advantages of using Adenovirus as a vector?
* Non-enveloped
* Limitations:
* causes potent inflammatory response
* Advantages:
* extremely efficient transduction of most tissues
109
What are the disadvantages and advantages of using Oncoretrovirus as a vector?
* Disadvantages:
* effectiveness only in proliferating cells
* Advantages:
* permanent expression of transgeen
110
What are the disadvantages and advantages of using Herpes virus as a vector?
* Disadvantages:
* stong inflammation
* neurotoxicity
* Advantages:
* large packaging capacity
111
