Genetics non-pics Flashcards
(94 cards)
1
Q
How does the concept of new mutation apply to Autosomal dominant diseases? what diseases does it occur commonly in?
A
= de novo mutations;
causes the AD to appear like an AR pedigree
AD de novo mutations = common in achondroplasia, HD, NF becausue all 3 mutations are located on “large” genes and therefore more likely for a new mutation to occur
2
Q
How does the concept of variable expression relate to AD?
A
affected individuals present differently and go unrecognized as “affected” and mislabeled on pedigree (ie: NF-1 presents with all sorts of different tumors)
3
Q
How does non-penetrance affect an AD pedigree?
A
makes the pedigree look like it skips a generation
4
Q
How does anticipation affect an AD pedigree?
A
age of onset occurs younger and younger with successive generations;
seen in HD because increase in expansions with each generation and increased expansions = decreased age of onset
5
Q
What are the genetic mutations that often present LIKE autosomal dominant (but they are not inherited likewise)
A
- Haploinsufficiency = when a diploid organizm only has a single copy (that is functional) of chromosome and thus the organism doesn’t producse enough gene product to bring out wild-type gene activity (dominant LOSS OF FUNCTION.. an allele is unable to produce its gene product so it is no longer considered “functional”)
- Dominant Negative Alleles = when a mutant allele doesn’t function normally and either directly inhibits the activity of wild-type proteins or inhibits the activity of another protein that is required for the normal function of the wild-type protein (ie: an activator downstream); *mutated protein acts with normal protein to block the normal proteins’ function.
- Dominant GAIN OF FUNCTION (GOF): mutations that result in elevated levels of gene activity or genes gain new activity:
for EX: cancer proto-oncogenes become mutated and become oncogene, stimulating massive growth (LOSS OF GROWTH CONTROL!)
6
Q
What are the characteristic patterns of AR inheritance?
A
- HORIZONTAL distribution of affected individuals (only sibships in one generation are affected, not typically seen in parents, offspring, or other relatives)
- risk of each sibling of an affected individual = INDEPENDENT; 25% chance affected, but 2/3 chance unaffected and CARRIER
- consanguinity and ethnicity increase risk
- males and females equally likely to be affected
7
Q
Explain the effect of consanguinity and ethnicity on the etiology and incidence of AR conditions
A
Ethnicity: groups of people who identify with each other through a common heritage; generally they are separated from larger populations by geographical, religious, or linguistic factors and are considered genetic isolates
- most mutant alleles are in heterozygotes who do not realize they have a mutant gene so the gene gets passed for several generations, perpetuating itself in these isolates.
- mating in ethnicity groups is not typically consanguineous
Consanguinity: mating between individuals related by blood, second cousins, or closer.
-increases the risk for mating between heterozygotes because consanguinity increases the chance that each offspring has inherited the same mutatnt allele from common ancesors (leading to birth of a baby with AR disease)
EX: ataxia with vitamin E deficiency (mutation in vit E absorbs protein, found in middle east where first cousin marriages are common)
8
Q
What is the basis for carrier detection screen across ethnic distributions?
A
carrier screening to identify couples at risk for having offspring with AR conditions that are more prevalent in their ethnic group
Ex: ashkenazi jews: Tay sachs, Gaucher
Africans = sickle cell disease
N. Europeans = cystic fibrosis
9
Q
How do gene modifiers impact the phenotype of a disease? (ie in an AR disease?)
A
EX: SMA:
SMN 2 = gene modifier so when SMN is mutated, SMA occurs because SMN2 cannot fully compensate for the lack of functional SMN protein, however, when the SMN2 copy number increase, small amounts of full length transcripts are generated by SMN2 and able to function thus resulting in a milder SMA II or III phenotype. If an individual has SMA, they will have a milder phenotype if there are greater than 3 copies of SMN2
10
Q
What is an example where carrier testing is complicate in an AR disease?
A
Testing for SMA:
98% of parents are heterozygotes and carry SMN1 mutation
2% de novo causing mutation (paternal origin);
Gets complicated when:
a parent has 2 copies of SMN1 on one chromosome and no copies on the other chromosome; testing involves dosage analysis (just looking for the number of copies.. so you think you have 2 copies, but really you have a chromo that doesn’t have a copy, so you can pass on a chromo without the gene!)
False negative: because 2 copies of SMN1 are on one chromosome
11
Q
What is x-inactivation and what is the lyon hypothesis?
A
x-inactivation= dosage compensation.. phenomenon of equalization of gene activity in spite of females having 2x the gene number of x-chromosomes
Lyon hypothesis: in early embryonic somatic (non-germ cells) female cells, one of 2 X chromosomes is randomly inactivated, such that only one is transcriptionally active and makes proteins and other is permanently inactivated in that cell and all progeny of that cell
Such that a female is a mosaic with 50% of the cells expressed maternally derived X and other 50% = paternally derived
Barr body = visibly inactive X-chromosome in non-mitotic cells as a dense clump of chromatin at the periphery of a cell’s nucleus
12
Q
What is XIST (X-Inactive-Specific Transcript)?
A
= has an important role in regulating inactivation process;
IT IS THE ONLY GENE THAT CAN BE EXPRESSED FROM AN OTHERWISE INACTIVE X-CHROMOSOME
**ONLY EXPRESSED IN THE INACTIVE X
-encodes non-coding mRNA transcripts that coat the chromosome and initiate transcriptional silencing through binding of repressor proteins
-maintained through subsequent cell divisions via DNA methylation
13
Q
How is X-inactivation involved in the etiology of X-linked diseases?
A
- if a woman has a deletion on one X-chromosome then the abnormal X-chromosome is INACTIVE
- If an X chromosome is translocated to an autosome: then the non-translocated X is inactivated, otherwise inactivation will spread to the autosome, creating functional monosomy
- pseudoautosomal region = share homology between X and Y chromosome
- gene escape X inactivation = mutations cause disease
14
Q
What are the characteristics of X-linked disorders (recessive vs. dominant)
A
X-Recessive:
-usually only males affected
-females = asymptomatic usually; may express condition with variable severity due to x-inactivation
-transmission = through unaffected female carriers to sons (such that the disease appears to SKIP generations)
NO MALE TO MALE TRANSMISSION
-affected males at risk of transmitting disorder to their grandsons through obligate carrier daughters
X-dominant:
- affected males have NO affected sons but ALL affected daughters:
- no male to male transmission
- both male/female children of a female affected
- have a 50% risk of inheriting phenotype (similar to autosomal dominant)
15
Q
What is the rationale for choosing a karyotype?
A
- need live tissue (blood sample/bone marrow)
- detect: chromosomal imbalances (numerical such as anaploidy or structural such as translocations/inversions/deletions/duplications)
16
Q
What is the rationale for choosing FISH?
A
DNA/RNA probe binds to specific gene of interest on chromosome;
Used for specific localization of genes + direct visualization of anomalies (ie: microdeletions) at molecular level (when deletion is too small to be visualized by karyotypes)
-known deletions/duplications, reciprocal/robertsonian translocations
17
Q
What is the rationale for choosing a microarray?
A
thousands of nucleic acids arranged in grids on glass. DNA/RNA probes are hybridized to the chip and a scanner detect the relative amount of complementary binding
Use: to profile gene expression levels of thousands of genes simultaneously to study certain disease treatments
Its able to detect SNPs for genotyping, predisposition of disease etc.
this allows for detection of ALL chromosomal imbalances that karyotyping can and few others;
uses DNA therefore done need a viable tissue/blood
CANNOT DETECT MOSAICISM OR BALANCED TRANSLOCATION!!
18
Q
When should an array based recommendation for detection of abnormality be the first line test?
A
for individuals with multiple anomalies (Not specific to defines syndrome)
non-syndromic developmental delay or intellectual disability
autism spectrum disorder
19
Q
What is the rationale for doing a single gene test?
A
for sequencing of genes associated with disease and interpretation of results based on degree that a particular sequence variation is/might be related to actual /future illness
“known disease causing variants”
20
Q
What is the rationale for whole exome sequencing?
A
-selectively sequence the coding region of genome
-come DNA to reference–compare variants and filter:
missense = mutation results in changed amino acid
nonsense = mutations base change results in a premature stop codon causing protein product to be truncated/incomplete
- only need 1% of genome
detects: base substitutions and small deletions and duplications– most but not all mutations
since only exons are sequenced, dont cover non-coding elements, untranslated regions, enhancers etc. does not cover copy number variations (ie: repeat expansions)
vs. whole genome sequencing –> sequences all nucleotides
21
Q
What are mutifactorial traits? polygenic inheritance? continuous traits? discontinuous traits?
A
- Multifactorial traits: multiple genes at different loci all have a small additive effect with multiple environmental factors and other trigger usually contributing to etiology (predisposition = inherited from both parents)
- Polygenic inheritance = additive effect of multiple genes and no environmental influences
- Continuous/quantitative traits = can be measured along an uninterrupted scale and tend to follow a normal or “bell-shaped” distribution in a population (ie: height, weight, BP, intelligence); when continuos traits have normal distribution, measurements with more than 2 standard deviations above or below average = “abnormal”
- Discontinuous traits = either present or absent; not measure on a scale/range, but severity of trait can range
22
Q
Explain the multifactorial threshold model/liability model; what concepts can the MFT model be used to explain?
A
all of the factors which influence the development of a multifactorial disorder (genetic or environmental) can be considered a single entity known as liability;
liabilities of all indviduals in a population form a continuous variable (has a normal distribution) but the curves are shifted right and the extend to which they are shifted relates their threshold for a disease/discontinuous phenotype (affect/not)
ABOVE THE THRESHOLD: abnormal phenotype expressed
In a general population: proportion beyond threshold = ‘population incidence’
in a relative population: proportion beyond threshold = ‘familial incidence’
MFT model assumes a susceptibility to a particular trait/disorder: susceptibility is normally distributed but not measurable: at one end of normal distribution = threshold of liability: individual who exceeds this threshold of liability/susceptibility will have the trait (ex: single congenital malformation)
MFT model can be used to explain:
1. Gender Bias: how different populations may have different thresholds; one gender may have a higher occurrence than the other; the susceptibility distribution is the same in both Male and female but the threshold beyond which an individual will have a trait is different (depending on gender)
2. Population Bias: how different distributions among populations is possible but the threshold is the same
(one population may have a higher occurrence for a disease than other populations.. explains the risks present in first degree relatives of an affected individual; frequency within a population is changed but the the threshold is the same)
23
Q
Apply the threshold liability model to underlying etiology of common congenital malformations and adult onset diseases
A
Explains the gender/population bias in relation to:
spina bfida = more common in F>M (gender bias)
population bias:
cystic fibrosis = more common in n.europeans + ashkenazi jews
sickle cell = more common in africans
thalassemia = more common in mediterranean, african, indian, and asians
24
Q
What is the difference between absolute risk and relative risk?
A
family aggregation = occurrence of more cases of a give disorder in close relatives of a person with disorder than in control families; due to shared genetic or shared environmental factors (familial aggregation cant distinguish between the two)
Absolute risk = an individuals risk for developing a given disease over a period of time
relative risk = used to compare risk between two groups of people: one group has a certain risk factor (ie: family history) and the other does not; ie: someones risk compared to general population risk (if relative risk = 1 then no difference)
relative risk = incidence in relatives of proband / incidence in general population
since relatives share a portion of their genes, the multifactorial trait is seen in proportion to the degree of relationship (ie: more first degree relatives affected than second degree)
Monozygotic twins = share 100% of genes
Parents/siblings/dizygotic twins = share 50% of genes
25
How do twin studies help to determine the genetic contribution of multifactorial conditions and traits?
1. monozygotic twins = identical genetics, therefore any differences = due to environment (1 egg, 2 sperm)
2. Dizygotic twins = differ by environment AND genes (2 eggs, 2 sperm)
by comparing MZ and DZ, can figure out genetic component
```
concordant = if both twins share a discontinuous trait
disconcordant = if both twins do NOT share discontinuous traits
```
if a disease is genetic: 100% of MZ will be concordant and 50% of DZ will be concordant
If a trait does NOT have a genetic contribution, there is no difference in concordance
Correlation coefficient = measure of association of a CONTINUOUS train between two relatives (if correlation coefficient = 1 (in MZ) = trait is entirely genetic
26
what is heritability
the measure of total phenotype variance contribute by genetic variance
h^2 = heritance = Variance genetic/ (variance genetic + variance environment)
27
What do adoption studies reveal about genetic contribution?
= children born to parents who have a particular condition but adopted by parents who do not have the condition are studied to determine effect of genetics on condition
28
Describe the basis for emperic risk estimates, their limitations, and influencing factors
incidence of a multifactorial trait among 1st degree relatives of an affected person ~ approx = to the squareroot of the incidence in general population;
*used to estimate recurrence risk
emperic risk = statistic that represents the average risk that is specific to the population that was tested; NOT NECESSARILY specific for a particular family because heterogeneity of many disorder requires consideration of other, non-functional etiologies;
Limitations:
- skewed populations test (ie: town near radiation plant)
- small population
- heterogeneity (locus): other nonfunctional etiologies
Influences:
- recurrence risk depends on the number of people who exceed the threshold
- risk decreases with further away from proband (therefore relative other an the primary relatives can be ignored)
so: things that increase the recurrence risk:
- increased number of people affected (relatives)
- increased severity of affected proband
- if one sex is more often affected, then, if the affected is of the OPPOSITE SEX (if proband is in the less affected gender)
29
Describe the function of mitochondria and their role in energy production
= make ATP by using electrons from intermediary metabolism (from H+ brough in primary by NADH from glucose breakdown) and also by FADH2 from FA breakdown and removing energy in a controlled manner as electrons move down the ETC
energy released is used by complex I, III, cyt C, IV, to pump protons through the mitchondrial innermembrane
this creates a charge and pH gradient such that mito = charged and acts as a capacitor (storing potential energy); the potential energy drives ATP synthase (complex V), which couples the reaction of ADP + Pi to ATP with inflow of protons
30
Describe mitochondrial DNA characteristics, including maternal inheritance, threshold, heteroplasmy, and segregation during cell division
1. Maternal Inheritance:
"uniparental inheritance": non-mendelian; ALL offspring carry trait if its present on mom's DNA; none carry it if its present on fathers mtDNA (because all mitochondira are inherited in oocyte and sperm only carries DNA, no mtDNA)
2. Heteroplasmy = presence of a mixture of more than one type of mtDNA with in a cell/individual; since eukaryotes contain hundreds of mitochondria with hundreds of copies of mtDNA, it is possible that both wild-type and mutant molecules in the same cell will exist (heteroplasmy) because the mtDNA ploidy is so high, heteroplasmy can encompass virtually continuous variation in proportion of mutant molecules
3. Threshold: genotypic blending of wild type and mutant mtDNA (Heteroplasmy) does not lead to equivalent phenotypic blending. A significant decrease in energy production appears not to occur until the proportion of mutant molecules rises enough that some mitochondria contain few or no-wild type molecules; a threshold exists in the expression of deleterious mtDNA mutations (~70% or more mutant molecules need) in vitro; in vivo, depends on: energy needs of a particualr tissue and on specific mutation
4. Segregation (during cell division):
different tissues can harbor different proportions of mutant and wild type molecules: depends in part on the developmental time and place of the original mutation as this will affect to which daughter cells the mutation partitions during cell division;
phenotype severity depends on the wild type to normal fraction and how aerobic a given tissue is and whether or not the mutation occurred early (potential and sever affect) or at terminal differentiation (little affect)
31
LIst the general clinical features and different etiology of mitochondrial diseases
Main features: seizures, heachache, muscle weakness, eye/hand corrdination problems, hearing loss
etiology: energy deficiency --how energy defects manifest themselves as pathology depends on variety of factors
including: nature of mutation (nuclear vs. mtDNA)
nature of tissue involve (how aerobic==how much ATP)
age of individual
point mutations (inherited, maternally) vs. deletion mutations (do not show family history)
32
Describe the role of mitchondria in etiology of complex diseases
- single disease = either nuclear or mtDNA mutation
- complex chronic = assume mitochondrial component due to energy importance in highly oxidative tissues
(ie: diabetes)
```
2% of T2DM = due to mtDNA mutations; also insulin resistant adults = mtDNA polymorphism in the noncoding D-loop
other associations (w/mito) = AD, PD, cancer, hypertrophic cardiomyopathy
*homoplasmic mtDNA mutations found frequently in several different tumor types
```
33
What are the different probability laws that are associated with providing a risk assessment in genomics?
1. Mutual Exclusivity: two or more events cannot occur in a single event (ie: heads or tails in one coin toss... can't get both)
2. Independent: the probability of two or more events is not influenced by the other (each event's probability is independent of the other)
3. Addition Rule: the probability that one OR the other of any mutually exclusive events will occur is the SUM of their separate probabilities
4. Multiplication Rule: the probability that two or more independent events occur TOGETHER ("AND") is the PRODUCT of their separate probabilities
34
What is the difference between gene frequency, genotype frequency and phenotype frequency?
Gene frequency = proportion of chromosomes that contain a specific gene or allele (ie: A or a)
Genotype frequency = proportion of INDIVIDUALS that carry a specific genotype (ie: homozygotes or heterozygotes)
Phenotype frequency = proportion of INDIVIDUALS who present a specific phenotype (ie: affected or unaffected)
35
How are Hardy-Weinberg Laws useful in calculating gene (allele) and genotype frequencies? Explain for different types of inheritance patterns (ie: AR, AD, X-linked)
Best used when the dominant homozygotes are indistinguishable from the heterozygotes:
p = probability of A (gene frequency A)
q = probability of a (gene frequency a)
p+q = 1
probability of A+a or a + A = (pq) + (pq) = 2pq
probability of A+A = p*p = p^2
probability of a+a = q*q = q^2
In Autosomal Recessive: (gene freq = q; carrier freq =2q; disease freq = q^2)
Disease incidence = aa = q^2
so gene frequency = sqrt(q^2)
since p+q = 1, then p = 1-q which is about 1
thus the frequency of hetero (carrier frequency) = 2*q (1)
In Autosomal Dominant (gene freq = p = disease freq/2)
Disease frequency = AA + Aa, but typically AA = 0 because it is too extreme and person dies off
so Aa = disease frequency = 2pq
and AA = p^2 = 0; so p is basically = 0 and thus p+q = 1, so q = 1 approx. so, disease frequency = 2p (1)
thus gene frequency (p) = disease frequency (2p) / 2
In X-linked:
Males: disease frequency = gene frequency = q
Females: disease frequency = q^2 = (male disease freq)^2
gene frequency = q
carrier frequency = 2pq (follow similar to AR/AD)
36
How can the H-W equilibrium be disturbed by: Mutation
ADDS genes to the gene pool;
SOURCE OF VARIABILITY
(in balance with selection to balance gene frequency changes/microevolution)
37
How can the H-W equilibrium be disturbed by: Selection
REMOVES genes from the gene pool by DECREASING gene frequency (in balance with mutation to balance gene frequency)
selection = the differential fitness of an individual with a certain genotype (f = 1 -s) such that if fitness = 0, then the selection is complete; if fitness = 1 then there is no selection (fitness between 0 and 1 = incomplete selection)
38
Achondroplasia has a reduced fitness since only 20% of affected individuals reproduce. What is the selection against the gene that causes achondroplasia? Why is the steadyincidence of achnodroplasia maintained?
1. selection = 80% (of genes lost during reproduction)
| 2. incidence maintained due to new (de novo) MUTATIONS
39
How can the H-W equilibrium be disturbed by: small populations?
smaller the population = greater the chance for random fluctuations in gene frequency;
Genetic drift = gene frequency of a gene may not be representative of the parent population, causing random fluctuations in its frequency (often occurs when small subgroups of populations isolated from general population)
VIA:
1. Founder Effect: if one of the original members of the new small population happens to carry a rare gene, this gene may become established in this population with a relatively high frequency (someone in one population, brings a gene to a new small population and the gene starts to grow; ie: ashkenazi jews)
2. Bottleneck effect: if there is a large population and then a natural cause (ie: tsunami, earthquake etc) causes a decrease in the number of individuals, then mutation can populate the new population easily
40
How can the H-W equilibrium be disturbed by: Nonrandom mating?
= departures from random mating usually occur because of their:
1. Assortative Mating: choose mate based on similar characteristics (ie: similar medical problem mates tend to mate; ie: deaf, short stature)
2. Consanguinity or Inbreeding: leads to a decrease of heterozygosity and a corresponding increase in homozygosity (ie: greater likelihood of an autosomal recessive disorder) can be measured by the coefficient of relationship (r) = proportion of genes shared by two related individuals and the inbreeding coefficient (F) which is the probability that an individual is homozygous as the result of consanguinity in his or her parents
41
Describe the consequences of heterozygote advantage and give examples?
= explains why disorders have a significantly high mutant gene frequency even through there is a substantial selection agains homozygous affected individuals. Could have been explained by extraordinarily high mutation rate, but more likely that there are environmental situations where heterozygotes are at a selective advantage in comparison to both homozygote phenotypes
EX: sickle cell anemia and cystic fibrosis; in SCA heterozygotes are resistive to malaria, giving them a higher reproductive fitness leading to a higher gene frequency in the gene pool. Selective forces (OPERATING IN BOTH DIRECTIONS towards the maintenance and removal of a deleterious gene = BALANCED POLYMORPHISM)
42
Understand the conditional probability and when Bayesian analysis is used to better refine a risk calculations
Conditional probability = probability that something will happen given that a previous event occurred. Provide overall probability of an outcome by considering all initial probabilities and then modifying these by incorporating additional information
Takes into account:
Prior probability = mendelian risk calculation (contrabands parent must have the mutation for the contraband to be at increased risk)
Conditional probability = chance of new information given gene carrier or not
Joint probability = probability that both of the two independent events will occur (product of the probabilities of each event)
Posterior probability = standardize the joint probability so the other two probabilities add to 1 (common denominator by adding two joint prob and then each of the joint probs = numerator)
Used: for risk calculations in diseases with later ages of onset, X-linked inheritance, non-penetrance, negative laboratory results (especially when carrier testing is not 100% sensitive)
43
Explain why it is difficult to change population frequencies by medical interventions
??
| because the genes still prevail even though you are treating the condition?
44
Explain the concepts of genetic imprinting and uniparental disomy
BOTH: heritable gene changes that DO NOT ENTAIL A CHANGE IN DNA SEQUENCE
Genetic imprinting = differential expression ("marker") of genetic material depending on whether it was inherited from the male or female parents; such that the EXACT SAME genetic material can result in a DIFFERENT phenotype depending on which parent the gene was inherited from; results in a mono-allelic gene expression caused by allele specific DNA methylation of an inactive or silent (imprinted) allele; can be tissue specific (imprinted in some tissues, but not in other) and/or developmentally regulated (imprinted in early embryonic development but biallelic as adult) but it is established during gametogenesis
IMPRINTED GENES ARE SILENCED:
Maternal imprinted = genes inherited from MOM are SILENCED
Paternal imprinted = genes inherited from DAD are SILENCED
Uniparental disomy = the inheritance of BOTH chromosomes of one homologous pair from a SINGLE parent; the offsprings total number of chromosomes is normal.
**NO GENETIC MUTATION OR IMBALANCE IN THE AFFECTED INDIVIDUAL, instead the problem is related to the parental origin of normal genetic material
UPD's are insignificant if the imprinted gene is lost; they are significant if the non-imprinted gene is lost
UPD most likely aries when a trisomy attempts to "rescue" the cell and transforms to disomy (1/3 of the time uniparental disomy will be produced).
For example: in Prader-Willis: maternally imprinted chromosome 15 disease, so normally, the chromosome from the mom is silenced and the chromsome from the dad is expressed; but then the paternal chromosome is deleted so its almost like "no chromo 15" information OR can occur due to UPD in which BOTH of chromo 15 are from the mom (maternal UPD) and so both are silenced and it appears like "no chromo 15 " information
(opposite gender for Angelman's syndrome)
UPD can also involve a segment (region) of the chromosome: thought to occur post-zygotic (somatic) recombination error
EX: UPD 11p (beckman-Wiedemann) in which both p arm of 11 are inherited from dad (Paternal UPD); occurs during MITOSIS (NOT GAMETOGENSIS)
UPD can result in the imprinting effects and greater risk of an autosomal recessive disorder (because you inherit both from one parent)
Heterodisomy = pair of non-identical chromosomes are inherited from one parent (due to meiosis I nondisjunction)
Isodisomy = two homologous chromosomes are genetically identical (due a meiosis II nondisjunction) . If a parent is a carrier for an autosomal recessive condition, and the gene is located on the chromosome involved in UPD then there is a higher chance for the offspring to get the disease (two copies of gene with mutation carried by the parent)
occurs in cystic fibrosis: UPD with isodisomy: two chromo 7's are maternally derived and identical -- offspring is homozygous for mutation
45
Describe the possible mechanisms of uniparental disomy
INSERT PICTURE!!!
1. Trisomic rescue:
a) heterodisomy: trisomy as a result of a non-disjunction in meiosis I (not identical) + fertilization; rescue result in heterodisomy UPD 1/3 of the time and successful rescue 2/3 of the time
b) . isodisomy: trisomy as a result of non-disjunction meiosis II (identical) + fertilization; rescue results in isodisomy UPD 1/3 of the time and successful rescue 2/3 of the time
2. Robertsonian translocation: in this instance there is also trisomy rescue but the possible outcomes are:
Trisomy Rescue = biparental disomy (normal with blanaced translocation) or uniparental disomy (with balanced translocation)
OR
Monosomy rescue (duplication of a single chromosome in a monosomic embryo) = uniparental isodisomy (via isochromosome formation)
3. Gamete complementation: the union of a gamete with two copies of a specific chromosome with a gamete that has no copies of that same chromosome.
46
Discuss the concept of mosacism (both somatic and gonadal) and its implications in phenotypic expression and recurrence risk
Mosacism = results from POST-ZYGOTIC mitotic nondisjunction event, giving rise to populations of cells with different chromosomal complement. The event can occur in somatic cells (somatic mosaicism) or in the germline cells (gonadal mosacism)
Phenotypic expression: phenotype characteristics depend on the proportion of normal and abnormal cells and in what tissues the abnormal cell lines predominate
It can occur at a single gene level (ie: NF-1 mutation causes some somatic cells to be normal ad other affected.. such that only some regions of the body demonstrate the manifestations of NF)
Recurrent risk: gonadal mosaicism is relatively common and need to be always mentioned as a possible etiology when providing recurrence risk information to families who have a family member affected with a genetic condition which appears to have arisen because of a “new” mutation or “sporadic” occurrence. Typically, the parent is asymptomatic (unless somatic mosaicism as well) and the presence of a genetic condition in the offspring is considered to be “sporadic”
gonadal mosaicism leads to an increased risk for an apparently unaffected parent to have more than one child with a dominant or X-linked disorder (gonadal = some of the gamete carry the mutation, others do not)
47
How is cancer is a genetic disease? How does it go from a single cell to a malignant tumor?
Evidence that cancer is a genetic disease
• Most carcinogens are mutagens
• >50 types of inherited cancer predisposition syndromes
• some types of cancers are caused by chromosomal abnormalities
• mutations in oncogenes and tumor suppressor genes enhance growth
• defects in DNA repair increase the probability of cancer
Cancer is a multi-step process
• Begins with a single mutation in a single cell that provides a growth
• Once initiated cancer progresses by the accumulation of additional mutations
• Takes an estimated 3-7 mutations for single cels to transform into malignancy
• 6 hallmarks of cancer
o self-sufficiency in growth signals
o insensitivity to anti-growth signals
o evading apoptosis
o sustained angiogenesis
o limitless replication potential
o tissue invasion and metastasis
48
What are oncogenes? what is their role in oncogensis?
```
proto-oncogene = a normal gene that promotes cell growth and survival;
oncogene = mutated form of the cellular gene that stimulates uncontrolled cell division and proliferation;
```
Function of the proteins encoded by proto-oncogenes: growth factors and their receptors, cytoplasmic signal transducers, transcription factors, telomerase, anti-apoptotic proteins
MUTATIONS THAT ACTIVATE ONCOGENES ARE DOMINANT AND RESULT IN A GAIN OF FUNCTION (cause the production of a gene product that is increased in gene expression)
49
What are the mechanisms by which oncogenes lead to cancer?
1. Production of modified or NOVEL product
A). Point mutations, small insertions/deletions:
KRAS = intracellular GTP-binding protein that is mutated in many cancers; it acts a molecular "on/off" switch that is activated with GTP and inactive with GDP; POINT MUTATIONS IN KRAS LEAD TO ABNORMAL CELL GROWTH AND PROLIFERATION
B). Translocations leading to gene fusion:
Chronic Myelogenous Leukemia (CML): a reciprocal translocation between chromo 9/22 that results in the fusion of two genes (BCR and ABL1); fusion causes encoding of protein to INCREASE TYROSINE KINASE ACTIVITY resulting in abnormal proliferation (leukemia)
2. Increase in the amount of NORMAL product
A). translocation to an active chromatin domain:
Bukitt's Lymphoma (B-cell tumor of jaw): translocation between chromo 8 and 14,22, or 2 brings c-MYC gene under control of the immunoglobin regulatory elements; c-MYC upregulates expression of genes involved in cellular proliferation
B). Regulatory Mutations
Telomerase = adds telemers on; normally it has decreased activity in somatic cells ( telomers are lost with each division), but in some tumors, DNA is mutated to upregulate expression of TERT (gene that encodes telemerase)
3. Copy Number Increases
A). Gene amplifications: many additional copies of a segment of the genome are present in the cell
two mechanisms:
1. Double minute: very small accessory chromosomes
2. Homogenously staining regions: tandem chromosomes
50
What are the mechanisms by which tumor suppressor genes lead to cancer?
= Knudson's two hit model
First "hit" = many different types of mutations: missense, nonsense, insertions/deletions (can be inherited or sporadic)
Second "hit":
1. Mutation of the normal allele
2. Transcriptional silencing of the non-mutated allele:
In DNA that is actively transcribed: DNA is unmethylated and histones are acetylated (DNA is less compact and can be transcribed)
During epigenetic silencing of TSGs, the DNA is hypermethylated at CpG nucleotides and histones are deacetylated this DNA is compacted and cant be transcribed
3. Los of heterozygosity (LOH) = loss of non-mutated allele by multiple mechanisms
51
How do current cytogenetic and DNA technology establish a diagnosis, prognosis, and treatment of cancer?
* Karyotyping: large deletions, duplications, inversion, ploidy, some solid tumors difficult to culture, can’t be performed on fixed tissue, analyze 20 cells, need dividing cells
* FISH: dividing or non dividing cells, shorter time, rearrangements, deletion/duplication, can be performed on fixed tissue, 200 cells analyzed (higher sensitivity), need to know abnormalities that you are looking for, only use 3-4 probes at once
* Array CGH: can perform on isolated DNA and assay entire genome for gains/losses in copy #, higher resolution than karyotype or FISH, if includes SNP can find areas where there is loss of heterozygosity. BUT cannot detect structural rearrangements, normal cells and tumor heterogeneity can complicate data analysis, many variants of unknown significance
Molecular genetics:
• Allele specific PCR: PCR using primers specific for WT or mutant allele. Sensitivity down to 1-5% a mutant, targeted, detect point mutations
--Locus specific primers can be used in combo with fluorescent labels allele-specific reported primers
* Measure fluorescence of report on a real time PCR machine
* Detect point mutations, small insertions/deletions
• Reverse Transcriptase Quantitative PCR (RT-qPCR)
o Detect and quantify fusion transcript produced by chromosomal translocations (BCR-ABL t(9;22) and PML-RARA t(15;17). Monitor residual disease in patients undergoing therapy. Sensitivity 1/100,000 cells
* Gene expression microarrys: compare gene expression in tumor samples to normal tissue can be whole genome or targeted. Diagnosis of tumors of unknown origin, evaluation of diagnostic markers and establishing treatment ex: oncotype DX Breast, prostate, or colon cancer arrays
* Sanger sequencing: PCR amplification of target gene followed by sequencing, detect pt mutations, small duplications, ins/dels, sensitivity 20-25% mutant DNA
* Nextgen: sequencing multiple genes for multiple patients at once: ideal for when little tumor is available for testing, detect pt mutations, small insertions, or deletions, sensitivity <1%, expensive and complicated analysis
EX: of how cytogenetics/molecular genetics play a role in cancer diagnosis:
Acute myeloid leukemia (AML): genetic variation in AML is measured using tests, and the results are used to identify AML subtype for patient risk stratification and to gude patient management
Cytogenetics and molecular genetics are used to monitor response to therapy by monitoring hematological malignancies, and as the patient responds to therapy, measuring the percentage of the cells with the genetic abnormality (should decrease)... relapse is often caused by NEW cytogenetic or molecular genetic abnormalities
also used to identify if the patient starts to become resistant to the treatment, and thus a different treatment option is necessary
52
What are Tumor Suppressing genes? what is their role in oncogensis?
* Loss of function genes (turn off gene expression of a protein)
* Control of cell growth by regulating progression through the cell via checkpoints or by promoting apoptosis
* Two mutations required to inactivate TSGs
* Knudson’s two hit model first hit can be sporadic or inherited
Cell cycle checkpoints (three check points: G1/S, G2/M, Mphase)
1. G1/S: phase checkpoint: is the environment favorable for cell division? Is there DNA damage?
• RB1 (protein RB; when active (unphosphorylated) it binds transcription factor E2F and prevents transcription of genes necessary for S phase. It is inactivated by phosph. Releasing E2F to transcribe target genes and to progress to S phase. Loss results in inability to arrest cell cycle here in response to DNA damage. Common in sporadic and inherited cancers
BASICALLY: RB1 makes pRB which stops transcription; if the cell is ready for cell division than pRB is inactive and the cell continues to S phase
2. G2/M: Is DNA replication complete? Is the environment still favorable for cell division?
3. M phase: Are all chromosomes attached to the spindles?
** TP53 encodes P53 a Transcription factor that accumulates in response to DNA damage. Regulates cell cycle at G1/S and G2/M pts and activates DNA repair pathways and can initiate apoptosis. One of most common mutations in cancer (no p53 = can't stop cell growth of damaged DNA)
53
What are DNA repair genes? what is their role in oncogensis?
= "caretaker TSGs"
they encode proteins responsible for detecting and repairing DNA mutations;
Mutations result from DNA damage that is NOT repaired; many types of DNA damage including spontaneous loss of the base, spontaneous deamination f cytosines, base adducts formed by chemicals, UV lights, ionizing radiation, mistakes in DNA repliacation
THEY PROTECT THE INTEGRITY OF THE GENOME!!!
loss of function mutations permit the accumulation of mutations in oncogenes and TSGs and INDIRECTLY PROMOTE CANCER (because no longer making proteins to detect and get rid of proto-onc/TSG mutations/malfunctions)
54
What are some of the DNA repair pathways that help prevent cancer?
1. Base excision repair -- repairs chemically altered bases
2. Nucleotide excision repair (NER)-- removes thymine dimers and chemical adducts: 4 major steps: 1). recognize damage 2). cleave DNA 3). remove affected segment 4). fill gap in DNA using template
Inherited defects in the NER pathway can cause Xeroderma Pigmentosum (AR disease characterized by photosensitivity and predisposition to skin cancer)
3. Mismatch Repair-- correct nucleotides misincorporated during DNA replication or repeat mismatches due to strand slippage
EX: Four mismatch repair genes are mutated in Lynch: MLH1, MSH2, MSH6, PMS2
4. Double strand break repair-- caused by errors in replication or recombination and ionizing radiation
Two major pathways:
1. Homologous recombination: homologous chromosomes used as a template to synthesize DNA that was lost (involved in BRCA1/2 and Fanconi Anemia)
2. Non-homologous recombination: broken ends are ligated together (error prone)
55
Define the different etiologies of cancer in families: sporadic, familial, and hereditary and the genetic basis of each
Sporadic:
single occurance of a specific cancer in the family with typical age of onset and a single primary tumor; the relatives are generally not at an increased risk
etiology: accumulation of somatic (acquired) mutations due to chance or environmental risk factors (smoking, obesity, UV radiation etc)
Familial:
two close relatives with a specific type of cancer at the typical age of onset; single primary tumor, and other close relatives are at a moderately increased risk
Etiology of familial cancer: due to:
-multifactorial influences, low penetrance single gene alleles, shared environmental risk, clustering of sporadic cases, underreporting of cancer history
**predisposition genetic test is insignificant for familial and sporadic cancers!
Hereditary
Two or more relatives in the same lineage with the same or related cancers; EARLY AGE OF ONSET, multifocal or BILATERAL tumors, usually AUTOSOMAL DOMINANT in inheritance
56
Describe the clinical features in the personal and family medical history that aid in identifying families at increased risk of cancer
Explains the features observed in hereditary cancer:
- Early age of onset: fewer events required for cell to be transformed from the normal to malignant phenotype
- increased incidence of individuals with two or more primary tumors/bilaterality in paired organs: all the cells in the body carry the germline mutation, including oocyte/sperm
- cancer in multiple individuals and generations in the family
- Reduced penetrance: requires additional somatic mutations for a person with a germline mutation to develop cancer
57
Describe the medical management approach to individuals with, and at risk for, hereditary cancer syndromes and contrast it to population screening guidelines
ex: BRCA1 and 2 mutation CARRIERS:
For Breast Cancer Risk:
- monthly breast self exam starting at AGE 18
- clinical breast exam semiannually starting at age 25-35
- annual mammography AND MRI starting at 25
- discuss prophylctic mastectomy
- consider chemo-prevention options
For Ovarian Cancer Risk
- recommend risk reducing salpingo-oophorectomy ideally between 35-40
- concurrent transvaginal ultrasound and serum CA-124 every 6 months starting at age 35
- consider chemo-prevention options
compared to Li Fraumeni (TP53) syndrome: similar to BRCA 1/2 with regard to BREAST CANCER, but start at 20-25 yrs old (not 18) and dont do ovarian cancer risk management
58
Compare and contract how somatic versus inherited genetic mutations lead to to the development of cancer. How does the model explain the characteristic etiology of hereditary cancer?
Knudson's two hit hypothesis for tumorigenesis involving a TSG
Sporadic cases: a person has two normal copies of the gene; both copies of the genes have to be lost/turned off through somatic mutation to start the process of tumorigenesis:
--takes two events to start the process (born with two wild-type genes, then first hit deletes one copy and second hit deletes the other)
--mutations only present in the tumor tissue
Hereditary cases: a person has a GERMLINE mutation in the gene (first hit) ; if the other copy of the gene is lost through somatic mutation, this start the process of tumor developing (second hit).
- -one event to start the process
- -the germline mutation, by definition, is present in all the cells of the body, including gametes (so it can be transmitted to FUTURE OFFSPRING), and the lymphocytes ( so through genetic testing of a blood sample, it is possible to identify the germline mutation)
Explains the features observed in hereditary cancer:
- Early age of onset: fewer events required for cell to be transformed from the normal to malignant phenotype
- increased incidence of individuals with two or more primary tumors/bilaterality in paired organs: all the cells in the body carry the germline mutation, including oocyte/sperm
- cancer in multiple individuals and generations in the family
- Reduced penetrance: requires additional somatic mutations for a person with a germline mutation to develop cancer
59
What syndrome is associated with each: BRCA1, BRCA2, PTEN, TP53, CDH1, STK11?
BRCA1/2: hereditary breast and ovarian cancer
PTEN: Cowden syndrome (benign/malignant cancers in: breast, thyroid, endometrial, skin)
TP53: Li-Fraumeni Syndrome (osteosarcome, soft tissue sarcome, breast cancer, brain cancer and other cancers including colon)
CDH1: Hereditary diffuse gastric cancer (lobular breast cancer + diffuse gastric cancer)
STK11: Peutz-Jeghers: gastrointestinal polyps, mucucutanous pigmentations, increased risk of colorectal/gastric/breast/pancreatic cancer
60
Which cancer gene is transmitted as an autosomal recessive gene?
MUTYH
61
Lynch syndrome is associated with an increased risk in which cancers? What are the screening recommendations for individuals with this condition?
= colon cancer, endometrial, ovarian, stomach cancers
screenings: start colonoscopies at age 20-25 and repeat every 1-2 years with removal of polyps (even though "non-polyposis disease")
Screening for gene:
1. family history: with molecular testing for mutation in MLH1 or MSH2
2. Tumor Tissue Screen (universal):
a). Microsatillite instability: look if more than 2 alleles per locus
b). Immunohistochemical stain: look for 4 DNA repair proteins (MLH1, MSH2, MSH6, PMS2); if one missing then suspect but not necessarily means Lynch because 10-15% of sporadic colon cancer has an abnormal ICH (so just because you have colon cancer and a missing protein does not mean that your cancer was due a hereditary disease.. ie: lynch); would need to do more tumor testing and molecular testing of a mismatch repair gene to identify a germline mutation
62
Describe the basic principles of genetic control of metabolic pathways
- If there is a defect/mutation in the genes that encode for either the enxyme or cofactors of a pathway, the disease may occur; most IEM are recessive (few exceptions).
- the pathological and clinical features resulting from an enzyme defect are often shared by dieases due to enzymes that function in the same pathway (locus heterogeneity)
- Different clinical effects may result from mutations in the same enzyme (allelic heterogeneity)
- The pathophysiological consqeuences of enzyme disorders can be attributed to:
1. accumulation of substrate
2. Deficiency of the product
3. Substrate accumulation and product deficiency
4. Accumulation of alternate products
(because precursor --> substrate --> product (via enzyme/cofactor)
so if this last arrow is not working, then either an alternate pathway or a defective product is formed) (see pg. 244)
63
Using common examples, apply the concepts related to the degradation of cellular components within organelles to explain the rationale for diagnosis and treatment of certain inborn errors of metabolism
Lysosomal storage diseases: (and sphingolipidosis)
lysosomes contain acidic degradative enzymes;
inability to degrade macromolecules leads to accumulation of substrate in lysosome, leading to cellular disfunction and eventually cell death; gradual accumulation = "unrelenting progression" of these diseases;
increases in masses of affected tissue/organs (normal patients at birth then they show a plateau and regression as material accumulates)
EX:
1. Tay Sachs disease = GM2 breakdown not working (ganglioside).. affects brain
2. Mucopolysaccharidosis (MPS) = heterogenous group of storage diseases:
Mucopolysaccharides = polysaccharide chains synthesized by connective tissue; their degradation requires multiple enzymes; defects in any enzymes result in substrate accumulation
All are autosomal recessive EXCEPT hunter syndrome (X-linked recessive)
64
Apply what is known about the role of co-factors in enzymatic reactions to the rational for diagnosis and treatment of certain inborn errors of metabolism
•Defects in co-enzymes:
o Class of diseases due to defects in cofactors, such as vitamins
deficiency in conenzyme can result in metabolic block
o Diagnosis of an inborn error due to a specific cofactor, such as a vitamin, is essential, b/c these disorders may be “vitamin-responsive” (megadose treatable)
treat with a large does of the vitamin cofactor to ameliorate all symptoms (ie: treat with vit b12 or biotin)
o Methylmalonic Acidemia (MMA) & Biotinidase Deficiency: See Disorder Sheet
65
Apply the general approaches leading to the diagnosis and treatment of patients with inborn errors of metabolism
Typical neonate findings: usually full term, normal birth, well interval before symptoms present (usually a few days)< family history is usually negative (be suspicious if consanguinity (since most are AR) or unexplained sudden infant death)
Acute Neonate Symptoms = persistant vomiting, poor feeding/failure to gain weight, abnormal breathing rates, jaundice, irritable, seizures, lethargy, unusual odors (maple syrup or musk for PKU)
Once you suspect the possibility of an IEM, 5 parts to evaluation of the patient:
1. history
2. Physical examination
3. Initial screening
4. Advanced screening tests
5. Definitive diagnosis (using various lab studies)
* measuring ammonia, bicarb, pH and glucose can also help: if blood ammonia is elevated then suspect urea cycle disorder (even though normal pH and bicarb), if abnormal pH and bicarb and elevated ammonia then suspect acidosis; if ammonia is NORMAL but pH and bicarb are high then suspect galactosemia
Management of acute metabolic disease:
GOAL: prevent catabolism and limit intake of the accumulating substrate via:
IV glucose, stop dietary protein/carb/fat source (respective to suspected disorder), remove toxin via hemodialysis if needed, vitamin supplementation (to increase residual enzyme activity), avoid fasting etc.
Acute Treatment:
o Supportive care immediately: halt catabolism (IV glucose), BP med’s, assisted breathing
o Stop dietary source of protein while investigating cause
o Search for & treat infections
o Immediate toxin removals (hemodialysis for hyperammonemia)
o Diagnose & specific therapy (special diets, drugs, vitamins, etc.)
o Add’l thereapies: allow outlet by alternate pathways: include vitamin supplementation, carnitine, and specific substrates.
Chronic Treatment
o Limit the accumulating substate
o Vitamin supplementation if vitamin-responsive (increase residual enz. activity)
o Avoidance of fasting & immediate intervention during times of stress/catabolism with the use of emergency protocols.
Organ transplant:
1. liver transplantation for urea cycle defects
2. bone marrow transplants for mucopolysaccharide storage
Enzyme replacement therapy
BH4 (to treat PKU by stimulating PAH)
66
Describe the characteristics and justification for newborn screening programs that detect inborn errors of metabolism
principle: to identify infants with genetic disease for which early treatment could prevent, or at least ameliorate the consequences
GOALS:
1. prediction: identify patients BEFORE they manifest disease
2. prevention: initiate therapeutic interventions to forestall the course of the disease
3. personalization: individualize patients' therapies to optimize their outcomes
-early recognition and prompt treatment remain critical
-early signs and symptoms are often non-specific
- neonatal response to overwhelming illness is limited: poor feeding lethargy, FTT
• Episodes of metabolic decompensation can lead to irreversible neurologic impairment.
• Irreversible damage if untreated
• Prevents damage if begun early
• Natural history is well known
• Increased population incidence
67
Recognize the clinical features suggestive of a urea cycle disorder and apply what is known about the sequence of the reaction within the urea cycle to rationale for treatments
```
Clinical features:
high ammonia, normal pH and normal bicarb (via advanced screening test)
poor feeding
vomiting
lethargy
convulsion
coma
```
Treatment:
Increase the amount of NH3 excreted & decrease the amount of NH3 produced
Acute Treatment:
o Supportive care immediately: halt catabolism (IV glucose), BP med’s, assisted breathing
o Stop dietary source of protein while investigating cause
o Search for & treat infections
o Immediate toxin removals (hemodialysis for hyperammonemia)
o Diagnose & specific therapy (special diets, drugs, vitamins, etc.)
o Add’l thereapies: allow outlet by alternate pathways: include vitamin supplementation, carnitine, and specific substrates.
Chronic Treatment
o Limit the accumulating substate
o Vitamin supplementation if vitamin-responsive (increase residual enz. activity)
o Avoidance of fasting & immediate intervention during times of stress/catabolism with the use of emergency protocols.
Alternative pathways for ammonium excretion.
• Benzoate: binds glycine → hippurate (excreted)
• Phenylacetate: binds glutamate → phenylacetyglutamine (excreted)
Organ transplant:
1. liver transplantation for urea cycle defects
68
What is the importance of a family history in genetic testing? How can a family history improve patient care?
family history helps identify people with an increased risk of specific disorders who may be the best candidates for genetic testing;
histories identify those who may benefit from increased screening, lifestyle changes, and prophylactic measures whether or not genetic testing is available.
Improvement of patient care:
1. Early identification of families at increased risk of chronic disases can improve, delay or prevent advcerse outcomes
2. Risk assessment is unique for each disease and requires periodic re-evaluation
3. Personalized prevention programs shoudl be based on individual (not population) assessment
5. Encouraging patients to generate and update their family history promotes a partnership
69
With regard to family history, what are targeted questions?
targeted questions = focused on disease (specific to the symptoms or condition you are assessing); they help in identifying people who may be affected or at risk
70
What targeted questions should you ask when assessing a family history of cancer?
organ of tumor, number of tumors, age of diagnosis, pathology of tumors, treatment
71
Why is asking the age of onset of an adult onset condition, like cancer or coronary artery disease an important component of risk assessment?
suggests a hereditary inheritance
72
When doing genetic testing for hereditary breast ovarian cancer, or other cancer syndrome, why is it important to test an affected relative BEFORE the one that is affected?
because of genetic heterogeneity and testing all genes is not plausible; also many tests are not 100% sensitive; so by testing the affected individual you can find the mutation and compare the unaffected to see if they share the same mutation, and so see if the affected has one of the classic mutations instead of running every single mutation check on the unaffected
73
What family history characteristics might be indicative of genetic susceptibility to coronary artery disease? Describe two ways in which clinical management is different in people at average risk vs high risk of coronary artery disease
age of onset, angiographic severity, multiple vessels, 1' or 2' relative, lots of risk factors (ie: HTN)
at low risk: asses CAD risk every 5 years
at high risk: consider early detection strategies every 2-3 years
74
Elicit a family medical history by asking targeted questions to help establish a diagnosis, identify at risk family members and perform a risk assessment.
* Targeted questions: Not only does the physician need to ask if anyone in the family has ever been diagnosed with the particular disease/disorder in question, but he/she needs to ask if anyone has ever had known signs/symptoms of the disease/disorder. This helps to identify people who may have been affected by the disease unbeknownst to the patient and/or the patient’s relative. (Marfan Syndrome example p. 298)
* At Risk Family Members: Based on etiology of the disease & mode of transmission
* Risk Assessment: STUDY the population genetics risk assessment chapter and the chapters on the individual modes of transmission.
75
Elicit a family medical history by asking targeted questions for the purpose of categorizing cancer in a family as either sporadic, familial or hereditary in order to make medical management decisions (using breast cancer as an example).
Cancer can be “sporadic” (patient is not at increased risk of developing cancer), “familial” (patient has a modestly increased risk of developing a specific type of cancer) or “hereditary” (patient has a significantly increased risk of developing specific cancers).
Categories:
* “sporadic”: no apparent vertical transmission, no early age of onset, 1 or 2 distant people in the family tree affected. No related cancers.
* “hereditary”: > 1 person in family affected, in a vertical pattern & with early ages of onset. Other cancers that may be related to the disease (e.g. thyroid cancer occurs a lot in families with breast cancer).
* “familial”: somewhere between sporadic and hereditary.
Target Questions:
• All relatives:
oAge
o Personal history of benign or malignant tumors?
oMajor illnesses?
oHospitalizations?
o Surgeries (including prophylactic ones)?
Biopsy History?
oReproductive history (important for women at increased risk for breast/ovarian/endometrial cancer)?
•Relatives who have had cancer:
oOrgan in which tumor developed?
o Age at time of diagnosis?
o Number of tumors (important for women at increased risk of breast, ovarian, or endometrial cancer)?
o Pathology, stage, and grade of malignant tumor?
o Pathology of benign tumors
o Treatment regimen (important b/c some relatives may say they had cancer, but it was a benign tumor)?
o Primary or recurrence?
76
Use the family medical history as a tool to determine the approach to genetic testing in the consultand and other at-risk family members.
* Proband: First affected or possibly affected (fetus) family member coming to medical attention.
* Consultand: Individuals (apparently unaffected) seeking genetic counseling/testing.
• Approach: When should molecular testing for predisposition to cancer be offered? –when ALL 5 of the following ARE MET:
o When patient has a significant personal an/or family history of cancer (as previously described-suggestive of hereditary or less often familial cancer).
o When the test can be adequately interpreted.
o When the results will affect medical management.
o When the clinician can provide or make available adequate genetic education and counseling.
o When the patient can provide informed consent.
77
Use the family medical history as a tool to stratify the risk for common adult onset conditions that have a genetic component in order to make medical management decisions (using coronary artery disease as an example).
• Absolute CAD risk estimates (% risks) based on family history are not yet readily available, therefore, family information is used to stratify risk of CAD.
•Stratums:
o “Low Risk”: no apparent vertical transmission, no early age of onset, one maybe two distant people in the family tree affected. No or very few females affected (usually occurs more often in men, therefore, an affected female indicates a higher genetic load and hence greater risk) Also, no other related cancers (e.g. thyroid cancer occurs a lot in families with breast cancer).
o “Moderate Risk”: Somewhere between Low and High risks.
o “High Risk”: more than one person in family affected, in a vertical pattern & with early ages of onset. Many females affected (usually occurs more often in men, therefore, an affected female indicates a higher genetic load and hence greater risk). Also, characteristic patterns of disease (other than the specific suspected one) that may indicate a specific genetic etiology (e.g. Inherited predisposition to thrombosis might be suspected in a pedigree that has multiple relatives with CAD, stroke and other thromboembolic events).
•Medical Management Decisions:
o ON-GOING
o Test for important familial risk factors: thrombotic genetic markers (prothrombin G20210A, MTHFR,C677T)
o Stratum specific management (more intensive, frequent visits/assessment of risk for higher risk candidates)
78
How do the four ethical principles (autonomy, nonmalefiance, beneficence, and justice) apply to medical genetics practice and informed consent?
1. Autonomy: a person's right to self governance; freedom to act without interference as long as harm is not done and good consequences are promoted over bad ones; (goal of genetics is to enhance autonomy)
2. Nonmaleficence: DO NO HARM; avoid harm or at least minimize it: permitting harm when unavoidable and ensuring there is a corresponding benefit. **informed consent allows clients to make their own decisions about the benefit harm ratio and promotes autonomy.
3. Beneficence: help others further their important and legitimate interests: includes: protecting their rights, avoiding and preventing harm from occuring to others, helping or saving people. Needs to be explored with informed consent because genetics often involves a psychosocial benefit that interferes with medical best interests and need to be able to distinguish between beneficence and paternalism (not engaging the patient in decision.. paternalism challenges autonomy)
4. Justice = equitable distribution of burdens and benefits of healthcare. Includes preventing discrimination regarding access to services and equally serving all who seek services. Challenging when rests are costly and not fully accessible
79
Provide examples of how genetic information has been appropriately used and misused historically and the impact on patient perceptions and current practice
```
Appropriately used:
1. newborn screen
2. ethnicity based carrier screening*
3. universal screening of lynch disease
4. maternal serum screening *
(* = not viewed as positive by everyone because it promotes the identification of reproductive risks)
```
Misuse:
1. Eugenics : aimed at improving the health of society
ie: in the US: involuntary sterilization of "imbeciles" and "feeble minded"/mentally ill/ epileptic
2. Nazis sterilized and killed mentally retarded and huntington disease patients (in order to try and eliminate these disease and create a "healthy society")
Currently:
aim is to improve the lives of INDIVIDUALS not SOCIETY and to promote freedom of choice with regard to how to use genetic information by providing adequate and unbiased information
still: spector of eugenics still affects people's perceptions of medical genetics
80
Identify the potential impact of genetic exceptionalism and arguments against it
genetic exceptionalism = treating genetic information (includes family history) different or separate from of the medical information.
GINA = prohibits discrimination in health coverage and employment based on genetic information
Arguments against exceptionalism
= passing genetic specific laws reinforces the stigma associated with genetics;
thus in order to expectionalism to be successful need:
1. to define the term genetics
2. to have an efficient way to separate genetic from non-genetic information in health records
3. to have a possible treatment for genetic information and a compelling reason to do so
81
recognize the familial nature of genetic information and how this can lead to an ethical dilemma when the need to disclose genetic test results to prevent harm to relatives (duty to warn ) is in conflict with a patients desire to maintain confidentiality
Duty to Warn = obligation if any to warn family members about genetic condition in the family for which they are at risk
AT FEDERAL LEVEL: can override patient/physician confidentiality agreement (HIPAA) if:
1. serious or imminent threat to the health or safety of a person or the public
2. the threat constitutes an imminent, serious threat to an identifiable third party
3. The physician has the capacity to avert harm
Situations when the physician can warn the relative:
1. high likelihood of harm if relative is not warned
2. the patient despite encouragment refuses to inform
3. relative is identifiable
4. the harm of nondisclosure outweighs harm of disclosure
5. current technology renders the disease preventable, treatable, manageable
6. only the necessary information is released
7. There is no other reasonable way to avert harm
82
State the importance of informed consent in adequately addressing the issues and challenges to informed consent
Informed consent includes:
1. purpose of the test
2. description of limitations of the test
3. discussion of benefit and risks of the test (including medical, psychological and insurance risks)
4. information about the meaning of the possible test results and how the results will be disclosed
5. Discussion of who will have access to the remaining biological sample and how any leftover sample may be retained by the laboratory
6. Information about who will have access to the genetic test result which is a part of the confidential medical record
7. Statement that above have been reviewed and had their questions answered
Challenges to informed consent:
1. Children: wait to test until the kid is of age to make decision
2. Testing the affected relative: typically need to test affected before unaffected in order to identify a causative mutation in the family (can lead to familal pressure for testing)
3. Identical twins or parent-child: usually the right of one party not to know does not supersede the other partys right to know, but such situations require comprehensive genetic counseling to discuss how test results will be managed
83
What are the indications for (based on different abnormalities/inheritance types) and utility of prenatal testing?
GOAL: to help parents learn what they need to know about the health of their unborn child to help them make informed decisions about themselves and their family within the context of their own value system
Indications for prenatal diagnosis:
1. Chromosomal abnormality
a. Advanced maternal age
b. Abnormal biochemical screen
c. Previous child with chromosomal abnormality
2. Single gene defect
a. Previous child with inherited metabolic disorder
b. Heterozygous couples detected prospectively by a screening program
c. Previous child with abnormality detected through ultrasound
3. Multifactorial disorders
a. Previous child with neural tube defect
b. Elevated MSAFP
c. Previous child with developmental defect
d. Malformation syndrome detected by ultrasound
4. Environmental defect
a. Previous exposure to teratogenic drug, chemical, or infectious agent
Utility of prenatal diagnosis
• Reassure and reduce anxiety especially in high risk groups
• Manage the pregnancy
• Plan appropriate management at birth (psychological, delivery management, post natal care)
• Determine potential outcomes
• Decide whether to continue the pregnancy
• Discover conditions that may impact future pregnancies
Things to be aware of
• Normal test =/= healthy child
• Gestational age matters
• Must consider cultural, moral, religious values of family
• Decision to terminate never easy
• Must provide non-judgmental non-directive genetic counseling
84
When should women be offered aneuploidy screening? What criteria do they need to meet? How is the screening performed?
give before 20 weeks of gestation regardless of maternal age;
need to meet 3 criteria:
1. identify women are are at increased risk, prior to having a definitive diagnostic test
2. offered systematically to all pregnant women, who are considered only to be at population risk
3. be beneficial to those who receive it.
performed via analysis of maternal serum analytes at first and second trimesters and screens for trisomy 18, 21, (and neural tube defects, and if you have twins!)
85
What are the different methods of prenatal diagnosis?
1. Invasive (diagnostic) = Amniocentesis, Chorionic Villus Sampling (CVS), Fetal Blood Sampling, Fetal Tissue Sampling
2. Non-invasive (Screening) = screening for neural tube defects, screening for down syndrome and other aneuploidies (first-trimester screen, second trimester screen), ultrasound, maternal cell free fetal DNA (take a blood sample of mom and can extract the free fetal DNA in order to sequence the fetus's DNA)
screening = the identification among apparently healthy individual of those who are sufficiently at risk of a specific disorder to justify a subsequent diagnostic test or procedure **if the mom receives a positive first trimester screen, NEVER do a second screening; instead AUTOMATICALLY send to diagnostic test (because if the second screening (non-diagnostic) test is negative then you could have potentially missed an affect fetus
86
When should maternal serum be analyzed? what disorder is it trying to screen?
Advanced maternal age causes oocyte meiotic apparatus to deteriorate with age and thus predisposes nondisjunction of chromosome 21 predominantly at first meiotic division.
Increased maternal age is a risk for having pregnancy with trisomy 21, 13, 16, and 18, 47 XXX and 47XXY
By screening maternal serum analyates: can identify risk for trisomy 21, 18, neural tube defects (NTD)
In Trisomy 21: AFP and uE3 is decreased, HCG is increased
In trisomy 21: all (AFP, uE3 and HCG) are decreased
in NTD: AFP is super increased
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What is the purpose in pregnancy?
non-invasive screen technique for dating the pregnancy and measure the nuchal translucency (found increased in down syndrome), and looking at the nasal bone (down syndrome patients have a decreased nasal bone/absent)
90% of infant with a congenital anomly are born to women with no risk factors; all pregnant women should be offered routine ultrasound screening (helps identify key features in trisomy 21, 18 (ie: polyhydraminos, clenched fist), 13 (polydactyl, holoprosencephaly), turners syndrome (45X0)
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What are the applications, risks, benefits, timing, and limitations for: Chorionic Villlous Sampling (CVS)
Procedure: placental villi obtained through transcervical or transabdominal access to placent
Timing: 10-13 completed weeks (*available early in pregnancy (allows for further testing and potential pregnancy termination))
Risk: 1%
Limitations: Does not test for Open Neurl Tube Defect
Tests: chromosome and DNA
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What are the applications, risks, benefits, timing, and limitations for: Amniocentesis
Early
* Procedure: Transabdominal
* Timing: 9-12.9 weeks
* Risk: 2-3%
* Limitations: NOT RECOMMENDED, increased culture failure
Mid-Trimester:
• Procedure: Transabdominal; Test for ONTD
• Timing: 15-20 weeks
• Risk: 0.5%
• Limitations: Minimal (**easiest to perform)
• Tests: Chromosome & DNA, AFP & Acetylcholinesterase
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What are the applications, risks, benefits, timing, and limitations for: Percutaneous umbilical sampling (PUBS)
Procedure ultrasound guided, the fetal umbilical vessel is sampled with 22 gauge needle
Timing: 18+ weeks
Risk: 1-2%
Limitations: the hardest to perform, risk of fetal loss and later in gestation
Tests: full fetal karyotype in 48 hours, all fetal hematology and serology, used in assessing CVS mosacism
91
Identify common teratogens and their effects on pregancy
Drugs:
1. Alcohol: FAS, intrauterine growth restriction (IUGR), mental retardation, microcephaly, short palpebral fissure, long philtrum, cardiac defects
2. Phenytoin: fetal hydantoin syndrome
3. Thalidomide = limb detects in exposed fetus
Infectious disease:
1. Rubella = cardiac malformations, eye defets, micocephaly
2. Cytomegalovirus = non-immune hydrops, splenomegaly, chorioretinitis, intracranial calcifications
3. Varicella = fetal demise, growth restriction, cutaneous scars
Uncontrolled pregestational diabetes: causes a 4x higher rate of major malformations (cardiac, neural tube, renal, caudal regression)
obesity = higher rate of neural tube defects, cardiac malformation, oro-facial clefts, limb reductions, hydrocephaly
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What are the four different categories of congenital anomalies? what is a sequence? association?
1. Malformations = defect in morphogenesis (development) of an organ or structure; usually occurs before 10 weeks gestation (ie: hypoplasia (underdeveloped) organ/structure, cleft lip/palate, synactylyl)
2. Deformations = alterations in shape, position, or structure of a part of the body which was previously normally-formed; caused by MECHANICAL FORCES (intrinsic factors impinging physically on the fetus during development) EX: oligohydraminos, uterine malformation, causing a deformation
3. Disruptions = destruction of tissue that was previously normal, caused by factors EXTRINSIC to the developing structure; like due to a vascular insufficiency, trauma, teratogens; EX: amnionic bands (fibrous bands of ruptured amnion, that dont let fingers constrict)
4. Dysplasias = abnormal cellular organization within tissue resulting in structural changes. EX: protein structural changes in cartilage or bone resulting in skeletal dysplasia (ie: achondroplasia)
sequence = a pattern of multiple defects resulting from a single primary pathophysiological mechanism (EX: clubfoot and hyrocephalus can result from a neurla tube defect, Pierre Robin sequence)
Association = non-random occurrence of a combination of several anomalies occurring together more often than by chance alone; no specific sequence, syndrome or other etiology yet identified (EX VACTERL association)
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What is the difference between a major and minor anomaly?
Major = impairs normal body function and often requires surgery for management (ie: congenital heart defect, cleft palate)
Minor = have little or no surgical medical, or cosmetic significance (are of little or no clinical significance)
**but still need to consider them becuase they can serve as markers of altered morphogenesis and clues to patterns of malformation (because patterns of minor anomalies can suggest a syndromic diagnosis)
presence of multiple minor anomalies increases the likelihood of major anomaly (recognized or unrecognized), chromosome abnormality, or genetic syndrome
15% of all newborns have 1 minor anomaly
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Describe the critical period of morphogenesis
= exposure to teratogens at certain periods is more likely to cause birth defects
(teratogen = a drug, infection, or environmental agent that causes a birth defect)
Each organ system has a different critical period: ie; CNS = wks 3-16, heart = 3.5 wks to 6.5 wks; during this critical period, major defects are more likely
ex:
Thalidomide: exposure on day 30 = upper and lower limb defects
exposure on day 35 = only lower limb defects
