Path - Genetics - Exam 3 Flashcards
How can single gene recessive/dominant disorders occur?
- Recessive:
- homozygous
- compound heterozygous - Dominant:
- heterozygous inherested
- de novo
Explain the standard patterns of mendelian inheritance
The modes of Mendelian inheritance are autosomal dominant, autosomal recessive, X-linked dominant, and X-linked recessive.
- Autosomal dominant: 50 percent chance of having an affected child with one mutated gene (dominant gene) and a 50 percent chance of having an unaffected child with two normal genes (recessive genes).
- i.e. huntingtons – CAG repeat in HD gene on chromosome 4 - Autosomal Recessive – need two carrier parents
- X-Linked Dominant: X-linked dominant traits do not necessarily affect males more than females (unlike X-linked recessive traits). The exact pattern of inheritance varies, depending on whether the father or the mother has the trait of interest. All daughters of an affected father will also be affected but none of his sons will be affected (unless the mother is also affected). In addition, the mother of an affected son is also affected (but not necessarily the other way round).
- X-Linked Recessive - X-linked recessive inheritance is a mode of inheritance in which a mutation in a gene on the X chromosome causes the phenotype to be expressed in males (who are necessarily hemizygous for the gene mutation because they have one X and one Y chromosome) and in females who are homozygous for the gene mutation, see zygosity.
Explain the cell biological basis of mendelian inheritance
- loss of function – much more common and more likely to be recessive
- gain of function - more likely to be dominant
- biallelic – both in phenotype.
- dosage sensitive or insensitive
- monoallelic – one will be silent
- dosage sensitive
- maternal or paternal
a) M/P Allelic Expression – blocks other allele
b) M/P Imprinting – blocking itself
For a loss of function mutation:
- heterozygotes for dosage insensitive gene will be phenotypically normal = RECESSIVE
- heterozygotes for dosage sensitive genes are haploinsufficient. = DOMINANT.
- can be increase or decrease in dosage
- i.e. Charcot-Marie-Tooth Disease – a duplication leads to 3 alleles. Nerve condition.
Haploinsufficiency is the phenomenon where a diploid organism has only a single functional copy of a gene – not enough protein is made.
What is the molecular basis of dominance?
- Gene is “dosage” sensitive
A. reduced gene dosage, expression, or protein activity (haploinsufficiency)
B. increased gene dosage - Gene mutation causes “gain of function”
A. Ectopic or temporally altered mRNA expression
B. Increased protein activity
C. Toxic protein alterations
D. Altered structural proteins
E. Dominant negative effects
F. New protein function
Define Penetrance and Expressivity:
Penetrance: – Proportion of individuals with a mutation that develop disease = no. of people with disease/no. of people with mutation.
I.e. BRCA1. Appears recessive, but is actually just low penetrance.
Expressivity:
Given that the disease is present, this refers to the degree to which the disease is expressed (number and severity of clinical features). Genetic and environmental factors.
Explain the biological basis for variable penetration and expressivity (modifiers of mendelian inheritance)
Variable penetration – gene is penetrative in some and non-penetrative in others. Expressivity – severity.
Why the difference?
- Stochastic (random probability of distribution, i.e. required ‘second hit’)
- environmental
- genetic – variants in other genes
- heterogenetic?
- Constitutional or mosaic?
I.e. Autosomal Dominant polycystic kidney disease (APKD).
What is Genotype-phenotype correlation?
- like between specific genetic mutation (genotype) and disease characteristics (phenotype)
- observed genotype-phenotype correlations can sometimes be explained by considering the specific effect that the genotype has on consequent or residual protein function
- genotype-phenotype correlation is not always observed – other factors affecting gene expression may interfere, i.e.:
- modifier genes
- chance effects
- environment
/What is Duchenne muscular dystrophy (DMD) and what causes it?
- x-linked, therefore hemizygous males and homozygous females
- wheelchair dependent by 12
- cause: mutations in DMD gene which encode dystrophin – structural protein – muscle cell membrane.
- Deletions that result in frame-shifts – produce unstable mRNA and no dystrophin protein
- If deletion occurs but no Frameshift – becker muscular dystrophy (milder)
/What is AATD and what causes it?
- alpha1-antitrypsin (protease inhibitor) deficiency
- increased risk of liver and lung disease
- due to:
a) missense mutations – results in ATT polymer formation (bad)
b) null alleles (nonsense or Frameshift) - AAT deficiency but no polymer formation so no risk of liver disease.
What is Mosaicism?
Post-zygotic mutations resulting in two or more genetically distinct cell lines.
If it arises later – more localized.
Phenotype will depend on the proportion of mutant cells.
Typically results in milder disease
EXAMPLE: Monosomy X (turner syndrome)
What is Mono-allelic and bi-allelic expression ?
biallelic – both in phenotype. A + a
- dosage sensitive or insensitive
monoallelic – one will be silent: A OR a
- dosage sensitive
- dependent on parent of origin OR random
- Dependent on parent of origin:
a) M/P Allelic Expression – blocks other allele??
b) *M/P Imprinting – blocking itself - Random:
c) X-inactivation
d) autosomal monoallelic gene expression
- How does dosage affect clinical outcomes? What is haploinsufficiency? Vs Dominant Negative?
For a loss of function mutation:
- heterozygotes for dosage insensitive gene will be phenotypically normal = RECESSIVE
- heterozygotes for dosage sensitive genes are haploinsufficient. = DOMINANT.
Haploinsufficiency is the phenomenon where a diploid organism has only a single functional copy of a gene and it is not tolerated:
- insufficient protein hypothesis
- balance hypothesis (imbalance of protein complex subunits)
Vs Dominant Negative – protein loss of normal function that interfered with normal function of other proteins
Gene functions that are inherently dosage sensitive:
- products that are rate-limiting
- competitive products that determine a developmental or metabolic switch
- fixed stoichiometry
EXAMPLE: autosomal dominant osteogenesis imperfect – heterozygous loss of function
a) mild – haploinsufficiency – no alpha chain
b) severe – dominant negative – abnormal alpha chain production
What is Imprinting?
Gene expression according to parent of origin:
- maternal: allele from mother switched off
- paternal: allele from father switched off
Reset each generation
EXAMPLE: Prader-Willi syndrome
What is X-inactivation?
Steps:
- X chromosomes counted
- Xist is transcribed from the future inactivated X chromosome/s
- Xist RNA then coats the body of the chromosome
- Expression of Xist is considered necessary and sufficient for inactivation; it recruits other silencing proteins
- usually random
- XCl ensures correct dosage of X-linked genes – some genes on X chromosome escape inactivation (pseudoautosomal regions, need 2n)
- Human females = ‘functionally mosaic’ as 2 different cell lines differentiated by which X chromosome is expressing
- EXAMPLE: DMD in females – some muscle fibers stain positively for dystrophin, others not.
What is skewed vs random X-inactivation?
Usually random, but may be skewed towards non-mutant chromosome, therefore could explain phenotypic variability in females.
EXAMPLE: DMD – mutant allele favored, therefore most cells mutant.
Explain characteristics of genetic variation in human populations (small and large scale genomic variants)
- low mutation rate, we each have 8-12 new variants
- most variants therefore inherited
- ~1:8 of all base positions in protein coding exome have been observed to vary
- many variants not functionally important and occur at minor allele frequencies (MAF) of >0.1% or 1% in the population. If >1% - benign variation (polymorphism). As opposed to pathogenic variation
Small scale (bp):
- substitutions
- base deletions
- base insertions
Large scale (kb-Mb)
- insertions
- deletions
- inversions
Genome scale:
- chromosomal aneuploidy (wrong number of chromosomes)
- polyploidy (wrong number of sets)
Explain factors determining genetic population structure
Hardy-Weinberg principle:
If population is:
- large (therefore genetic ‘random’ drift minimized)
- randomly mating
- no migration
- no selection pressures on a particular genotype
- mutation rate remains constant – new mutation rate = rate of mutation loss
Then, genotype frequency will remain unchanged from one generation to the next.
NAME:
- mutation rates
- selection
- migration
- random drift
Explain frequency of genetic diseases in populations
p + q = 1 (q = recessive allele frequency)
P2 + 2pq + q2 = 1
Explain history of uses and misuses of genetics in medicine
- genetic determinism
- genetic discrimination
- Future: genetic cloning – what is perfect?
Explain deviations from random mating - assortive mating; consanguinity
Assortive mating: individuals with similar genotypes and/or phenotypes mate with one another more frequently than would be expected under a random mating pattern.
Consanguineous union: second cousins or closer
Coefficient of inbreeding (F) = P (two alleles identical by decent)
For first cousins, spouses share 1/8 of genes, therefore progeny autozygous at 1/16 of loci, therefore F=0.0625.
Coefficient of Relationship (R) = proportion of genes that consanguineous spouses share as a result of common decent.
R = 2F, therefore R = 1/8 for first cousins.
Siblings: R = 1/2 and F = 1/4.
First: R= 1/8 and F =1/16
Second: R = 1/32 and F =1/64
What causes variation?
- DNA repair mechanism to contend with damage due to environmental agents
- DNA replication errors
- Homologous DNA recombination during meiosis
- Retrotransposition (regions of DNA that can copy and reinsert themselves somewhere else)
Compared to ‘reference genome’
What are the consequences of variation?
- no change in phenotype
- alternative phenotypes of no medical consequence
- disease susceptibility
- pathogenic
What is the difference between DNA damage and mutation?
Damage = physical change in structure of DNA
- endogenous or exogenous
Mutation = change in the base sequence of DNA
What factors can cause DNA damage?
a) exogenous factors, i.e.
- UV light
- ionizing radiation
- chemical agents - human mad (alkylating agents, heavy metals tobacco etc), chemo, medical exposures
b) endogenous factors, i.e.
- cellular metabolism
- replication errors
How does ionizing radiation induce DNA damage?
- Unique feature: clustered damage that can result in DSBs
- Degree/type of damage related to energy level:
a) low energy – isolated lesions
b) high energy – clustered damage - bystander damage to surrounding cells
- E.g. – Chernobyl. Increased frequency of chromosomal rearrangements in thyroid cancer – consistent with DSBs + subsequent repair resulting in fusion genes.
How do alkylating agents induce DNA damage?
Sources:
- certain industries
- smokers
- HCPs with chemo
Cause direct damage to DNA by adding an alkyl group to N and O atoms of purines and pyrimidines.
Consequences:
- base mismatches (i.e. methyl group to guanine)
- crosslinking
- strand breaks
What are the possible cell responses to DNA damage?
a) Cell cycle arrest – until repair
b) DNA repair – independent of cycle
c) Apoptosis – irretrievable damage
d) Transcription – induction of proteins and ncRNA involved in cell cycle, signaling and DNA repair)
What are the types of DNA damage?
- base loss
- base modification
- inter-strand X-links
- DNA protein C-links
- Strand breaks
What are the types and mechanisms of DNA repair?
- Single strand breaks
a) base excision repair
- glycosylases sense damage and break the sugar-base done.
- short patch or long patch
b) nucleotide extension repair
- corrects thymine dimers and other large chemical adducts
- i) global (anywhere in genome)
- ii) transcription coupled (at actively transcribed regions)
- removes large patch around error, so good for repair of bulky lesions
c) mismatch repair
- repairs mismatched and insertion/deletion loops that are created during DNA replications
- errors sensed by mismatch proteins
- nicks strand at closes GATC site to error
- Double strand breaks:
No template to use
a) non-homologous end joining
- G0 and G1 phase
- protein complexes assemble at broken ends and rejoin them using ligases, regardless of sequence
b) homologous recombination
- S phase (synthesis dependent – sister chromatid)
- single strand from damaged DNA invade the undamaged homologue, which is used as a template for repair
Where are DNA damage checkpoints in the cell cycle and how do they work?
- designed to detect DNA damage, replication errors and spindle defects and arrest cell cycle to facilitate repair
- checkpoint activation controlled by two master kinases: ATM and ATR
a) G2/M: unreplicated or damaged DNA?
b) G1/S: damaged DNA?
c) Intra-S: Damaged DNA, replication errors or incomplete replication?
Describe examples of diseases caused by defects of DNA repair and replication
Xeroderma Pigmentosum:
- acute susceptibility to UV light-induced skin cancer due to mutations in genes involved in nucleotide excision repair
Li-Fraumeni Syndrome:
- AD cancer predisposition syndrome
- Cancer predisposition syndrome
- Loss of function mutations in TP53 gene
Lynch Syndrome:
- AD cancer predisposition syndrome
- Increased risk of colon cancer + more
- Loff of function mutations in MLH1, MSH2, MSH6, PMS2
Appreciate how cancer therapeutics manipulate DNA damage and repair mechanisms
Mechanism:
a) direct DNA damage (i.e. radiation, alkylating agent)
b) inhibition of DNA replication/repair
Resistance can occur through increased DNA repair.
Negative consequences:
- drug toxicity, i.e. untargeted effects
- teratogenicity – affects growth of embryo/feotus
Briefly define different types of genetic testing
- Diagnostic – confirms diagnosis in an affected person, and may be prognostic as well
- Predictive – testing of unaffected individuals, usually in the absence of corroborating evidence, for:
- pre-symptomatic (will they develop the disease?)
- carrier
- prenatal/pre implantation - Screening – testing of individuals at population-level risk of disease (i.e. newborn), where there is an advantage of detecting conditions early
- Somatic – testing of tumor tissue (not germline) for:
- diagnostic
- monitoring
- choice of therapeutic agents - Pharmacogenetic – metabolism/drug toxicity
Be aware of appropriate sample sources for genetic testing
- Peripheral blood (whole blood)
- DNA extracted from WBCs
- preferred source of DNA for testing – plentiful and easy to access, minimally invasive - Buccal cells, urine, skin
- collected by swab inside cheek, early morning urine or biopsy
- used as a second source of DNA is suspicion of mosaicism,
- used for comparison of tumor DNA to constitutional DNA, OR
- used when it is difficult to get blood for some reason - Chorionic villus Sampling (placenta, 11-14 weeks) and Amniocentesis (amniotic fluid, 15-18 weeks)
- invasive, therefore risks of bleeding, infection, loss of pregnancy and incorrect results due to contamination with maternal cells
- used for chromosomal or molecular testing
- used for studying metabolic diseases - Cell free DNA (cfDNA)
- DNA not contained by membranes but floating free in circulation can be isolated
- Sources of cfDNA:
- haematopoeitic cells
- foetal cells
- tumor cells
- used for non-invasive prenatal screening – aneuploidies, can be used early in pregnancy
- used for tumor detection and monitoring – not widely available
