Human Genetics Flashcards
Limitations of cytogenetics
- only large abnormalities seen
- labour intensive
- specially trained staff
Reasons for cytogenetics referral
Infertility
Recurrent miscarriage
Primary and secondary amenorrhea
Amniotic fluid for advanced maternal age
4 main samples used in cytogenetics
- blood
- amniotic fluid
- chorionic villus
- bone marrow
3steps in the sample processing
- culture
- harvest
- analysis
What is used to arrest cells in metaphase?
Colcemid
What does the potassium chloride do?
Hypotonic, so cells swell
Name 6 main types of structural chromosome abnormalities
- deletion
- ring chromosome
- duplication
- isochromosome
- inversion
- translocation
Two types of deletion
- terminal
- interstitial
Types of staining
- Giemsa banding
- reverse banding
- telomeric banding
- centromere banding
- NOR banding
- quinacrine banding
4 things needed to name a band
- chromosome number
- arm symbol
- region number
- band number within that region
Use of FISH
- microdeletions/duplications
- aneuploidy
- haematological disorders
Why is FISH useful for blood samples?
- rapid, specific and accurate
- not necessary to have good metaphases
- able to combine several techniques and detect different nucleic acid targets in the same preparation
- greater number of signals can be counted
Advantages of using FISH for haematological disorders
- can detect a number of translocations
- can be used to monitor minimal residual disease after treatment
- can detect gene amplifications associated with an adverse prognosis for certain tumours
- can be used to confirm engraftment
Describe a dual-fusion assay
- utilizes large probes that span 2 break points
- optimal for detection of low levels of nuclei possessing a simple balanced translocation
- greatly reduces the number of normal background nuclei with an abnormal signal pattern
Describe break-apart assays
- useful in the evaluation of genes known to have multiple translocation partners
- differently coloured probes hybridize to targets on opposite sides of the breakpoint of the affected gene
Definition of monogenic disease
Diseases that result from modifications in a single gene occurring in all cells of the body
What may influence pedigrees in monogenic disorders?
- reduced penetrance
- variable expression
- anticipation
Define reduced penetrance
When a person carrying a gene mutation manifests no signs
- AD ectrodactyly
Define variable expression
The way in which the disorder manifests differs between affected individuals
- tibial aplasia
Define anticipation
Presentation worsens with successive generations
What does MECP2 do?
It is a multifunctional epi genetic modulator
- binds to forms of DNA that have been methylated
- condenses the chromatin structure and form a complex with histone deacetylase or directly block TFs
- May function as a transcriptional activator
- highest levels of expression in neurons
What type of inheritance is Rett syndrome?
X linked dominant
Stages of female Rett syndrome
- normal period
- sudden decrease in interaction and slowing of progress
- rapid developmental regression
- deterioration slows, hand stereotypies, more interaction
- loss of ambulation, spasticity
Features of PPMX syndrome
- severe ID and psychosis
- parkinsonian features
- pyramidal signs
- macro-orchidism
Features of MECP2 duplication syndrome
- hypotonia
- severe ID
- epilepsy
How to explain Rett syndrome
- X inactivation pattern
- depends on type of mutation (nonsense worse than missense)
- depends of site of mutation
- other genes can also be responsible
Possible functional modifiers in Rett syndrome
- alterations in the dopaminergic system
- oxidative stress burden
- mitochondrial dysfunction
Types of microarrays
- DNA
- protein
- tissue
- cellular
- chemical compound
- antibody
- carbohydrate
Types of DNA arrays
- expression chips
- array CGH (comparative genomic hybridization)
- mutation/ genotyping microarrays
Features of stargardt macular degeneration
- autosomal recessive
- juvenile onset
- mutations in ABCA4 gene
Pros and cons of ABCR400 microarray
- molecular diagnosis is unequivocal
- raw microarray data cannot be delivered to patients without verification
- chips only detect mutations at known points
Definition of an adverse effect
Undesired events causing harm to patients, not by the underlying disease, but as a consequence of examination, treatment or care
Definition of pharmacogenetics
The study of the role of inheritance in individual variation in response to xenobiotics
Role enzymes in metabolizing drugs
- modify most of the chemicals to which humans are exposed
- convert them into more readily water-sol metabolites to be removed from the body
- some reactions lead to formation of highly reactive intermediates
What can genetic polymorphism lead to
- abolished enzyme activity
- reduced enzyme activity
- increased enzyme activity
- no change
Aspects of pharmacokinetics
- absorption
- distribution
- metabolism
- excretion
Aspects of pharmacodynamics
- receptors
- ion channels
- enzymes
- immune system
Problems with poor metabolizers
- too slow drug metabolism
- too high drug conc at standard dose
- high risk for adverse reactions
- no response from pro drugs
Problems with ultra metabolizers
- too rapid drug metabolism
- no drug response at standard dose
At what levels can genetic variation occur?
- chromosomal
- DNA sequence
- nucleotide
What is a haplotype?
A combination of alleles at adjacent locations on a chromosome that are inherited together
Types of mutations
- missense
- synonymous
- nonsense
- sense
- frame shift
- mutation affecting polyA
- splice site mutation
- unstable mutations
Factors affecting a pedigree
- disease may not have shown phenotypically or person deceased prior to onset
- spontaneous mutations
- family size (small shows fewer)
- variable gene expression
- protective effect on mutation carrier
Define detoxification
Conversion of lipid soluble chemicals into water soluble metabolites
Define metabolic activation
Converting inert compounds into highly reactive molecules
What is special about CYP?
- single CYP can metabolize many compounds
- many CYPs metabolize same compound at different sites
- many CYPs metabolism same compound at same site at different rates
Factors influencing drug metabolism
- age
- lifestyle
- genetic polymorphisms
- health status
Definition of genetic polymorphism
The recurrence within a population of 2 or more genetic variants of a specific trait in such proportions that they cannot be maintained by simple mutation
How are effects of polymorphisms measured?
- phenotypically
- metabolic ratios
Possible effects of polymorphisms
- increased enzyme induction
- altered enzyme activity
- altered enzyme stability
- altered enzyme specificity
Genetic determinants of HIV progression
- genetic diversity of HIV
- host genetic susceptibility
- host pharmacogenetics
Why is pharmacogenetics considered in HIV?
- the prevalence of toxicity
- long term treatment
- complexity of multi drug treatment
Possible issues with pharmacogenetics
- takes time to test
- uptake by clinicians
- clinical utility
Define xenobiotics
A foreign compound/chemical found in an organism that is not normally produced or expected to be found in that organism
Process of using a microarray
- take a sample
- isolate the mRNA
- make DNA copies of mRNA and tag each sample with a different colour
- apply labelled DNA to microarray
- scan microarray
What of expression chips do? (Microarray)
Determine the volume at which genes are expressed
What do array CGHs do?
Determines genomic gains and losses (copy number variations)
