Mutations & Diagnostic Tools Flashcards
What is a mutation?
A mutation is a heritable alteration in a gene or a chromosome, caused by a change in the sequence of amino acids
Name a major source of ionising radiation.
Radon
Describe what a transposable element is, and define some of their characteristics.
A transposable element is a specific DNA sequence (usually containing more than 1 gene) that move (as a discrete unit) to a random site - they’re always contained within DNA and are never in a free form, and can insertion ally inactivate target genes
Are larger or smaller genes more susceptible to transposable elements?
Larger genes, as they have a greater area and usually are composed of a greater number of genes
What is the difference between a ‘micro’ and a ‘macro’ mutation?
A ‘micro’ mutation is a mutation of a single nucleotide base (insertion, deletion, substitution etc) while a ‘macro’ mutation is a mutation that describes changes on a chromosomal level
What is the difference between a transition and a transversion?
A transition is a nucleotide change to the same type of base (e.g. purine-purine or pyrimidine-pyrimidine), while a transversion is a nucleotide change to a different type of base (e.g. purine-pyrimidine or vice versa)
What mutation produces sickle cell anaemia?
A substitution mutation (missense) in the 6th amino acid on codon 7 from a glutamic acid to a valine
What is a mis-sense mutation?
A mutation that leads to a change in the amino acid in a polypeptide sequence
What is a silent/silence mutation?
A mutation that causes no change in the amino acid sequence coded for
What is a nonsense mutation?
A mutation that causes a (premature) stop codon
What is a frameshift?
A change in the nucleotide reading frame, by either a deletion (-1) or an addition (+1)
What is an inversion?
The rearrangement of a chromosome where a segment of it is reversed
Does an insertion of 3 nucleotides cause a frameshift?
No, as the frame will be read the same across the whole DNA sequence, only now there is a new codon inserted
What is the difference between a missense and a nonsense mutation?
- a nonsense mutation is a change in the nucleotide sequence where a stop codon is formed
- a missense mutation is a change in the nucleotide sequence where a different a amino acid is coded for
What is the difference between an oncogene and a proto-oncogene?
A proto-oncogene is a wild-type gene that regulates cell division, while an oncogene is a mutated form that is often unable to adequately regulate cell division (and as such is highly implicated in many cancers)
Why is a ‘gain of function’ mutation more likely to infer a dominant trait than a recessive trait?
If a ‘gain of function’ mutation was recessive there would be no gain in function as it would still be secondary to the dominant allele - a ‘gain of function’ mutation must therefore be dominant as to gain the function, the protein it codes for must still work, only in an enhanced way - if it wasn’t enhanced, either the other allele would attribute to ensuring the old proteins function, or the cell wouldn’t be viable and die (meaning there would be no gain of anything)
Are all mutations harmful?
No, as some may infer evolutionary advantages (the whole principle of evolution is based on genetic mutations)
How is nitrous acid formed? How does this cause genetic mutations?
It is formed from the nitrates and secondary amines formed in the stomach under acidic conditions -
What is cytogenetics?
The study of the genetic constitution of cells through the visualisation and analysis of chromosomes
Concerning leukaemia, why might cytogenetics be a useful diagnostic tool?
Various chromosomal translocations can infer the specific type of leukaemia an individual is suffering
What is aneuploidy? Give 4 specific examples.
Aneuploidy is an abnormal number of chromosomes, due to errors in cell division at meiosis:
- Down syndrome - a trisomy, an extra chromosome 21
- patau syndrome - a trisomy, an extra chromosome 13
- Edwards syndrome - a trisomy, an extra chromosome 18
- Turner syndrome - a monosomy, female missing an X chromosome
How would you write the Karyotype of a standard female in a chromosome report? What about a standard male?
- 46,XX
- 46,XY
How would you write the Karyotype of a male with Down syndrome in a chromosome report?
47,XY+21
What is unique about Turner syndrome?
It is the only monosomy that is still viable
What is amniocentesis? When should it be carried out? Is there a risk of miscarriage?
Amniocentesis is a test a female can undergo during pregnancy to check whether the embryo has a genetic disorder - it involves removing and testing a small sample of cells from the amniotic fluid, which surrounds the foetus in the womb - this is carried out after around 15 weeks, and gives a 0.8% chance of a miscarriage
What is chorionic villus sampling? When should it be carried out? Is there a risk of miscarriage?
Chorionic villus sampling is a test a female may be offered during pregnancy to check if the embryo has a genetic order - this involves removing and testing a small sample of cells from the placenta - this is carried out around 11-12 weeks after gestation, and gives a 1.2% of miscarriage
What is polyploidy? How would you write this in a chromosomal report?
Polyploidy is the gain of a whole haploid set of chromosomes, producing triploidy
- 69,XXX
What is the most common cause of polyploidy?
Polyspermy - fertilisation of an egg by more than one sperm (usually 2 sperm)
What percentage of pregnancies result in triploidy? What about tetraploidy?
Triploidy occurs in around 2-3% of all pregnancies (most of these embryos are not viable) - tetraploidy occurs in 1-2% of all pregnancies
How is the viability of an individual with aneuploidy determined?
By which chromosomes are involved in the non-disjunction event
What is the cause of aneuploidy?
A non-disjunction at meiosis, leading to an abnormal number of chromosomes in a gamete - one gamete will have an extra chromosome, while one will be missing a chromosome
What is anaphase lag?
Anaphase lag describe a delayed movement during anaphase, where a chromatid/chromosome fails to attach to the mitotic spindle, or its migration towards the pole is delayed, and overall fails to be included in the reforming nucleus
What does X activation ensure?
That across both males and female species, only one X chromosomes complement is active
In spite of their differences, what allows the X and Y chromosomes to join as a pair during cell division?
Homologous PAR1 and PAR2 regions
In Turner syndrome, what gene has been linked to the stunted growth seen in affected individuals?
The SHOX gene
List 2 observable features of a newborn baby with Turner syndrome.
- puffy/swollen feet
- excess skin at the back of the neck
What is mosaicism? How is it caused?
Mosaicism is the presence of 2 or more cell lines in an individual - it results from a non-disjunction event in mitosis at an early stage of development, forming a new converging cell line
What is a reciprocal translocation?
The transfer of genetic material between 2 non-homologous chromosomes
What is the difference between a balanced and an unbalanced gamete?
A balanced gamete has undergone a reciprocal translocation, but overall no genomic data has been lost from the genome - an unbalanced gamete has undergone reciprocal translocation, and has lost/gained part of the genome it, and so is missing DNA
What is a Robertsonian translocation?
A robertsonian translocation involves the fusion of 2 acrocentric centromeres, resulting in the loss of a chromosome (the genetic material will still remain however)
What 5 chromosomes are most susceptible to robertsonian translocations? Why?
Chromosomes 13, 14, 15, 21, & 22 - all these chromosomes are acrocentric, and have very short p arms
List 4 types of FISH probe. What stage(s) of cell division are they
Locus/gene specific probes, telomere probes, centromere probes, whole chromosome paints - the probes are usually used in metaphase (and sometimes interphase)
How many days may prenatal aneuploidy screening take? What chromosomes are FISH probes normally used for?
Up to 14 days - probes are usually designed for chromosomes 13, 18, 21, and the X & Y chromosomes, are these are more likely to result in aneuploidy
What is the difference between a germline mutation and a somatic mutation?
A germline mutation is one that occurs in gametes, can be passed on and effect all cells within the body - a somatic mutation occurs in a body cell and is not passed on to any offspring
Why are errors in RNA far more common than errors in DNA? Why is this not a huge problem?
RNA polymerases do not have a built-in proof-reading mechanism that DNA polymerases do - this isn’t a problem as many RNA copies will be produced, most of which will be correct - therefore, the majority of the protein produced will be correct an should have no major consequence to the cell - RNAs are also quickly degraded, so the mutated copy should be removed relatively quickly
Why is a mistake on DNA much more deadly than a mistake in RNA?
RNA is not inherited, and is not passed on to the next generation - therefore, making an incorrect copy of RNA will have less consequences than an incorrect copy of DNA, which is universal, coding for mutated RNA and a mutated protein that is lasting and permanent
Where do symptoms of mitochondrial disease mainly occur?
In organs that require large amounts of energy (and so have a high abundance of mitochondria) such as the heart, brain, and skeletal muscle
How may somatic mutations in mitochondria lead to a disease phenotype?
Mitochondrial DNA has a limited ability to repair itself, so somatic mutations tend to build up over time - a build up of these mutations has been linked with Alzheimer’s, Parkinson’s, and heart disease
Are the majority of germline cell mutations inherited or spontaneous?
Inherited
What event do insertion and deletion mutations lead to?
A frameshift
What stage of nuclear division are chromosomes usually in upon analysis?
Metaphase
What is the systematic sorting of chromosomes called?
Karyotyping
What type of phenotype will a carrier of unbalanced gametes display?
They will always display an abnormal phenotype
How would you write the karyotype of an individual who has had a reciprocal translocation in chromosomes 5 & 12 in a chromosome report? What about a reciprocal location in chromosomes 1 & 18?
- 46,XX,t(5,12)
- 46,XX,t(1,18)
Do deletions and duplications on a chromosomal level give rise to balanced or imbalanced gametes?
Imbalanced (as there is either more genetic information that usual or less genetic information as usual)
What would you write in a report describing abnormal Karyotype results?
- give the correct ISCN (46,XX)
- describe the abnormality in words
- balanced/unbalanced?
- monosomy/trisomy?
- relate the abnormality to clinical problems
What is uniparental disomy?
The presence of homologous chromosomes from a single parent lineage (ie an offspring as both chromosomes from either their mother or father)
What is the difference between isodisomy and heterodisomy?
An isodisomy is a uniparental disomy where an individual inherits an identical homologous chromosome pair from one parent - a heterodisomy is where an individual inherits 2 homologous chromosomes from one parent
In what stages of meiosis would a isodisomy and a heterodisomy occur?
An isodisomy would occur in meiosis II, while a heterodisomy would occur in meiosis I
What are the 4 mechanisms that generate uniparental disomy? What do they all require?
- trisomy rescue
- monosomy rescue
- gamete complementation
- mitotic error
- all require 2 separate abnormal events
Can a microarray detect balanced chromosomal rearrangements?
No - it can only check for imbalanced rearrangements
Can microarrays look for changes in DNA at a single nucleotide level?
No, as the signal they would give off would be too small
What amplification step is seen in most genetic analysis?
PCR
List 2 pro’s and 2 con’s of next generation sequencing.
Pros
- increased read length
- high throughput
Cons
- insufficient IT capacity
- lack of knowledge to fully interpret findings - lot of information, however don’t always understand what all this information means
What is non-invasive prenatal testing? List a pro and con of this technique.
Non-invasive prenatal testing involves analysing the maternal plasma, which contains around 5% foetal DNA (to 95% maternal DNA) - foetal DNA is isolated and analysed
- a pro includes the removal of any risk of miscarriage
- a con however includes that the process is technically challenging
How may no -invasive techniques be applicable to some cancers?
90% of metastatic cancers have circulating cancer cells and cell free DNA - the levels of circulating tumor DNA in plasma may be used as a diagnostic tool
What is the difference between the exome and genome?
The genome comprises all the genetic information of an organism, while the exome comprises all the coding portion (exons) of an organisms genome
What does whole exome sequencing analyse?
The coding portion of an organisms genome (it’s exome)
At birth, what is the approximate number of primordial germ cells in males and in females?
In males there are around 4 million primordial germ cells, while in females there are around 1 million primordial germ cells at birth
Why do primordial germ cells only begin to differentiate into spermatozoa in males at puberty?
They are only needed when oocytes are available to fertilise (in females of the same age)
How does the mutation rate of male gametes compare to female gametes?
The mutation rate in male gametes is 5x higher
What percentage of pregnancies result from chromosomal abnormalities (structural or numerical)?
75%
Why do male gametocyte mutations increase with age? What about female gametocyte?
- in males, spermatozoa is continually made - the gametocytes have been exposed to mutagens for a much lone time than in younger males
- although a similar explanation may be true, the real answer for mutations in female gametocytes is actually unknown
What are 3 possible outcomes if a very early embryo was exposed to mutagens?
- abortion (death)
- teratogenesis (developmental abnormalities in embryo)
- born with a cancer
In general, what do recessive mutations do?
Recessive mutations cause loss of function and usually effect biochemical pathways
In general, what do dominant mutations do?
Dominant mutations cause gain of function and generally cause structural abnormalities
What disorder does a mutation in type I collagen often result in?
Osteogenesis Imperfecta
What are cystine residues commonly associated with?
The formation of disulphide bonds (bridges)
Why may a patient display both abnormal and normal types of a protein?
They may be heterozygotes
What is the difference between an endogenous and an exogenous mutagen? Give an example of each.
An endogenous mutagen is one produced by the body (DNA replication errors) - an exogenous mutation is a mutagen that is an external agent from the environment (UV light)
What is the most toxic form of DNA damage?
A double stranded break
What is an apurinic/apyrimidinic site?
A site on the DNA helix that contains neither a purine or pyrimidine - this can act as a mutagen and propagate cancer
What are the 4 main DNA damage response steps?
- signal
- sensor
- transducer
- effector
In regards to DNA damage, what can the checkpoints after G1 and G2 provide?
Time for the cell to check and repair any abnormal DNA
What is senescence?
Permanent arrest of the cell cycle
Define DNA replication stress.
DNA replication stress is defined as inefficient replication that leads to replication fork slowing, stalling, and/or breakage
What 3 factors may contribute to replication stress?
- defect in the replication machinery
- factors may hinder the replication fork progression
- defects in the response pathways
What is slippage? Where does it normally occur?
A for, of mutation where DNA polymerase inserts or deletes less/extra nucleotides into a sequence - this often happens at microsatellites where there are tandem repeats of DNA
What is nucleotide misincorporation? What is the most common cause of this type of mutation persisting?
Simply where DNA polymerase inserts the wrong base - an abnormal endonuclease activity will allow these mutations to persist
What are 2 widely considered consequences of DNA double strand breaks?
- genomic mutations - cancer
- cell growth inhibition - ageing
Name a disorder associated with trinucleotide tandem repeats? What is the tandem repeat?
Huntington’s disease - due to CAG repeats (35-121 repeats)
What does an excessive accumulation of mutations in a cell lead to?
Cancer
What adverse effect may single strand annealing lead to?
Deletion of part of the DNA sequence
What is a key regulator that is mutated in many cancers?
p53
What does the evolution of therapy resistance suggest? What is clonal expansion?
The heterogeneity of cancers means that continually mutating cells produces a certain cell line which develops resistance to cancer treatment - this leads to clonal expansion, selecting for this particular clone (by killing of other cancer cells), and propagating its existence
How may the DNA damage response shape the evolution of a cancer?
The DNA damage will kill off certain cell lineages in a cancer and leave others, shaping the cells who thin the cancer which will shape how it acts and grows
How may a lot of current cancer treatment seem highly paradoxical? How may this be an issue?
They themselves induce DNA damage in an effort to kill cancer cells - this may be a problem if the radiation begins to damage excessive amounts of healthy DNA in healthy cells, who’ll may produce more cancer and/or propagate them further
What is a holiday junction?
A cross-shaped structure that forms during genetic recombination, where 2 DNA double-strands become separated into 4 strands during homologous recombination (crossing over) in meiosis
At birth, how many primordial germ cells in males compared to females?
At birth there are around 4 million primordial germ cells in males, while in females there are around 1 million primordial germ cells
In females, when do primary oocytes undergo prophase Impf meiosis?
At birth
What is spermatogenesis? When does it occur?
Spermatogenesis involves the differentiation of primordial germ cells in which spermatagonia are transformed into spermatozoa - this occurs around the time of puberty
Why do progenitor germ cells only begin to differentiate into spermatozoa at puberty?
They are only needed when oocytes are available to fertilise
What features would allow a germ cell mutation to be heritable?
- it would not be lethal to the gamete
- it would not impair gamete function
- it would not be lethal at fertilisation
- it would allow the production of a viable adult with normal reproductive capacity
What is the Philadelphia chromosome? Where does it arise, and what specifically does it cause?
The Philadelphia chromosome develops due to a reciprocal translocation of genetic material between chromosome 22 and 9, causing fusion of the BCR-ABL1 genes - this codes for a tyrosine kinase that is permanently on, causing the cell do divide uncontrollably - this abnormality leads to leukaemia
What is the Philadelphia chromosome? Where does it arise, and what specifically does it cause?
The Philadelphia chromosome develops due to a reciprocal translocation of genetic material between chromosome 22 and 9, causing fusion of the BCR-ABL1 genes - this codes for a tyrosine kinase that is permanently on, causing the cell do divide uncontrollably - this abnormality leads to leukaemia
