Theme 1 - Intro to pathology and genetics Flashcards
____ is used for information transfer
RNA
____ is used for information storage
DNA
Why is RNA much more unstable than DNA?
RNA is transient (short lasting) because the -OH on C2 in RNA attacks the phosphodiester bond
What is the sense strand?
The strand that ends up in the mRNA
What is a synonym for the short arm of chromosome 7?
7p
What is a synonym for the long arm of chromosome 7?
7q
What are haploinsufficient genes? Which genes are haploinsuffient and which aren’t?
Genes that don’t tolerate the loss of one copy of the pair of chromosomes
All autosomes are haploinsufficient, sex chromosomes are not
What are pseudoautosomal regions?
homologous regions where identical genes are shared between X and Y
Are there more unique genes on the X chromosome or Y?
X chromosome
Very few unique genes on Y chromosomes
Give two features of mitochondrial DNA
Circular DNA not linear
Cytoplasmic DNA not nuclear
Maternal (oocyte inheritance)
What is satellite DNA?
Large blocks of repetitive sequences
What is the structure of a gene?
Lecture 1 page 6
What are the 5 steps for forming a protein?
- Transcription (RNA polymerase)
- Cleavage and Polyadenylation
- Splicing
- Translation
- Post translational modification
What is alternative splicing?
Most genes can encode more than one type of protein by using axons in different combinations
What are processed genes?
Intronless copies of other genes. Most are non functional
What is alphoid DNA?
- A type of satellite DNA found at centromeres
- required for assembly of the centromere
- repeat unit sequence shows chromosome specific sequence variation
What is a polygene?
A gene whose individual effect on a phenotype is too small to be observed, but which can act together with others to produce observable variation
What are the 5 classifications of genetic disorders
- Multifactorial - The interaction of multiple genes in combination with environmental factors e.g type II diabetes, ischaemic heart disease
- Single gene - mutation in a single gene (AD, AR, XL -mendelian inheritance) e.g cystic fibrosis
- Chromosomal - an imbalance or rearrangement in chromosome structure e.g aneuploidy, deletion, translocation
- Mitochondrial - mutation in mitochondrial DNA
- Somatic mutations - mutations within a gene in a defined population of cells that results in disease e.g breast cancer
What type of inheritance are myotonic dystrophy, Marfan syndrome and Huntington’s disease?
Autosomal dominant
What is penetrance?
The frequency with which a specific genotype is expressed by those individuals that process it, usually given as a percentage e.g Huntington disease by 80 years is 100% penetrance
What is incomplete penetrance?
Not all relatives who inherit the mutation develop the disorder e.g BRCA1 mutations 80% life time chance of developing breast cancer
What is expressivity?
Variation in expression - the extent to which a heritable trait is manifested in an individual
What is anticipation?
The symptoms of a genetic disorder apparent at an earlier age as it is passed from one generation to the next
This occurs in myotonic dystrophy and Huntington’s disease
What type of inheritance is CF, Haemachromatosis and sickle cell disease caused by?
Autosomal recessive
What type of inheritance is Duchenne Muscular dystrophy, fragile X syndrome, colour blindness and haemophilia caused by?
X-linked inheritance
What is lionisation?
- X-Inactivation
- the process of random inactivation of one of the X chromosomes in cells with more than one X chromosome
- occurs in every female in early embryogenesis
- leaves a Barr body
What are the two types of X linked inheritance?
XL Dominant (rare) XL Recessive
How would you go about drawing a family pedigree?
- record names and dates of birth
- marriage - joined directly
- sibling - stick up then joint
- arrow - probing
- spontaneous abortion = miscarriage
- double line = consanguineous couple
What are the ingredients for PCR?
- Primers (small, synthetic, “oligonucleotides”)
- nucleotides
- DNA polymerase
- Target DNA - usually genomic DNA isolated from a blood sample
What are the 3 steps of PCR?
- Heat denaturation (94*): separates strands
- Primer annealing (55*): primers anneal to single stranded templates
- Primer extension (72*): templates are copied to generate a new strand of DNA which is complementary to the target
What are the ingredients for Sanger sequencing?
- 1 primer
- nucleotides (dNTPs)
- DNA polymerase
- dye terminator nucleotides (ddNTPs)
How does Sanger sequencing work?
- denaturing, annealing, extension
- products separated based on size
- excited with laser and each dye gives off a different signal which is collected and decoded and shown on a chromatogram
How do clonal sequencing machines work?
- generate clones of our target DNA using PCR
- attach a primer and start sequencing clones
How do we work out which of the many variants are disease causing? (6 ways)
Variant prioritisation:
- Linkage based strategy - if families share the same variant, it is likely to be disease causing
- Homozygosity based strategy - look for a homozygous region e.g if there is consanguinity
- Double-hit based strategy - if its recessive and there is no consanguinity we can start filtering
- Overlap based strategy - used when looking for new mutations/ diseases. If we have two patients who have the same mutation and the same disease
- De novo based strategy
- Candidate based strategy
What is comparative genome hybridisation (array CGH) ?
- Sample DNA - green
- Reference DNA - red
- Red and green will mix together to give us yellow if there is the same proportions of DNA
- This shows any copy number variations in the genome
What is the best way to work out structural variation?
WGS - however, there is a large amount of variants
What are the 6 methods to detect copy number variation (CNV)?
- Whole genome
- G-banding
- Next-generation sequencing
- Microarrays (aCGH) - Targeted testing
- FISH
- MLPA
- QF-PCR
What are the 4 types of diseases of the blood?
- Conditions with two few blood cells e.g anaemia
- Conditions with too many blood cells e.g leukaemia
- Conditions with abnormal function of blood cells e.g sickle cell disease
- Disruption of blood clotting e.g thrombosis, haemophilia
What are some common allergy conditions seen in clinics?
- aeroallergies
- food allergies
- bee/wasp venom allergies
- idiopathic anaphylaxis
- chronic urticaria
- drug allergies
- desensitisation
What is an autopsy?
An examination of a body after death to determine the cause of death
What does the coroners and justice act 2009 state?
That a coroner has a duty to investigate death if:
- a coroner is made aware a body is in the area
- the cause of death is unknown
- the deceased died a violent or unnatural death
- the deceased died whilst in custody or state detention
What are some examples of ‘violent or unnatural deaths’?
- surgical/medical intervention
- drugs
- acute alcohol toxicity
- suicide
- car crash
- occupation related
What are the differences between the two types of post-mortem?
Coroners: -undertaken at request of coroner -family informed but do not need consent -most common Consent/hospital PM: -undertaken at request of doctors/ relatives -every part of autopsy needs consent -rare
State (in descending order) the qualifying order of relationships to be able to give consent
- spouse or partner
- parent or child
- brother or sister
- grandparent or grandchild
- niece or nephew
- stepfather or stepmother
- half brother/sister
- friend of long standing
What are the benefits of post mortem?
- For society - document accurate data about health of population, notification of communicable diseases, evidence in murder cases
- For medicine - education, identifying adverse effects of new treatment
- For relatives - aid grieving process, genetic testing, compensation claims in occupational deaths
What is sequelae?
a condition that is the result of a previous disease or injury
Explain how a tissue sample is prepared for a pathologist to examine
- Tissue arrives in labelled pots to the lab
- Tissue needs to be ‘fixed’, preventing breakdown
- specimen dissected and tissue processed
- Specimen cut and made into a slide. standard routine stain is H&E
What colours are haematoxylin and eosin?
Haematoxylin - purple
Eosin - pink
What does the 2004 human tissue act state?
A legislation that regulates activities related to the removal, storage, use and disposal of human tissue
What are the advantages and disadvantages of genetic testing?
Advantages: -early diagnosis -carrier testing (reproductive choices) -prenatal testing Disadvantages; -do you want to know you're going to get cancer sometime? -alzheimer's- no treatment -affecting insurance prospects
What is genetic counselling?
An education process to help affected or at risk individuals to help understand the nature of a genetic disorder, how it is transmitted ad the options for management and family planning
What is pharmacogenetics?
studying an individuals genetic make up in order to predict responses to a drug and guide prescription
What are pharmacogenomics?
analysing entire genomes, across groups of individuals, to identify the genetic factors influencing responses to a drug
KRAS mutation leads to what type of cancer?
pancreatic
colon cancer
non small cell lung cancer
What does the prefix -ana mean?
absence e.g anaplasia
What does the prefix -meta mean?
change from one state to another e.g metaplasia
What does the suffix -penia mean?
a lack of e.g thrombocytopenia
What does the suffix -cytosis mean?
increased number of cells e.g leukocytosis
What is meant by the suffix -ectasis?
dilation e.g bronchiectasis
What is CAR-T therapy?
modifying patients own T cells to allow them to recognise and attack their chancer cells
What is Sanger sequencing?
also known as “chain termination method”
method for determining the nucleotide sequence of dna
