Genetic Disease Flashcards
What is Pathology?
Study of Disease
What is Morbid anatomy?
Large scale overview analysis of organs and visible disease. Diseased organs and tissues
What is Cellular / Histopathology?
Cellular level - microscopic study - histology - tissues, cytology - cells
What is molecular pathology?
Analysis of molecules and pathways within the cells - Application of molecular biology. Analysis of DNA, RNA, Protein, Lipids, sugars, metabolites
What is the Anatomical pathology?
Clinical pathology - macro and micro study. Observational
What is Aetiology?
Cause or origins of disease
What is pathogenesis?
The mechanism of disease development
Cyto means
cells e.g cytotoxicity
Dys means
Disordered eg dysplasia
Hyper means
More than normal eg hyperplasia
Hypo means
Less than normal eg Hypothyroidism
Leuko means
White e.g leukocyte
Meta means
A change of one state into another eg metaplasia
Neo means
New eg neoplasia
aemia means
Relating to the blood eg anaemia
cytosis means
Increase number of cells (in blood) leukocytosis
itis means
an inflammatory process eg appendicitis
oid means
Having resemblance to something eg epitheliod
oma means
Swelling or growth eg atheroma
opathy means
a diseased state eg adenopathy
osis means
a state or condition eg acidosis
penia means
a lack of something eg lymphopenia
plasia means
a disorder of growth eg anaplasia, metaplasia
Crohn’s Disease
Inflammatory Bowel Disease
Crohn’s Disease - histology
Disruption to organised epithelial structure - repeated inflammation / chronic
Formation of granulomas - areas of cell death, large scale cell death or necrosis
Aetiology of Crohn’s Disease
Genetic Susceptibility e.g Inherited genetic variants in NOD2
Gut flora/microbiota e.g Altered communities of commensal microbes
Environmental Factors e.g diet, NSAIDs, tobacco, increased hygiene
Host Immune Response e.g Overactive TH1 cells, underactive Treg Cells
Pathogenesis of Crohn’s disease
- Environmental trigger: infection, NSAID -> mucosal damage
- Damage/bacterial invasion -> acute inflammation and healing
- Genetic deficiency in innate immunity or barrier function genes -> unable to repair damage or kill invading microbes
- Uncontrolled immune responses to bacteria damage colon wall -> chronic inflammation and persistent infection
Genetic factors in disease of Crohn’s disease
Increased recognition of inheritance of gene(s) which predispose towards disease or modifies disease
What is Cystic Fibrosis?
Autosomal disorder
Mutation in CFTR gene
Thick mucous secretions - recurrent chest infection, lung damage
Environment factors in disease (Asbestosis)
Work related exposure to asbestos fibres, lung and pleural fibrosis. Mesothelioma (a malignant tumor of the mesothelium)
Cells respond to insult via…
Degeneration and atrophy
Apoptosis and necrosis
Inflammation
Regeneration, hyperplasia, hypertrophy
Dysplasia and neoplasia
Structural changes - gross changes, microscopic
Study of the disease process technique
Investigation of a mass/abnormal tissue or organ. -> Fine needle aspiration of biopsy tissue (retains architecture of cells)
Antigen expression
Stain tissue with labelled antibodies. Flow cytometry
Molecular genetic studies
Karyotype, FISH, DNA sequencing
Breast cancer pathology
Over expression of HER-2 protein -> Target of the monoclonal antibody - Antibody Herceptin
Her2 and Herceptin
Genetics: Her2 is a proto-oncogene. Her2-activated mechanisms of tumour cell growth
Pathology: Activation of Her2 in some breasts tumours. Identification of which patients are suitable for herceptin treatment since their tumours have Her2 gene amplification
Targeting therapy to a specific mutation in melanoma
B-RAF mutations in 50% of melanoma patients. B-RAF is a potent tyrosine kinase. Vemurafenib is a selective inhibitor of mutant B-RAF
What are pseudogenes
Genes that appear like they are genes for typical functional proteins but in fact code for non functional proteins
What advantage does polymerase chain reaction have over cloning?
It allows DNA to replicated much faster
Other than they typical Polymerase Chain reaction, what are the 2 other types of PCR and what are their advantages?
Reverse Transcriptase PCR which extracts RNA and then converts it to cDNA viathe reverse transcriptase enzyme allowing it to be determined what genes are actually being expressed in a tissue
Real time PCR, this involves the use of a marker allowing you to track the amount of DNA strands made which in turn allows you determine the amount of starting material which means you can gather some information about the gene expression in the tissue
What are the 3 steps in PCR
Denaturation, Anealing primers, DNA synthesis
What is the most important factor in the denaturation phase?
The temperature to which the solution is raised too must be determined by the enzyme used. 94-98C
What is the factor that needs to be regulated closely in the annealing phase?
The lowering of the temperature otherwise, the primers may join to sections of the DNA other than the target sequence resulting in the replication of unwanted material. 55-70C
What factor must be tightly controlled in the DNA synthesis phase of PCR?
The time allowed for elongation as this will control the length of the DNA fragment produced. 65-72C
What are the three types of Gel Electophoresis?
Polyacrylamind Gels, Agarose Gel, Pulse-field Gel Electrophoresis
What type of Gel electrophoresis uses single stranded DNA of less that 500 nucleotides?
Polyacrylamid Gels
What type of Gel electrophoresis is used for long DNA strands?
Pulse field gel electrophoresis
What is the name of the special nucleotides used for DNA sequencing?
Dideoxynucleotides
What 6 molecular techniques rely highly on hybridisation?
Dot Blot, Southern Blot, FISH, SNP arrays, Microarray, Array CGH
What is the purpose of FISH?
To identify potentially harmful mutations that have occured in the cell such as deletions
What are SNP arrays used for?
To look for point mutations in order to examine the relationship between this mutation and the observable phenotype
What is a microarray?
A microarray is a slate with lots of slots of immobilized known DNA sequences in the form of single stranded molecules, this then allows sample DNA to be washed across the slate so complementary basepair binding will be able to determine if any of the sequences are present
What is array CGH used for?
Creation of a karyotype for chromosomal analysis
What is the western blot (immunoblotting)
involves detection of polypeptides after size-fractionation. Size and amount but not location
What is the function of an Immunoassay?
Where antibodies are used to determine the quantity of a specific protein in a cell
What is Immunohistochemistry?
A test using immunoglobulins to check for the genexpression of the proteins in the cell
What is a GWAS
Genome wide association study - looks at thousands of nucleotide variants at once
What is an aCGH used for?
Used to scan a complete genome for imbalances. Can simultaneously detect aneuploidies, deletions and duplication.
What is a De Novo mutation?
Variation in DNA sequences results as a result of new mutations
What are the two main causes of mutations?
Endogenous mutations and mutagens
What is an endogenous mutation?
A mutation which is caused due to spontaneous errors in DNA replication and repair
What is a mutagen?
A chemical that induces damage to damage to DNA causing mutations to occur
What are the three types disorders that can arise from mutations?
Single gene disorders
Chromosome disorders
Complex/multi factorial disorders
What are the 6 types of chromosomal mutations?
Translocations,
Deletions,
Inversions,
Chromosome loss
Chromosome duplication
What are the two classes of substitution mutations?
Transition mutations and transversion mutations
What is a transition mutation?
When a purine is exchanged for another purine (A with G), or a pyrimidine is exchanged with another pyrimidine (C with T)
What is a transversion substitute mutation?
When a purine is replaced by a pyrimidine or vice versa (A to C) or (G to T) etc
What is the hotspot that differs from theoretical predictions of transversions being more common?
C to T mutation. Triggered by UV damage in cancer
What ate the three effect based classifications of substitution mutations?
Silent mutations,
Nonsense mutations,
Missense mutations
What is premature protein truncation?
When the effect of a mutation results in a stop codon appearing earlier than it should resulting a shortened protein that may or may not be functional
What are the two types of Missense mutations?
Synonymous where a similar type of amino acid is replaced resulting in little effect on function
Non-synonymous where the amino acid replaced is dissimilar so a serious effect on function can occur
Where are the three regions where pathogenic mutations occur?
The coding region
Areas affecting gene regulation
Mutations affecting RNA stability of splicing
What is a frame shift mutation?
When an insertion or deletion of a base pair results in a change in the reading frame usually causing premature truncation and severe deleterious effects
What are the three factors that affect the phenotype seen from a premature truncation?
The stability of the polypeptide product
The extent of truncation
The functional importance of the missing amino acids
What are the inheritance features of an autosomal recessive disease?
The carriers are asymptomatic, typically not seen in parents, males and females equally affected
Risk 1:4
What are the inheritance features of an Autosomal Dominant Disease?
Phenotype typically appears in every generation, Risk 1:2 at least one parent will display the phenotype
What are the inheritance features of a recessive x-linked disease?
Sons only inherit this from the mother, A male will pass on condition to all daughters, the incidence of disease is much higher in males
Disease is milder in women due to random X inactivation
What are the inheritance features of a dominant x-linked disease
Male parents have no affected sons but all daughters affected
Females typically have a less severe disease
More common for females to have the disease
What are the inheritance features of a Y linked dominant disease?
Disease can only pass from male to male
Only males are affected
All sons of affected male are affected
Trisomy 13-Patau Syndrome
3 chromosome 13. 95% of cases initiate a miscarriage. Dysmorphology, seizures, disability
Numerical abnormalities - Aneuploidies
Meiotic disjunction at Meiosis II (A) or Meiosis I (B)
Cri Du Chat syndrome or 5P monosomy
Monotone, small head, high palate, low ears, round ears.
Structural abnormalities of chromosomes
Due to errors in cell division when chromosomes align. Homologous recombination frequently causes deletions and duplications. A severe phenotype if multiple genes are involved.
Mutation in coding region
Majority of recorded pathogen mutations. Mutations disrupting RNA stability or splicing
Mutations affecting gene regulation or dosage
Promoter/enhancer region mutations - 1% of total.
What are the three types of genetic testing
Direct testing, Cytogenetic testing, Biochemical testing
What is direct testing?
Looking at the DNA or RNA that makes up a gene
What is a Cytogenetic test?
When the chromosomes are examined
What is biochemical testing?
When you assay for particular metabolites
What are the two uses of genetic testing?
Diagnostic and Predictive
What is the purpose of predictive testing?
So that potentially life style changes can be made in order to improve the health outcome
What are the two forms of genetic heterogeneity?
Locus Heterogeneity and Allelic heterogeneity
What is locus heterogeneity?
When multiple mutations can cause the same phenotype from different loci
What is allelic heterogeneity?
many mutations within the same gene can result in similar phenotypes
What is the concept of penetrance?
How likely it is that the gene will result in a phenotype as it can vary dramatically between individuals
What is expressivity?
The idea that a gene will manifest itself in different ways between individuals even if the gene is identical
What is the process of Prenatal Diagnosis?
when chromosomal and genetic analysis is achieved through either culturing cells from amniotic fluid or through analysis of hormones or proteins in the mothers blood etc
What are the non-invasive prenatal diagnostic methods?
Maternal Serum alpha-fetoprotein,
Maternal serum screen,
Ultrasonography
What does Maternal Serum alpha-fetoprotein test for?
Tests for levels of AFP which are elevated in neural tube defects and reduced in downs syndrome
What does the maternal serum screen test for?
AFP to detect neural tube defects (rise)/ downs syndrome (fall)
High levels of hCG and inhibin A are seen in downs syndrome
Oestriol is low in downs syndrome
What are the two methods of invasive prenatal diagnosis?
Amniocentesis
Chorionic Villus Sampling
How does the test of amniocentesis work?
A small amount of amniotic fluid is collected for studies
How does Chorionic Villus Sampling work?
Biopsy is performed on the villus area of the chorion either transabdominally or transcervically
What is the advantage of chorionic villus sampling as opposed to amniocentesis?
Results can be obtained at an earlier date
What is pre implantation diagnosis?
Several embryos are cultured and then are tested through FISH and other genetic techniques and only those found without mutations will be implanted
What are the two key things required to prove that a gene is linked to a disease?
Mutation screening and Functional proof
What is mutation screening?
Failure to notice the gene in a large sample of controls
The gene can be observed with a clear and relevant inheritance pattern in a pedigree chart
What is functional proof with regards to linking a gene to a disease?
There must be proof thorugh things such as computer modelling that the change the mutation has on the final product is important or relevant with regards to the original proteins function
What is the only currently avaliable treatment for those with genetic diseases
Primary prevention where changes in lifestyle or potentially some drug treatments may prevent onset of the disease
