Genetic diseases Flashcards
1
Q
What does low penetrance of a genetic variant imply?
A
Only a few patients with the gene have a phenoytpe associated with that gene.
2
Q
How large in base pairs does an insertion need to be to be considered a copy number variant?
A
> 50 base pairs
3
Q
What is a nonsense variant?
A
One that introduces a stop codon
4
Q
What is a frame shift variant?
A
An insertion or deletion that shifts the codon reading frame
5
Q
What is nonsense decay?
A
Describes that destruction of RNA due to the presence of a nonsense variant.
6
Q
What is a missense variant?
A
One that causes the insertion of different residue in the protein, which may lead to misfunction
7
Q
What is a splice altering coding variant?
A
Variant that causes a change to specific splicing marker on the RNA, leading to it being incorrectly spliced and the resultant protein being dysfunctional.
8
Q
How are metabolic conditions usually inherited?
A
Autosomal recessive. This is because the there is usually redundancy for the production of enzymes involved in metabolic function, and one copy of the gene is usually adequat to prevent disease.
9
Q
Why is it that negative autosomal dominant diseases exist?
A
They exist where the proteins that are produced by the health and vairant DNA need to work together to acheive their function. An example is osteogenesis imperfecta where the affected colagen gene prodcues proteins that need to make a triple helix with the healthy collagen gene, leading to no functional collagen.
10
Q
What is male and female drawn as in a pedigree?
A
Circle is female. Square is male.
11
Q
What’s the diferenec between variabel expression and incomplete penetrence?
A
Variable expression means that all those with the effected gene (s) show the phonetype with varying degrees of severity, but incomplete penetrance means that only some gene variant affected infdividuals will have no evidence of the disease.
12
Q
What is gonadal mosacisim?
A
When the parents gonadal cells have a mutation that the other cells of their body do not.
13
Q
What is somatic mosacisim?
A
Where some of the cells in a person have variant, but other cells do not.
14
Q
What is pseudodominance?
A
It’s where the carrier frequency is so common that a truly autosomal recessive disease appears autosomal dominant.
15
Q
Why might you only see an X-linked condition in females? E.g. Rett sydnrome.
A
When the condition is lethal in males.
Where the condution is Turner Syndrome.
Note that X-inactivation may lead to females having an X-linked disease phenotype, but males will have this as well.
16
Q
What is anticipation?
A
It’s the slowly increasing severity of the phenotype as the generation number increases.
17
Q
Heteroplasmy is important for mitochondiral disease. What is this, why is it important?
A
The number of mitochondria with mutations is the defining factor that will influence the likelihood disease.
18
Q
What are the three survivable autosomal aneuplodies?
A
21, 18 (edwards), 13 (Patau)
19
Q
What is non-disjunction in meiosis?
A
The failure for chromatid pairs to separate, leading to double the genetic material being left in the daughter cell, causing aneuploides.
20
Q
Segmental aneuploides have have what type of inheritence?
A
Autosomal dominant
21
Q
What is a point mutation?
A
Single change in a base pair
22
Q
What is a point mutation referred to if it changes the amino acid sequence?
A
A missense mutation.
23
Q
If a missense mutation results in an amino acid change for a new amino acid of similar biochemical properties, it is referred to as what?
A
A conservative missense mutation. If the new amino acid is biochemically very different is is called a ‘non-conservative’ missense mutation.
24
Q
What DNA change occurs in sickle cell anaemia?
A
Nucleotide triplet in the beta-globin chain in haemoglobin is changed from CTC to CAC, which causes a glutamate to valine switch. This causes misfolding of beta-globin, haemoglobin, and a deformed resulting cell.
25
What are the two bases that seem to appear in trinucleotide repeats with great frequency?
Cytosine and guanine.
26
What is the gene called that has CGG repeats in it and leads to fragile X-syndrome if the there are too many repeats?
Familial mental retardation 1 (FMR1)
27
What's a nonsense mutation?
Introduction of a stop codon
28
What is difference between the word hereditary and congenital?
Hereditary means obtained from ones parents. The word congenital means born with. So huntington's disease is hereditary but not congenital, and congenital syphillis is congenital but not hereditary.
29
If a single gene leads to multiple effects- what is this referred to?
Pleiotropism
30
What is called when multiple gene defects producing the same phenotypic outcome?
Genetic heterogeneity
31
How does variable expressivity differ from penetrance?
Variable expressivity describes traits that different but attributable to the same dominant mutation. Penetrence refers to the degree to which the one trait is expressed as the result of a dominant mutation.
32
What does the term - dominant negative - allele mean?
It infers that not only is the resultant gene non-functional, that it also interferes with the function of normal genes. E.g. one mutated collagen chains leads to dysfunction of the other two as collagen needs to be a trimer to function.
33
What do Huntington disease, neurofibromatosis, myotonic dystrophy, tuberous sclerosis, polycystic kidney disease, familial polposis coli, hereditary spherocytosis, von willebrand disease, marfan syndrome, EDS, osteogenesis imperfecta, achondroplasia, familial hypercholsterolaemia, and acute intermittent porphyria all have in common?
Autosomal dominant conditions
34
Is incomplete penetrence more common in autosomal dominant or recessive disorders?
Autosomal dominant.
There is usually comoplete penetrence when the two defective (autosomal recessive) genes are present.
35
Inherited enzyme mutations tend to produce diseases with dominant or recessive inheritence?
Recessive
- in their hetrozygous form, recessive enzyme deficiencies are clinically silent because the normal gene makes enough enzyme to complete the physiological role of that enzyme.
36
What is the best explination for the absence of Y-linked inheritence?
Almost all the genes specific to the Y chromosome are involved in spermatogenesis. Mutations causing dysfunction here lead to infertility, and so cannot be inherited.
37
How is glucose-6-phosphate dehydrogenase deficiency (G6PD) inherited?
X-linked.
38
How do you explain females expressing traits associated with X-linked diseases?
Either homozygotes for the gene, or more likely, have a degree of X-inactivation leading to expression of the mutant allele.
39
What do haemophilia A/B, Duchenne muscular dystrophy, agammaglobulinaemia, Wiskott-aldrich syndreom, diabetes insipidus, LEsch-Nyhan syndreom and Fragile X syndrome all have in common?
All X-linked
40
What's special about vitamin D-resistant rickets and Alport syndrome?
The are both X-linked DOMINANT, conditions. X-linked conditions are almost always recessive.
41
What do thalasaemias, osteogenesis imperfecta, hereditary spherocytosis and muscular dystrophies have in common?
All caused by inherited mutations that cause defective STRUCTURAL proteins.
42
What gene is mutated in Marfan syndrome? How does it cause disease?
The fibrillin-1 gene FBN1.
Fibrillin-1, along with FBN2, are key components of microfibrils found in the ECM. When defective, the ECM is weak. This is problematic for connective tissues in the lens, the large arteries, the heart. Furthermore, TGF-beta availability is governed by microfibrills. In the presence of functional fibrillin-1 containing microfibrils, TGF-beta is sequestered in the ECM, and only available on injury to facilitate repair. In Marfan's, the TFG-beta is more available and leads to inflammatory and ECM augmenting activity that adds to derfomity of structures (e.g. the mitral valve) in Marfan's disease.
43
What is Marfan's syndrome type 2?
It's the phenotype of Marfan's that involves mutations in TGF-beta type 2 receptor that prevent it being sequestered, and allow it to be overactive as is seen in Marfan's syndromem type 1.
44
What are the morphological, syndromic, features of patient's with Marfan's syndrome?
Tall
Long extremites compared to height
Tapering fingers and toes
Long headed (dolichocephalic)
Bossing of the bones of the face, particularly the supraorbital ridge
Kyphosis or scoliosis
Slipping of the dorsal or lumbar vertebrae
Chest deformity (excavatum or cavinatum)
45
What is the ocular disease that is almost only seen in patients with Marfan syndrome?
Ectopia lentis - the subluxation or dislocation (usually upward and outward) of the lens.
It is due weakening of the ciliary zonules (the fibrous structures the hold and pull on the lens)
46
What are the two most prevalent cardiovascular abnormalities affecting patient's with Marfan's disease?
Mitral valve prolapse (40-50% of patients), and dilation of the ascending aorta due to cystic medionecrosis (necrosis of the media of the aorta) +/- aortic dissection.
47
What is the mechanism of mitral valve porlapse in Marfan's syndrome?
Defective microfibrils make up the cordae tendinae of the mitral valve. They become lax, leading to prolapse +/- regurgitation. Note that similar things can occur to the tricuspid valve, and rarely the aortic valve.
48
What are the subcategories of EDS?
Classic
Hypermobile (no genetic association)
Vascular
Kyphoscoliosis (most common)
Arthrochalasia
Dermatosparaxis
49
What do the vascular EDS subtypes result from?
Mutations in genes effecting the production of type III collagen.
50
What type of collagen is typically effected in classical EDS?
Type V collagen (usually defects in COL5A1/2)
51
Familial hypercholesterolaemia is caused by defects in what gene?
The gene encoding the low-densisity lipoprotein receptor (most common - about 85% of cases). A minority of cases are caused by apolipoprotein B-100 (the ligand for the LDL receptor in the LDL particles) affecting 5-10% of cases, and gain of function mutations in proprotein convertase subtilisin/kexin typ 9 (1-2% of cases) - PCSK9.
52
How does LDL-receptor dysfuntion lead to the phonetype seen in familial hypercholesterolaemia?
LDL receptor is responsible for binding to LDL/apoliporprotein B particles and removing them from circulation. This lowers circulating cholesterol and reduces the likelihood of the formation of atheromas.
53
What is the role of PCSK9 in normal people?
It regulates the expression of LDL-receptors. When active PCSK9 causes LDL receptor recycling and reduces it's ability to sequester LDL cholesterol from the circulation. PCSK9 inhibitors therfore enable the LDL receptors to function for longer and clear more cholesterol.
54
Outgoing cholesterol carrying particles from the liver, after initial acquistion of cholesterol from the gut as chylomicrons, is in what form?
Very low densisity lipoprotein - more triglyceride and proteain (Apo B/C/E) than LDL.
55
What happens to VLDL particles (with ApoC, B, E in situ) when it reaches its target tissue (e.g. muscles, adipose, solid organ)?
It undergoes lipolysis and the remanent intermediate-density lipoprotein goes into circulation. ApoC is lost in the process. ApoB and E remain.
56
What happens to the remanent Intermediate-density lipoprotein (IDL), the waste product after VLDL is used in tissue?
About 50% is taken up by LDL receptor (binds to ApoB/E, so also called the ApoB/E receptor) mediated transport into the liver for recycling back into VLDL. The remainder then is processed further by target tissues into LDL. The ApoE is lost, and most of the triglyerides are gone by this point.
57
In triglyceride and cholesterol trafficking to and from the liver, VLDL becomes IDL beomces LDL. What happens to the ratio of cholesterol to triglycerides accross this journey? What happens do the protein components of these molecules?
Triglycerides:Cholesterol ratio decreases from VLDL -> IDL -> LDL. So to do the surface proteins Apo B/C/E -> ApoB/E -> ApoB
58
IDL and LDL binding to LDL-receptors (binding ApoB/E or just ApoB respectively) leads to update of the lipids into a lysosome. How does the cholesterol escape the lysosome?
Two proteins facillitate the transfer NPC1 and NPC2.
59
What action does have cholesterol have in hepatocytes after being brought in as LDL/IDL and escaping the lysosome?
Suppresses furthre cholesterol synthesis by inhbition of HMG CoA
Activates acyl-coenzyme:cholesterol acyltransferase - this favours esterification and storage of excess cholesterol
Suppresses the synthesis of LDL receptors, thus protecting the cell from excess LDL uptake that could lead to steatosis.
Upregulartes expression of PCSK9, which further reduces the LDL receptor recycling and leads to their destruction.
60
Like CF, familial hypercholesterolaemia can be due to different parts of LDL gene of to genes that effect its processingl. How the LDL receptor malfunctions is classified as class I through VI. What do the classes represent?
Class I - failure to synthesis LDLR
Class II - failure to transport LDLR out of the ER
Class III - failure of LDLR to bind LDL or IDL properly
Class IV - failure to cluster around clathrin coated pits so can't endocytose.
Class V - failure to be able to be recycled
Class VI - failure to localise to the basolateral hepatocyte membrane
61
How do HMG-CoA receptors work to lower serum cholesterol?
They reduce intra-hepatocyte cholesterol synthesis, which in turn increases the number of LDL receptors on the basolateral surface of hepatocytes, increasing the ability to remove plasma LDL and IDL.
62
How do organelles receive the intra-organelle proteins they need?
They get them from lysosomes that are formed and then fuse with the organelle, dropping off the needed proteins.
63
What is the significance of mannose-6-phosphate groups being attached to the terminal ends of proteins processed in the golgi apparatus?
Binding of mannose-6-phosphate groups serves as an 'address' label recognised by specific resceptors found on the inner membrane of the golgi. Lysosomal enzymes now with their M6P groups bind these receptors and are then sequestered from the other secretary proteins being produced in the golgi. Small vessicles take these lysosomal enzymes to fuse with and deliver them to lysosomes.
64
Defects in lysosomal enzymes can lead to accumulation of their unprocessed or partially processed substrate. What happens to cells full of lysosomes with undigested substrate?
The lysosomes are unable to perform their critical cell homeostasis roles. Noteably they are unable to fuse with the autphagosomse to perform autophagy, and especially mitophagy (recycling of mitochondria). This leads to accumulation of inefficient and leaky mitochondria, which are inefficient at making ATP, produce reactive O2 species, and can trigger intrinsic apoptosis. Accumulation of other protein products is also slowed leading to accumulation of damaging substances such as alpha-synuclein and Huntingtin.
65
In Tay-Sachs disease, what enzyme is missing?
hexominidase A
66
The missing enzyme in Tay-Sachs disease is hexominidase. What does this enzyme do?
It usually degrades ganglosides - lipid/carbohydrate structures. The particular class of langliosides degraded by hexaminidase is called GM2. The disesae phenotype is the result of accumulation of this substance, and is so also called GM2 gangliosidosis.
67
What is are the enzymes involved in degradation of GM2 gangliosides that can be defective to give rise to GM2 gangliosidosis?
Hex A (alpha and beta subunits from different genes) and Hex B (2x beta subunits) and an activator enzyme GM2A are all needed to effecively breakdown GM2 Ganglioside. Therefore, a mutation in alpha hexosaminodase (Tay Sachs disease) beta subunit, or GM2A can all cause symptomatic gangliosidosis.
68
Which population in Tay-Sachs disease particularly high in?
Ashkenazi Jews. 1 in 30.
69
Which organ appears to be most affected by hexosaminidase deficiency?
Hexosaminidase deficiency leads to accumulation of GM2 gangliosides (lysosomal storage disease). Becuase these lipid/carbohydrate structures are most prevalent in nervous system tissue, this is where they accumulate cand cause the most damage and symptoms. This includes brain and eye dysfucntion.
70
What are 'whorled configurations'?
A whorl is a spiral. Under electron microscopy, whorled configurations are classic findings in the lysosomes of neurons of of Tay Sachs disesae and other gangliosidoses.
71
What is the significance of a retinal cherry red spot?
This is a classic finding on opthalmoscopy that appears in the retina in Tay-Sachs and Niemann Pick disease pts.
72
Niemann-Pick disease (A and B) is a lysosomal storage disease. What substance is accumulated in these patients?
Sphingomyelin.
73
What is the enzyme that is mutated in the lysosomal storage disease Niemann-Pick disease (types A and B)?
Spingomyelinase. Leads to an accumulation of sphingomyelin.
74
Which population have a particualarly high concentration of Niemann Pick disease?
Ashkenazi Jews
75
What are Zebra bodies?
These are the typical appearence of sphingomyelin clumps seen under electron microscopy when looking at the cells of patients with Niemann-Pick disease.
76
Why do patients with the lysosomal storage disease Niemann-Pick (A and B) and up with organomegally?
Defects in sphingomyelinase lead to accumulations of lysosomal sphingomyelin in all cells, but this particuarly impacts on circulating phagocytes, notably monocytes. These accumulate in the spleen and cause massive splenomegaly.
77
How is Niemann-Pick C different to types A and B?
A and B are diseases of sphingomyelin accumulation. Type C is caused by defective NPC1 or NPC2 enzyme fucntion - both are required for normal trafficking of lysosomal cholesterol into the cytoplasm of hepatocytes and other cells that have taken it up via LDL receptors.
78
What are the interesting adult medicine clinic features of Niemann Pick disease type C?
Can present as a chronic neurological disease. Ataxia, vertical supranuclear gaze palsy, dystonia, dysarthria and psychomotor regression.
79
What is themost common lysosomal storage disease?
Gaucher disease
80
What is the problem occuring in lysosomal storage disease, Gaucher disease?
Autosomal recessive disease with mutations in the gene encoding glucocerebrosidase. This normally cleaves glucose from ceramide. When defective, glucocerebrosides (byproduct of glycolipid breakdown from RBCs and WBCs primarily) accumulate in phagocytes, and in some rarer subtypes in the CNS. There are 3 subtypes.
81
What are the 3 subtypes of the glucocerebrosidosis lysosomal storage disease called Gaucher disease?
Type I (99% of cases) - no CNS involvement. Splenomegaly and skeletal issues (bone accumulation leading to erosive lesions) are prominent. Long lived.
Type II - infantile acute cerebral form. Death at early age.
Type III - intermediate between type I and II. Tend to present with progress central nervous system disease beginning in adolescence or early adulthood.
82
Gaucher cells (distended phagocytic cells) ar pathomneumonic of Gaucher disease (lysosomal storage disease). Where are mos likely to be found?
The places phagocytes coalesce - spleen, liver, bone marrow, lymph nodes, tonsils, thumis, peyer patches.
83
What is different in appearance about Gaucher cells (glucocerebroside accumulation) compared to other affected lysosomal storage disease cells?
Rather than vacuolated, fibrillary type cytoplasms that loos like crumpled tissue paper.
84
What common neurodegenerative disease is strongly associated with glucocerebrosidase gene variants and concomittant Gaucher disease?
Parkinson's disease.
85
Mucopolysaccharidoses are what type of diseases?
Lysosomal storage diseases originating from mutations in the genes encoding the lysosomal enzymes needed for degradation of mucopolysaccharides. There are 11 subtypes each with their own associated enzyme deficiency.
86
What are the typical morphylogical features of patients with mucopolysaccharidosis? (lysosomal storage disease)
Coarse facial features
Clouding of the cornea
Joint stiffness
Intellectural disability
-brain lesions
Hepatosplenomegaly
Skeletal deformities
Valvular lesions
Subendothelial arterial depositis
87
What enzyme is responsible for glycogen breakdown in lysosomes?
Acid alpha-glucosidase (AKA acid maltase)
88
Which enzyme is mutated in the lysosomal glycogen storage disease Pompe disease?
Acid alpha-glucosidase (AKA acid maltase).
89
What is the most prominent feature in patients with the glycogen lysosomal storage disease Pompe disease?
Cardiomegaly from accumulation of cardiomyocyte lysosomal glycogen.
90
Are glycogen storage diseasea all lysosomal storage disease?
No, deficicencies in the cytosolic enzymes involved in glycogen synthesis and breakdown in the cytoplasm can be defective and lead to glycogen accumulation not in the lysosomes.
91
What are the three types of glycogen storage disease?
1) Hepatic type (aka hepatorenal von Gierke disease type 1) - glucose 6 phosphatase deficiency - hepatoreanomegaly and hypoglycaemia.
2) Myopathic type McArdle disease - muscle phosphoylase deficiency - glycogen accumulation in skeletal muscles - failure to raise blood lactate, cramps, CK elevated, myoglobinuria, normal life span
3) Lysosomal - pompe - acid alph-galactosidase defect - Massive cardiomegaly, skeletal muscle issues heptamogealy
92
How are karyotyping studies done?
A mitotic spindle inhibitor freezes the cell in metaphase allowing for the condensed chromosomes to inspected and counted. They are arranged by length, and stained with banding stains (e.g. Giemsa or G stain for G banding), to establish their pair.
93
On karyotype notation: what does Xp21.2 indicate?
X chromosome
P (short) arm
Region 2
Band 1
Sub-band 2
Regions and bands are identified on the basis of Giemsa (G) staining.
94
What does aneuploidy mean?
Number of chromosomes in the cell is not a multiple of 23
95
What are the most common causes of aneuploidy?
Non-disjunction and anaphase lag
96
What is non-disjunction?
The gamete (post meiosis) with one more or one less chromosome participates in fertillisation leading to the abnormal number.
97
What is anaphase lag?
One homologous chromosome in meosis, or one chromatid pair in mitosis, lags behind is left out of the nucleus. The resulting cells are one with monosomy and the other with normal number of chromosomes.
98
Which chromosomes are most commonly involved in mosaicism?
The sex chromosomes. E.g. Turners syndrome from 45X/47XXX mosaicism
99
What does 46 XY del (16)(p11.2p13.1) mean?
A pt has cells with 46 chromosomes, XY sex chromosomes, with a deletion on the P (short) arm of chromosome 16 between region 1, band 1, sub band 2 and region 1, band 3, sub band 1.
100
What does 46, XY, r(14) mean?
It means that the patient has 46 chromosomes including X and Y sex chromosomes, and that the patient has had a deletion even at both ends of chromosome 14 leading to it forming a ring. Usually catastrophic.
101
What is meant by a paracentric or pericentric inversion (with regards to karyotyping)?
Paracentric invesrsion refers to 2 breaks occuring on one end of a chromosome cleaving a piece of genetic material that doesn't include the centromere. This is flipped and then re-inserted into the same gap in the chromosome.
Peri-centric inversion is the same, but the breaks are on either side of the centromere, and the inverted material involves the centromere.
102
What is an isochrome?
Sometiems, the long or short arm is lost. This results in duplication of the remaining arm, which new chromosome forming with 2 of the same arm about the centromere (either two short or 2 long arms). One compatible with life is i(X)(q10), where only the long arm of X is present, twice.
103
In a balanced translocation, no genetic material is lost as part of one chromosome swaps places with part of another chromosome. Why can these still be prolematice?
When gamete production occurs, some of the gametes will likely be left with insufficient genetic material from one of the chromosomes and too much from the other.
104
What is meant by 46,XX,t(2;5)(q31;p14)?
Pt has 46 chromosomes, including 2x X chromosomes. There is a balanced translocation from chromosome 2, long arm, region 3, band 1, to chromosome 5, short arm, region 1, band 4.
105
What leads to a robertsonian translocation?
Breaks on either side but near the centromere of 2 acrocentric chromosomes. The small centre pieces fuse and is usually lost. The long remaining pieices als fuse, greating a big long chromosome.
106
What is most common cause of trisomy 21?
Meiotic nondisjunction
107
Does meitoic nondisjunction leading to aneuploidy usually arise in the sperm or ovum?
Ovum. Maternal ages is the greatest risk factor.
108
How can a Robertsonian translocation lead to down syndrome?
Translocation of the long arm of chromosome 21 onto another acrocentric chromosome in the parent, which is then passed into the gamete, leads to a zygote with additional copy of genes from chromosome 21.
109
What are typical morphological features of a Down syndreome child?
Flate face
Oblique palpebral fissures
Oblique epicanthic folds
Simian crease
Gap between 1st and 2nd toe
110
What are the common morbidities of pts with Down Syndrome?
Intellectual disability
40% have congenital heart disease - AV septal defects mos commen, then VSDs, ASDs and tertralogy of Fallot.
Leukaemia (20 fold risk ALL, 500 fold risk of AML)
Alzheimer disease
immune dysfunction
111
What is trisomy 18 called?
Edwards syndrome
112
What are the morphological features of babies born with Edwards syntrome? (trisomy 18)
Low set ears
Prominant occiput
Micrognathia
Short neck
Overlapping fingers
Limited hip abduction
Rocker-bottom feet
113
What are the common morbidities associated with Edwards syndrome?
Renal malformation
Congenital heart defects
Intellectual disability
Very rarely do these children live beyond the first year of life
114
What disease is associated with trisomy 13?
Patau syndrome
115
What are the morphological findings of patau syndrome?
Micropthalmia
Microcephaly
Polydactyly
Cleft lipe and palate
Rocker bottom feet
116
What are the morbity causing features of Patau syndreom (trisomy 13)?
Cardiac defects
Renal defects
Intellectual disability
Death usually before the age of 1
117
What are the features of 22q11.2 deletion syndrome?
Variable. But often congenital heart defects, palate defects, facial dysmorphis, developmental delay, T-cell immunodeficiency (due to thymic hypoplasia), hypocalcaemia (due to parathyroid hypoplasia), psychotic diseases, ADD.
118
What is lyonisation?
X-inactivation. Originally described by Mary Lyon, thus Lyonisation.
119
When does X-inactivation happen?
About 5.5 days into embryogenesis. It happens at random, so all 'normal' females are mosaics of their mothers and fathers X chromosomes.
120
What is the Barr body?
Little clump of inactive X chromosome seen during interphase.
121
What does XIST doe?
Its the gene that produces long non-coding RNA, and facilitates X inactivation. It is present on the X-chromosome.
122
Are lyonised X chromosomes completely transcriptionally silent?
No. About 30% of p arm genes and 3% of q arm genes remain functional. This is obviously important, as patients with Turners have disease traits.
123
When is X-inactivation (lyonisation) reversed in normal women?
Oogenesis - to provide an active X chromosome for the ovum.
124
What is ther karyotype of patients with Klinefelter syndrome?
46 + n X(n>1)Y
E.g. 47XXY, 48XXXY and so on
125
With regard to sex chromosome number diseases, what is generally associated with increasing number of X chromosomes?
Increasing risk fo intelectual impairment.
126
What is the most common cause of hypogonadism in men?
Klinefelter syndrome
127
What are the common morbidities associated with Klinefleter syndrome?
Type 2 diabetes
Congenital heart disease (esp. mitral valve prolapse)
ASDs and VSDs
Osteoporosis
Extragonadal germ cell tumours
Autoimmune disease, SLE and breast cancer
128
What happens to hormones in Klinefelter patients?
Higher oestrogen
Higher FSH
Lower testosterone
129
Why is thought that androgen function is less in patients with Klinefelter syndrome?
Shorter CAG trinucleotide repeats in the androgren receptor lead to greater androgen sensititivity. The androgen receptor is encoded on the X chromasome. Whichever X chromosome has the fewest CAG repeats is inactivated by XIST though, so less sesnsitive androgen receptors end up being prioritised.
130
What are the most common causes of turner syndrome?
Meiotic non-dysjunction 57%
Structural X chromosome abnormalities 14% (isochromosomes, ring formation, deletions)
Mosaic 29% (45X/46XX, 45X/46XY, 45X/47XXX, 45X/46Xi(X))
131
What are the clinical features of Turner syndrome?
Internal:
Congenital heart disease
Coarctation of the aorta
Increased aortic dissection risk
Bicuspid aortic valve
Amenorrhea
Hypothyroidism (autoimmune)
Type 2 diabetes
NAFLD
Morphological
Neck webbing from intrauterine cyctic hygroma
Peripheral lymphoedema at birth
Failure to develop normal secondary sexual characteristics
Short stature
Obestity
Wide spaced nipples
Pigmented naevi
132
What are streak ovaries seen in Turner syndrome?
Unfortunately the lack of a second X chromosome is devastating to fertility. All oocytes are lost by age 2, and the ovaries becoms fibrosed streaks. In a sense, menopause occurs before menarche in Turner patients.
133
What is the SHOX region of the X-chromosome? Why is it relevant to Turner, Klinefelter syndreome, and X-inactivation?
It is conserved region between the X and Y chromosomes, and so it escapes X-inactivation in normal women to ensure balanced availability of its substrates. Its used to pair the X-Y chromosomes for cell replication in me. However, in Turner's syndrome the lack of second SHOX region leads to a gene dose deficiency, and in Klinefelters it leads to a dose excess.
134
When does triplet repeat expansion occur in the inheritence of fragile X?
During oogenesis in the mother.
135
When does triplet repeat expansion occur in the inheritence of Huntington disease?
During spermatogenesis in the father
136
What do fragile X syndrome, friedreich ataxia and myotonic dystrophy all have in common?
All triplet repeat inherited diseases involving NON-CODING genes.
137
What do spinobulbar muscular atrophy, Huntington disease, dentatorubralpallidoluysian atrophy, and spinocerebellar ataxia (1/2/3/6/7) have in common?
All triplet repeat inherited diseases involving CODIND DNA.
138
What amino acid seems to be involved frequently in inherited triplet repeat diseases involving coding DNA regions?
CAG - glutamate. Leading to polyglutamine regions in the resultant proteins. These case toxic gain of function for the protein.
139
What is the most common genetic cause of intellectual disability in males?
Fragile X syndrome.
140
What are the male fragile X morphological features?
Long face
Large mandible
Large everted ears
Large testicles (macroorchidism)
High arch palate
Behavioural challenges
- ASD, ADD
Epilepsy
Internal
Mitral valve prolapse
Hyperestensible joints
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Fragile X is a recessive X-linked disease associated with mutations in FMR1 gene. What is unusual about its inheritence pattern despite the above?
There is a very high proprotion of 1) carrier males (20%) who are clinically normal, 2) affected females (presumable to to inactvation, up to 50%). Another abnormality is 3) anticipation (increasing generational risk or worse disease earlier in life).
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How many CGG tandem repeats are typically seen in patients with symptomatic Fragile X?
Usually in excess of 200. (200-4000 in Robins)
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Where is FMRP, the protein produced by the triplet repeat affected gene FMR1 in fragile X syndrome, most prevalent?
Brain (involved in neurotransmitter availability - loss of neuroplasticity in fragile X pts) and testes (macro-orchidism)
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In fragile X syndrome, what happens after the tandem repeat number expands that leads to the symptoms? How does this differ to a disease of the same gene (FMR1) fragile X-associated tremor/ataxia?
The excess CGG repeats in fragile X syndreom patients FMR1 gene leads to gene silencing and loss of expression of FMRP, involved in neuroplasticity. In fragile X-associated tremor/ataxia, the CGG repeats continue to be transcribed and the mRNA transcipts are toxic - forming intranuclear inclusions in the central and peripheral nervous system leading to cell death and dysfunction.
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What body system to mitochondrial diseases usually impact?
Often the neuromuscular system due to their increased need for ATP.
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What type of disease is Leber hereditary optic neuropathy?
Mitochondrial disease. Neurodegenerative.
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What does maternal imprinting refer to?
Silencing of the maternally inherited allele of a gene.
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Where does imprinting occur?
In the parents, during gametogenesis. It's then passed on to the offspring.
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What's interesting about Prader-Willi and Angelman syndrome?
Both are autosomal dominant diseases caused usually by deletions at the same location, but the disease phenotype depends on which parent the affected allele was derived. If the allele with the deletion was from the father, the child will have Prader-Willi disease, if from the mother, they will have Angelman syndrome. The reason for this in different imprinting within men and women of the same chromsomal location. The imprinting doesn't overlap, so in the presence of two normally imprinted alleles (maternal and paternal), there is no issue.
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What is uniparental disomy?
When both copies of a gene are obtained from the same parent. Discovered in patient's with Prader-Willi who had apparently no deletions at the location of Prader-Willi/Angelman related genes. In these patients, they had 2 copies of these chromosomes from their mother, so maternal imprinting of both gene copies had led to the phenotype.
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What is defective imprinting?
When the imprinting is detrimental and not as it should be to maintain function. An example is when Prader-Willi is present due to maternal imprinting of the paternally inherited allele.
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How is it possible that unaffected parents could have two affected children with an autosomal dominant condition?
Gonadal mosacisim
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Which sequencing type (sanger or next generation) is more sensitive to detecting mutations in a milleu of cancer cells?
NGS
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What is single base primer extension used for?
Good for looking for known clinically signficant single base pair point mutations e.g. BRAF V600 mutation
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How does restriction fragment length analysis work?
If the site of an insertion, deletion, frameshift mutation is known relative to a specificed restriction site, then restriction enzymes can be used to detect the mutation by measuring the resulting DNA fragment lengths.
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What is amplicon analysis useful for?
Triplet repeat diseases. If the repeat is so long that it can't be done with PCR, then southern blot may need to be done.
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What is Fluorescence in Situ Hybridisation (FISH) used for?
FISH probes (up to 200 kilobases) are introduced to interphase located nuclear material that has been primed to accept the probe. The specific probe will bind to the chromosomal region of interest. If a translocation is suspected, the probes for the areas concened will light up on different chromosomes. They are also used to detect other structural or numerical chromosome abnormalities.
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Is FISH fast or slow?
Very fast. Can be used to rapidly detect mutations in acute promyelocytic leukaemia t(15:17) before giving vitamin A
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If you would like to do FISH to identify a suspected chromosomal abnormality, but aren't sure which one you are looking for, what technology should you use?
Cytogenomic array. You run 'normal' DNA and 'sample' DNA across the same plate of probes from accross the genome. Correct or incorrect binding leads to variable levels of dye production at each site. Lasers are used to measure any differences in dye production from the sample and the control. If the sample dye production is substanitally different, it suggests a mutation at the site corresponding to the probe.
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Why is single nucleotide polymorphism analysis helpful in the diagnosis of Prader-Willi syndrome?
In cases of unparental disomy (both alleles from the same parent - mother n Prader-Willi), the SNP analysis can identify loss of heterozygosity it the site of interest. The SNPs will be the same in both chromosomes.
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What is the use of micro and minisatellites of DNA?
For challenging to identify or sequence sections of DNA for hereditary diseases, the coinherited chromosomally adjacent mini/microsatellite regions can be used as surrogate markers for the presence of a mutant gene. Used in the testing for the presence of the autosomal dominant kidney disease mutationin PKD1.
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How is sodium bisulfate helpful in testing for fragile X syndrome?
In fragile X syndrome, the disease phenotype arises from the absense for FMRP following hypermethylation of the pahtologically long triplet repeat region of the FMR1 gene. Sodium bisulfate is able to change the cytosines to uracils IF they are unmethylated. Therefore, a sample of fragile X syndrome pt would have retained cytosines throughout the silenced FMR1 gene following treatment with sodium bisulfate, whereas a wild type DNA sample would have uracil throughout the FMR1 gene.
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What is cDNA?
Complementary DNA (cDNA) is representative of only the exons after postranscriptional modification (e.g. splicing). It is derived by trascribing a section of chromosome, then using the resultant mRNA to reverse transcribe back to DNA (more stable). This is then labelled cDNA.
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When might cDNA be diagnostically helpful?
Some mutations have very large intronic regions about them, making them difficult to process or find quickly with DNA based investigations. Allowing transcription to mRNA, then converting back to DNA, will remove the introns and make it easier to process. Further looking for splicing errors is fast if comparing cDNA to DNA of the same region.
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