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GiM 2 + Critical numbers Flashcards

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1
Q

What kind of variable is Height?

A

Numeric continuous

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2
Q

What kind of variable is Sex?

A

Categorical nominal

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3
Q

What kind of variable is number of children?

A

Numeric discrete

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4
Q

What kind of variable is severity of symptoms eg. Absent, mild, severe

A

Categorical ordinal

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5
Q

What kind of variable is types of degree?

A

Categorical nominal

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6
Q

What graph is an appropriate way to visually display the frequency distribution of continuous variables?

A

Histograms

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7
Q

What is the statistical value below which half of the distribution lies

A

Median

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8
Q

What can standard deviation be loosely described as?

A

a measure of the average distance of all of the data values from the mean.
- A useful measure of spread when there is a large amount of data

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9
Q

What are the lower and upper quartile?

A

Lower quartile = the median of the lower half of the data

Upper quartile = the median of the upper half of the data

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10
Q

What method can you use if a gene is too big for PCR?

A

Southern blotting

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11
Q

Why is fragile X mutation in FMR1 unsuitable for PCR and what should you use instead?

A

fragile X mutation in FMR1 gene is repetitive tract of (CGG)n sequence

GC-rich regions are difficult to PCR!

use Southern blotting

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12
Q

Which variants in apo-lipoprotein E (APOE) confer increase in susceptibility to Alzheimer’s or a protective effect?

A
  • E4 haplotype confers increase in susceptibility

* E2 haplotype confers a protective effect

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13
Q

When is the non-disjunction of chromosomes most likely to occur?

A

Meiosis I (80-90%)

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14
Q

What risk to gametogenesis increases with maternal age?

A

Aneuploidy

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15
Q

What are the trisomies of Down’s, Edwards and Patau’s?

A

21, 18, 13

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16
Q

What is Turner’s syndrome?

A

45 X

Phenotypically female
Short stature, no puberty, infertility

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17
Q

What is Klinefelter’s syndrome?

A

47 XXY

Phenotypically male - mostly undiagnosed
May be infertily, hypogonadism, gynaecomastia
Adults may have long legs and arms

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18
Q

What are the three origins of triploidy?

A

Digyny - 2N (egg) + N (sperm)

Diplospermy - N (egg) + 2N (sperm)

Dispermy - 1 egg + 2 sperm

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19
Q

What does the maternal genome focus on in comparison to the paternal genome?

A

Maternal genome for foetus

Paternal genome for placenta

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20
Q

How does a molar pregnancy occur?

A

Haploid sperm fertilises an empty egg

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21
Q

What can mitotic non-disjunction cause in the early embryo?

A

Mosaicism

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22
Q

What are the two types of chromosomal translocations?

A

Reciprocal - break & exchange
5-10% phenotype risk and reproductive risk

Robertsonian- whole arm fusion, only on acrocentrics (13, 14, 15, 21, 22)
no phenotype risk but reproductive risk

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23
Q

What are the two types of chromosomal inversions?

A

2 breaks, rotation, then rejoining

Pericentric - beaks on either side of the centromere

Paracentric - inversion on one arm (one side of the centromere)

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24
Q

In what direction is DNA and RNA synthesised?

A

5’ - 3’

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25
What is pseudogene?
Is from the same gene family as a functional gene but is mutated and no longer functional?
26
How are gene families created?
Duplication and Divergence
27
What are processed genes?
Intronless copies of other genes | mRNA undergoes Reverse transcription and reintegration
28
What is Alphoid DNA
A type of satellite DNA found at centromeres 171-bp repeat unit Repeat unit sequence shows chromosome-specific sequence variation
29
What is chromosome-specific alphoid DNA useful for?
identifying individual human chromosomes using probe hybridisation
30
What may be missed by PCR-based screening methods if heterozygous?
Large insertions or deletions eg. Duchenne muscular dystrophy (deletions) Charcot-Marie-Tooth disease (duplication)
31
Which nucleotide sequences signal the beginning and end of an intron?
GT = end of exon, beginning of intron AG = end of intron, beginning of exon
32
What are one third of point mutations caused by?
Hypermutability of CpG dinucleotides - Methylation - Deamination CG -> TG - Mismatched repair
33
What trinucleotide repeat expansion is seen in Huntington's disease and spinocerebellar ataxias?
Polyglutamine repeats (CAG)
34
What trinucleotide repeat expansion is causative in Fragile X syndrome?
CGG repeat expansion befor Fragile X mental retardation 1 (FMR1) gene on the X chromosome Normal: n = 5 - 50 Unstable pre-mutation: n = 50 - 200 Full mutation: n > 200
35
What syndrome is caused by a 22q11.2 deletion?
Di George syndrome 1 in 5,000 - Congenital heart defects - Learning difficulties
36
Describe Achondroplasia
Short stature Rhizomelic limb shortening Foramen magnum compression/ hydrocephalus 1 in 20,000 Autosomal dominant- often new mutation 80% Risk increases with paternal age
37
Describe Beckwith-Wiedemann syndrome
``` 1 in 10,000 Large tongue Ear pits/ creases Exomphalos Hemihypertrophy Neonatal hypoglycaemia Increased risk of Wilms tumour (nephroblastoma) ```
38
Describe Kabuki syndrome
``` 1 in 30,000 Persistent fetal finger pads (96%) Learning difficulties Congenital heart disease (50%) Poor growth Hearing impairment Cleft palate Premature breast development ```
39
What are Blaschko’s lines and what may cause them?
Mosaicism Hypo- &/ or hyper-pigmented patches
40
What is Peutz-Jeghers syndrome?
Otherwise known as hereditary intestinal polyposis syndrome
41
What is Treacher-Collins syndrome?
``` 1 in 50,000 Autosomal dominant Very variable Cleft palate Hearing impairment Downwards slanting eyes and absent cheekbones ```
42
What is Waardenburg syndrome?
``` 1 in 250,000 Sensorineural hearing impairment Iris heterochromia Premature greying White forelock Areas of skin hypopigmentation ```
43
What is William's syndrome?
7q11 deletion ``` 1 in 20,000 Elf like appearance Learning difficulties ‘Cocktail party’ speech Congenital heart disease Hypercalcaemia ```
44
What are three examples of whole genome testing?
G-banding Next generation sequencing Microarrays
45
What are three examples of targeted genetic testing?
Fluorescent in situ hybridisation (FISH) Multiplex ligation dependent probe amplification (MLPA) QF-PCR and qPCR
46
What are some applications of FISH
``` Copy number imbalance Aneuploidy Confirmation/ clarification of G-banding Confirmation of array CGH Identifying specific abnormalities in cancer ```
47
What are the advantages of array CGH?
Early diagnosis -1st line test, ” High resolution = increased diagnostic hit rate Greater accuracy of location/size of imbalances Information on relevant genes
48
What are the disadvantages of array CGH?
- Dosage changes only – not balanced rearrangements or mutations - Low level mosaics not detected - Non-pathogenic & uncertain pathogenic changes detected - Needs good quality DNA
49
What test is used for prenatal aneuploidy detection?
Quantitative fluorescent PCR (QF-PCR) If abnormal then G-banding DNA extraction from amniotic fluid or chorionc villi PCR amplification – primers from chromosomes 13, 18, 21, X and Y aneuploidy =>2 markers with abnormal dosage
50
What is a Philadelphia chromosome and what is it seen in?
t(9;22) )(q34.1;q11.2). Found in CML (also in some AML and ALL)
51
How does a Philadelphia chromosome occur?
Reciprocal translocation between chromosomes 9 & 22, Juxtaposition of BCR gene and ABL1 gene Creates a fusion gene BCR-ABL1 Codes for a hybrid protein - a tyrosine kinase signalling protein that is "always on" = uncontrolled cell division
52
What are the clinical features of Angelman syndrome?
Facial dysmorphism: - Prognathism, wide mouth, drooling - Smiling/laughing appearance Mental handicap: - Microcephaly - Absent speech Seizure disorder Ataxic, jerky movements ''Happy Puppet children''
53
What are the clinical features of Prader-Willi syndrome?
``` Infantile hypotonia: Feeding problems, Gross motor delay Mental handicap Male hypogenitalism/cryptorchidism Small hands and feet Hyperphagia - Obesity Stereotypic behaviour ```
54
What deletion is found in Angelman syndrome and Prader-Willi syndrome?
del 15(q11-q13) Always de novo
55
Loss of the paternal 15q11-13 contribution due to deletion or uniparental disomy (UPD) will cause what?
Prader-Willi syndrome
56
Loss of the maternal 15q11-13 contribution due to deletion or uniparental disomy (UPD) will cause what?
Angelman syndrome
57
What is the genomic imprinting of 11p15.5 in a normal child?
Maternal = No methylation Paternal = methylated Normal dosage of Insulin-like growth factor 2 – major fetal growth promoter
58
What does hypomethylation of the paternal 11p15.5 cause?
Hypomethylation = decrease in Insulin-like growth factor 2 Russell-Silver syndrome
59
What are the clinical features of Russell-Silver syndrome?
Growth retardation - Fetal (IUGR) - Persistent postnatal growth failure Triangular face - Brain size more preserved Asymmetry Sporadic occurrence
60
What does hypermethylation of the maternal 11p15.5 cause?
Hypermethylation = increase in Insulin-like growth factor 2 Beckwith-Wiedemann syndrome
61
Gene polymorphs in Thiopurine methyltransferase (TPMT) can cause what?
Reduces TPMT protein activity - TPMT inactivates certain drugs Increases toxicity of: Azathioprine, 6-mercaptopurine, 6-thioguanine
62
G>A mutation in mitochondrial gene MT-RNR1 which encodes for rRNA can increase the risk of what?
Mutation changes the structure of the rRNA to resemble E-coli rRNA Aminoglycosides more likely to bind to patients rRNA → Accounts for 30% of tendency to aminoglycoside ototoxicity
63
Genetic variation in CYP2C9 explains 50% of the variability of which drugs activity?
Warfarin
64
What is protein is over expressed in 20% of breast cancers?
Human epidermal growth factor receptor 2 (HER2)
65
What is Herceptin?
Trastuzumab a monoclonal antibody to the HER2 receptor
66
What are BRAF inhibitors used to treat?
Melanoma 50% of melanomas have a somatic mutation in the BRAF gene
67
Huntington's disease is caused by what?
an expansion of CAG repeats ≥ 40 in HTT gene at 4q16.3
68
What effect does an increase in CAG repeats have on the Huntingtin protein?
Increased number of Glutamine amino acids = polyglutamine (polyQ) expansion Changes structure and causes protein to form aggregates

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